From c2e1f45a14746299fda892be3e1a6567e491edcf Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 4 Nov 2024 10:48:53 +0000 Subject: [PATCH 01/22] draft adding list of cases to command line options --- test_suite/README.md | 6 ++++++ test_suite/process_test_suite.py | 12 +++++++++++- ...test_test_suite_compatibility_biosimulators.py | 15 +++++++++++++-- 3 files changed, 30 insertions(+), 3 deletions(-) diff --git a/test_suite/README.md b/test_suite/README.md index 2c26a5e6..6526fd78 100644 --- a/test_suite/README.md +++ b/test_suite/README.md @@ -47,6 +47,12 @@ The `process_test_suite.py` script provides various command-line options to cust **Usage:** `--limit ` **Default:** `0` (no limit) + `--cases` + **Description:** list specific cases to process + **Usage:** `--cases ` + **Default:** `[]` (no limit) + + - `--suite-path` **Description:** Specifies the path to the directory containing the test suite files. **Usage:** `--suite-path ` diff --git a/test_suite/process_test_suite.py b/test_suite/process_test_suite.py index 1a2862c6..0d3ca223 100755 --- a/test_suite/process_test_suite.py +++ b/test_suite/process_test_suite.py @@ -45,6 +45,14 @@ def parse_arguments(): help="Limit to the first n test cases, 0 means no limit", ) + parser.add_argument( + "--cases", + action="store", + type=list, + default=[], + help="Limit to the cases listed in the file. Empty list means no limit", + ) + parser.add_argument( "--suite-path", action="store", @@ -116,7 +124,9 @@ def process_cases(args): matplotlib.use("agg") # Suppress specific UserWarning caused by matplotlib (required to suppress interactive plots) warnings.filterwarnings("ignore", category=UserWarning, message="FigureCanvasAgg is non-interactive, and thus cannot be shown") - subfolders = os.listdir(suite_path_abs) if args.limit == 0 else os.listdir(suite_path_abs)[:args.limit] + subfolders = os.listdir(suite_path_abs) if args.limit == 0 else os.listdir(suite_path_abs)[:args.limit] + # do same for cases + subfolders = os.listdir(suite_path_abs) if args.cases == [] else os.listdir(suite_path_abs)cases for subfolder in subfolders: # if sbml_level_version is empty string (default), find the highest level and version in the folder diff --git a/test_suite/test_test_suite_compatibility_biosimulators.py b/test_suite/test_test_suite_compatibility_biosimulators.py index 1a1a590a..f7161680 100644 --- a/test_suite/test_test_suite_compatibility_biosimulators.py +++ b/test_suite/test_test_suite_compatibility_biosimulators.py @@ -15,7 +15,7 @@ import shutil sys.path.append("..") import utils -engines = utils.engines +engines = utils.ENGINES md_description = \ @@ -44,6 +44,14 @@ def parse_arguments(): help="Limit to the first n test cases, 0 means no limit", ) + parser.add_argument( + "--cases", + action="store", + type=list, + default=[], + help="Limit to the cases listed in the file. Empty list means no limit", + ) + parser.add_argument( "--suite-path", action="store", @@ -94,6 +102,7 @@ def process_cases(args): suite_path_abs = os.getcwd() # absolute path to test suite subfolders = os.listdir(suite_path_abs) if args.limit == 0 else os.listdir(suite_path_abs)[:args.limit] + # subfolders = os.listdir(suite_path_abs) if args.cases == [] else os.listdir(suite_path_abs)[args.cases] print(f"Processing {len(subfolders)} subfolders in {args.suite_path}") test_folder = 'tests' @@ -129,12 +138,14 @@ def process_cases(args): os.chdir(new_directory) print(f"Changed to {new_directory}") + + engines_list = list(engines.keys()) utils.run_biosimulators_remotely_and_locally(os.path.basename(sedml_file_path), os.path.basename(sbml_file_path), os.path.join(test_folder,'d1_plots_remote'), os.path.join(test_folder,'d1_plots_local'), - engines=engines, test_folder=test_folder) + test_folder=test_folder) if __name__ == "__main__": From cce679c21842f2e3425fdd54ce5f79c824d39557 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 4 Nov 2024 12:15:49 +0000 Subject: [PATCH 02/22] update test suite 00001 table and draft for 01186 table --- .../tests/d1_plots_local/amici_plot_1.pdf | Bin 9578 -> 9578 bytes .../tests/d1_plots_local/bionetgen_plot_1.pdf | Bin 5948 -> 5948 bytes .../tests/d1_plots_local/boolnet_plot_1.pdf | Bin 5948 -> 5948 bytes .../tests/d1_plots_local/cbmpy_plot_1.pdf | Bin 5948 -> 5948 bytes .../tests/d1_plots_local/cobrapy_plot_1.pdf | Bin 5948 -> 5948 bytes .../tests/d1_plots_local/copasi_plot_1.pdf | Bin 5948 -> 9591 bytes .../tests/d1_plots_local/gillespy2_plot_1.pdf | Bin 9592 -> 9592 bytes .../tests/d1_plots_local/ginsim_plot_1.pdf | Bin 5948 -> 5948 bytes .../d1_plots_local/libsbmlsim_plot_1.pdf | Bin 9597 -> 9597 bytes .../tests/d1_plots_local/masspy_plot_1.pdf | Bin 5948 -> 5948 bytes .../tests/d1_plots_local/pysces_plot_1.pdf | Bin 9590 -> 9590 bytes .../tests/d1_plots_local/rbapy_plot_1.pdf | Bin 5948 -> 5948 bytes .../tests/d1_plots_local/tellurium_plot_1.pdf | Bin 9580 -> 9575 bytes .../tests/d1_plots_remote/amici_plot_1.pdf | Bin 9584 -> 9584 bytes .../d1_plots_remote/bionetgen_plot_1.pdf | Bin 5954 -> 5954 bytes .../tests/d1_plots_remote/boolnet_plot_1.pdf | Bin 5954 -> 5954 bytes .../tests/d1_plots_remote/cbmpy_plot_1.pdf | Bin 5954 -> 5954 bytes .../tests/d1_plots_remote/cobrapy_plot_1.pdf | Bin 5954 -> 5954 bytes .../tests/d1_plots_remote/copasi_plot_1.pdf | Bin 5954 -> 9597 bytes .../d1_plots_remote/gillespy2_plot_1.pdf | Bin 9598 -> 9598 bytes .../tests/d1_plots_remote/ginsim_plot_1.pdf | Bin 5954 -> 5954 bytes .../d1_plots_remote/libsbmlsim_plot_1.pdf | Bin 9603 -> 9603 bytes .../tests/d1_plots_remote/masspy_plot_1.pdf | Bin 5954 -> 5954 bytes .../tests/d1_plots_remote/pysces_plot_1.pdf | Bin 9596 -> 9596 bytes .../tests/d1_plots_remote/rbapy_plot_1.pdf | Bin 5954 -> 5954 bytes .../d1_plots_remote/tellurium_plot_1.pdf | Bin 9586 -> 9586 bytes .../results_compatibility_biosimulators.md | 46 +- .../test_00001/tests/results_local.json | 1277 ++++++++++++++++ .../test_00001/tests/results_remote.json | 1326 +++++++++++++++++ .../results_compatibility_biosimulators.md | 75 + .../test_01186/tests/results_local.json | 307 ++++ .../test_01186/tests/results_remote.json | 356 +++++ ..._test_suite_compatibility_biosimulators.py | 14 +- utils/__init__.py | 10 + 34 files changed, 3382 insertions(+), 29 deletions(-) create mode 100644 test_suite/test_00001/tests/results_local.json create mode 100644 test_suite/test_00001/tests/results_remote.json create mode 100644 test_suite/test_01186/tests/results_compatibility_biosimulators.md create mode 100644 test_suite/test_01186/tests/results_local.json create mode 100644 test_suite/test_01186/tests/results_remote.json diff --git a/test_suite/test_00001/tests/d1_plots_local/amici_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/amici_plot_1.pdf index 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100644 --- a/test_suite/test_00001/tests/results_compatibility_biosimulators.md +++ b/test_suite/test_00001/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| | Engine | pass / FAIL (R) | pass / FAIL (L) | Compat (R) | Compat (L) | Type (R) | Error (R) | Error (L) | d1 (R) | d1 (L) | -|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------|:--------------------------------------------------------| -| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
| pass | pass |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
| | | | plot | plot | -| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```
| plot | plot | -| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```
| plot | plot | -| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
|
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```
| | | -| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```
| plot | plot | -| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```
| plot | plot | -| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
| pass | pass |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
| | | | plot | plot | -| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
| pass | pass |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
| | | | plot | plot | -| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```
| plot | plot | -| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
| pass | pass |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
| | | | plot | plot | -| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```
| plot | plot | -| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne
|
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```
| | | -| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
|
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```
| | | -| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
|
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```
| | | -| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
|
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```
| | | -| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
| pass | pass |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
| | | | plot | plot | -| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```
| plot | plot | -| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn
|
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```
| | | -| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
| pass | pass |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
| | | | plot | plot | -| 19 |
vcellhttps://github.com/virtualcell/vcell
| None | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
| | |
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```
| | | -| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
|
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```
| | | \ No newline at end of file +| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------|:--------------------------------------------------------| +| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']

Only following targets are supported:
- M_S1
- M_S2
- R_reaction1
- S1
- S2
- k1
- reaction1

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 19 |
vcellhttps://github.com/virtualcell/vcell
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/test_suite/test_00001/tests/results_local.json b/test_suite/test_00001/tests/results_local.json new file mode 100644 index 00000000..b4e8981e --- /dev/null +++ b/test_suite/test_00001/tests/results_local.json @@ -0,0 +1,1277 @@ +{ + "amici": { + "exception_message": "", + "log_yml": { + "duration": 14.945897, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 14.477085, + "exception": null, + "location": "tmp383126", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp383126:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp383126 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SUCCEEDED" + }, + { + "id": "c_S2_1", + "status": "SUCCEEDED" + } + ], + "duration": 0.301881, + "exception": null, + "id": "plot_1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SUCCEEDED" + }, + { + "id": "ds_S1_1", + "status": "SUCCEEDED" + }, + { + "id": "ds_S2_1", + "status": "SUCCEEDED" + } + ], + "duration": 0.070628, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000496", + "duration": 14.026971, + "exception": null, + "id": "task_1", + "output": "", + "simulatorDetails": [ + { + "key": "solver", + "value": "amici.amici.CVodeSolver" + }, + { + "key": "method", + "value": "amici.swig_wrappers.runAmiciSimulation" + }, + { + "key": "arguments", + "value": {} + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "brian2": { + "exception_message": "Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.124591, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "bionetgen": { + "exception_message": "Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1", + "log_yml": { + "duration": 0.652344, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Language for model `model_1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.|$)` such as `urn:sedml:language:bngl`).", + "type": "CombineArchiveExecutionError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` has warnings.\r\n - The model file `00001-sbml-l3v2.xml` has warnings.\r\n - 1 warning of type SBML unit consistency (99507). The following is the first warning at line 3, column 2:\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions.\r\n - 1 warning of type SBML unit consistency (99508). The following is the first warning at line 29, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20702). The following is the first warning at line 29, column 6:\r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n - 1 warning of type SBML unit consistency (99505). The following is the first warning at line 39, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type Modeling practice (80701). The following is the first warning at line 29, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp76442` has warnings.\r\n - Model `model_1` has warnings.\r\n - The model file `00001-sbml-l3v2.xml` has warnings.\r\n - 1 warning of type SBML unit consistency (99507). The following is the first warning at line 3, column 2:\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions.\r\n - 1 warning of type SBML unit consistency (99508). The following is the first warning at line 29, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20702). The following is the first warning at line 29, column 6:\r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n - 1 warning of type SBML unit consistency (99505). The following is the first warning at line 39, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type Modeling practice (80701). The following is the first warning at line 29, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 0.426688, + "exception": { + "message": "The SED document did not execute successfully:\n\n Language for model `model_1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.|$)` such as `urn:sedml:language:bngl`).", + "type": "SedmlExecutionError" + }, + "location": "tmp76442", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp76442:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp76442 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SKIPPED" + }, + { + "id": "c_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.248525, + "exception": null, + "id": "plot_1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SKIPPED" + }, + { + "id": "ds_S1_1", + "status": "SKIPPED" + }, + { + "id": "ds_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.055996, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.026353, + "exception": { + "message": "Language for model `model_1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.|$)` such as `urn:sedml:language:bngl`).", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "boolnet": { + "exception_message": "Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1", + "log_yml": { + "duration": 0.649471, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Simulation `simulation_1` is invalid.\n - Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).", + "type": "CombineArchiveExecutionError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` may be invalid.\r\n - The model file `00001-sbml-l3v2.xml` may be invalid.\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions. \r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp493084` may be invalid.\r\n - Model `model_1` may be invalid.\r\n - The model file `00001-sbml-l3v2.xml` may be invalid.\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions. \r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 0.39038, + "exception": { + "message": "The SED document did not execute successfully:\n\n Simulation `simulation_1` is invalid.\n - Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).", + "type": "SedmlExecutionError" + }, + "location": "tmp493084", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp493084:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp493084 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SKIPPED" + }, + { + "id": "c_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.226278, + "exception": null, + "id": "plot_1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SKIPPED" + }, + { + "id": "ds_S1_1", + "status": "SKIPPED" + }, + { + "id": "ds_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.061712, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.026888, + "exception": { + "message": "Simulation `simulation_1` is invalid.\n - Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cbmpy": { + "exception_message": "Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.875066, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n UniformTimeCourseSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:\n - SteadyStateSimulation", + "type": "CombineArchiveExecutionError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` has warnings.\r\n - The model file `00001-sbml-l3v2.xml` has warnings.\r\n - 1 warning of type SBML unit consistency (99507). The following is the first warning at line 3, column 2:\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions.\r\n - 1 warning of type SBML unit consistency (99508). The following is the first warning at line 29, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20702). The following is the first warning at line 29, column 6:\r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n - 1 warning of type SBML unit consistency (99505). The following is the first warning at line 39, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type Modeling practice (80701). The following is the first warning at line 29, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp734844` has warnings.\r\n - Model `model_1` has warnings.\r\n - The model file `00001-sbml-l3v2.xml` has warnings.\r\n - 1 warning of type SBML unit consistency (99507). The following is the first warning at line 3, column 2:\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions.\r\n - 1 warning of type SBML unit consistency (99508). The following is the first warning at line 29, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20702). The following is the first warning at line 29, column 6:\r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n - 1 warning of type SBML unit consistency (99505). The following is the first warning at line 39, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type Modeling practice (80701). The following is the first warning at line 29, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 0.376968, + "exception": { + "message": "The SED document did not execute successfully:\n\n UniformTimeCourseSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:\n - SteadyStateSimulation", + "type": "SedmlExecutionError" + }, + "location": "tmp734844", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp734844:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp734844 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SKIPPED" + }, + { + "id": "c_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.214746, + "exception": null, + "id": "plot_1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SKIPPED" + }, + { + "id": "ds_S1_1", + "status": "SKIPPED" + }, + { + "id": "ds_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.060416, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.025588, + "exception": { + "message": "UniformTimeCourseSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:\n - SteadyStateSimulation", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cobrapy": { + "exception_message": "Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.994398, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n UniformTimeCourseSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:\n - SteadyStateSimulation", + "type": "CombineArchiveExecutionError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` has warnings.\r\n - The model file `00001-sbml-l3v2.xml` has warnings.\r\n - 1 warning of type SBML unit consistency (99507). The following is the first warning at line 3, column 2:\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions.\r\n - 1 warning of type SBML unit consistency (99508). The following is the first warning at line 29, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20702). The following is the first warning at line 29, column 6:\r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n - 1 warning of type SBML unit consistency (99505). The following is the first warning at line 39, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type Modeling practice (80701). The following is the first warning at line 29, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp259661` has warnings.\r\n - Model `model_1` has warnings.\r\n - The model file `00001-sbml-l3v2.xml` has warnings.\r\n - 1 warning of type SBML unit consistency (99507). The following is the first warning at line 3, column 2:\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions.\r\n - 1 warning of type SBML unit consistency (99508). The following is the first warning at line 29, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20702). The following is the first warning at line 29, column 6:\r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n - 1 warning of type SBML unit consistency (99505). The following is the first warning at line 39, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type Modeling practice (80701). The following is the first warning at line 29, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 0.68093, + "exception": { + "message": "The SED document did not execute successfully:\n\n UniformTimeCourseSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:\n - SteadyStateSimulation", + "type": "SedmlExecutionError" + }, + "location": "tmp259661", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp259661:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp259661 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SKIPPED" + }, + { + "id": "c_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.341102, + "exception": null, + "id": "plot_1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SKIPPED" + }, + { + "id": "ds_S1_1", + "status": "SKIPPED" + }, + { + "id": "ds_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.060286, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.038447, + "exception": { + "message": "UniformTimeCourseSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:\n - SteadyStateSimulation", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "copasi": { + "exception_message": "", + "log_yml": { + "duration": 1.195088, + "exception": null, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` has warnings.\r\n - The model file `00001-sbml-l3v2.xml` has warnings.\r\n - 1 warning of type SBML unit consistency (99507). The following is the first warning at line 3, column 2:\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions.\r\n - 1 warning of type SBML unit consistency (99508). The following is the first warning at line 29, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20702). The following is the first warning at line 29, column 6:\r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n - 1 warning of type SBML unit consistency (99505). The following is the first warning at line 39, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type Modeling practice (80701). The following is the first warning at line 29, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp824256` has warnings.\r\n - Model `model_1` has warnings.\r\n - The model file `00001-sbml-l3v2.xml` has warnings.\r\n - 1 warning of type SBML unit consistency (99507). The following is the first warning at line 3, column 2:\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions.\r\n - 1 warning of type SBML unit consistency (99508). The following is the first warning at line 29, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20702). The following is the first warning at line 29, column 6:\r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n - 1 warning of type SBML unit consistency (99505). The following is the first warning at line 39, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type Modeling practice (80701). The following is the first warning at line 29, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 0.792452, + "exception": null, + "location": "tmp824256", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp824256:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp824256 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SUCCEEDED" + }, + { + "id": "c_S2_1", + "status": "SUCCEEDED" + } + ], + "duration": 0.383445, + "exception": null, + "id": "plot_1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SUCCEEDED" + }, + { + "id": "ds_S1_1", + "status": "SUCCEEDED" + }, + { + "id": "ds_S2_1", + "status": "SUCCEEDED" + } + ], + "duration": 0.063615, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000560", + "duration": 0.073808, + "exception": null, + "id": "task_1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `S2_1_c` has warnings.\r\n - XPath could not be validated.\r\n- Variable `S1_1_s` has warnings.\r\n - XPath could not be validated.\r\n- Variable `S1_1_c` has warnings.\r\n - XPath could not be validated.\r\n- Variable `S2_1_s` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `model_1` may be invalid.\r\n - The model file `/tmp/tmp5rjy3i1h/./00001-sbml-l3v2.xml` has warnings.\r\n - 1 warning of type SBML unit consistency (99507). The following is the first warning at line 3, column 2:\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions.\r\n - 1 warning of type SBML unit consistency (99508). The following is the first warning at line 29, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20702). The following is the first warning at line 29, column 6:\r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n - 1 warning of type SBML unit consistency (99505). The following is the first warning at line 39, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type Modeling practice (80701). The following is the first warning at line 29, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'LSODA/LSODAR hybrid method' (KISAO_0000560) will be substituted for 'CVODE' (KISAO_0000019) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "simulatorDetails": [ + { + "key": "methodName", + "value": "lsoda" + }, + { + "key": "parameters", + "value": null + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "gillespy2": { + "exception_message": "", + "log_yml": { + "duration": 0.824948, + "exception": null, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` has warnings.\r\n - The model file `00001-sbml-l3v2.xml` has warnings.\r\n - 1 warning of type SBML unit consistency (99507). The following is the first warning at line 3, column 2:\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions.\r\n - 1 warning of type SBML unit consistency (99508). The following is the first warning at line 29, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20702). The following is the first warning at line 29, column 6:\r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n - 1 warning of type SBML unit consistency (99505). The following is the first warning at line 39, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type Modeling practice (80701). The following is the first warning at line 29, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp391390` has warnings.\r\n - Model `model_1` has warnings.\r\n - The model file `00001-sbml-l3v2.xml` has warnings.\r\n - 1 warning of type SBML unit consistency (99507). The following is the first warning at line 3, column 2:\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions.\r\n - 1 warning of type SBML unit consistency (99508). The following is the first warning at line 29, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20702). The following is the first warning at line 29, column 6:\r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n - 1 warning of type SBML unit consistency (99505). The following is the first warning at line 39, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type Modeling practice (80701). The following is the first warning at line 29, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 0.508623, + "exception": null, + "location": "tmp391390", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp391390:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp391390 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SUCCEEDED" + }, + { + "id": "c_S2_1", + "status": "SUCCEEDED" + } + ], + "duration": 0.311967, + "exception": null, + "id": "plot_1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SUCCEEDED" + }, + { + "id": "ds_S1_1", + "status": "SUCCEEDED" + }, + { + "id": "ds_S2_1", + "status": "SUCCEEDED" + } + ], + "duration": 0.062732, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000088", + "duration": 0.044193, + "exception": null, + "id": "task_1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `S1_1_c` has warnings.\r\n - XPath could not be validated.\r\n- Variable `S1_1_s` has warnings.\r\n - XPath could not be validated.\r\n- Variable `S2_1_c` has warnings.\r\n - XPath could not be validated.\r\n- Variable `S2_1_s` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/kisao/utils.py:477: AlgorithmSubstitutedWarning: \u001b[33m'LSODA' (KISAO_0000088) will be substituted for 'CVODE'' (KISAO_0000019) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "simulatorDetails": [ + { + "key": "method", + "value": "gillespy2.solvers.numpy.ode_solver.ODESolver" + }, + { + "key": "arguments", + "value": { + "integrator": "lsoda" + } + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "ginsim": { + "exception_message": "Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.767792, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Simulation `simulation_1` is invalid.\n - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:\n Output start time: 0.0\n Output end time: 5.0\n Number of steps: 50", + "type": "CombineArchiveExecutionError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` may be invalid.\r\n - The model file `00001-sbml-l3v2.xml` may be invalid.\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions. \r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp717238` may be invalid.\r\n - Model `model_1` may be invalid.\r\n - The model file `00001-sbml-l3v2.xml` may be invalid.\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions. \r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 0.520654, + "exception": { + "message": "The SED document did not execute successfully:\n\n Simulation `simulation_1` is invalid.\n - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:\n Output start time: 0.0\n Output end time: 5.0\n Number of steps: 50", + "type": "SedmlExecutionError" + }, + "location": "tmp717238", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp717238:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp717238 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SKIPPED" + }, + { + "id": "c_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.318909, + "exception": null, + "id": "plot_1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SKIPPED" + }, + { + "id": "ds_S1_1", + "status": "SKIPPED" + }, + { + "id": "ds_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.063617, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.026382, + "exception": { + "message": "Simulation `simulation_1` is invalid.\n - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:\n Output start time: 0.0\n Output end time: 5.0\n Number of steps: 50", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "libsbmlsim": { + "exception_message": "", + "log_yml": { + "duration": 1.30786, + "exception": null, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` may be invalid.\r\n - The model file `00001-sbml-l3v2.xml` may be invalid.\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions. \r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp711766` may be invalid.\r\n - Model `model_1` may be invalid.\r\n - The model file `00001-sbml-l3v2.xml` may be invalid.\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions. \r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 0.750966, + "exception": null, + "location": "tmp711766", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp711766:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp711766 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SUCCEEDED" + }, + { + "id": "c_S2_1", + "status": "SUCCEEDED" + } + ], + "duration": 0.312021, + "exception": null, + "id": "plot_1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SUCCEEDED" + }, + { + "id": "ds_S1_1", + "status": "SUCCEEDED" + }, + { + "id": "ds_S2_1", + "status": "SUCCEEDED" + } + ], + "duration": 0.084254, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000086", + "duration": 0.06945, + "exception": null, + "id": "task_1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `S1_1_s` may be invalid.\r\n - XPath could not be validated.\r\n- Variable `S2_1_c` may be invalid.\r\n - XPath could not be validated.\r\n- Variable `S1_1_c` may be invalid.\r\n - XPath could not be validated.\r\n- Variable `S2_1_s` may be invalid.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `model_1` may be invalid.\r\n - The model file `/tmp/tmpn8yusbf5/./00001-sbml-l3v2.xml` may be invalid.\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions. \r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/kisao/utils.py:477: AlgorithmSubstitutedWarning: \u001b[33m'Fehlberg method' (KISAO_0000086) will be substituted for 'CVODE'' (KISAO_0000019) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "simulatorDetails": [ + { + "key": "method", + "value": "simulateSBMLFromFile" + }, + { + "key": "arguments", + "value": { + "dt": 0.001, + "method": 51, + "print_amount": 0, + "print_interval": 100, + "sim_time": 5.0, + "use_lazy_method": 0 + } + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "masspy": { + "exception_message": "Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1", + "log_yml": { + "duration": 1.128796, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n \t`(model, errors) = validate_sbml_model(filename)`\n If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .", + "type": "CombineArchiveExecutionError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` has warnings.\r\n - The model file `00001-sbml-l3v2.xml` has warnings.\r\n - 1 warning of type SBML unit consistency (99507). The following is the first warning at line 3, column 2:\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions.\r\n - 1 warning of type SBML unit consistency (99508). The following is the first warning at line 29, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20702). The following is the first warning at line 29, column 6:\r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n - 1 warning of type SBML unit consistency (99505). The following is the first warning at line 39, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type Modeling practice (80701). The following is the first warning at line 29, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp359632` has warnings.\r\n - Model `model_1` has warnings.\r\n - The model file `00001-sbml-l3v2.xml` has warnings.\r\n - 1 warning of type SBML unit consistency (99507). The following is the first warning at line 3, column 2:\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions.\r\n - 1 warning of type SBML unit consistency (99508). The following is the first warning at line 29, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20702). The following is the first warning at line 29, column 6:\r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n - 1 warning of type SBML unit consistency (99505). The following is the first warning at line 39, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type Modeling practice (80701). The following is the first warning at line 29, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\u001b[0m\r\n", + "sedDocuments": [ + { + "duration": 0.532317, + "exception": { + "message": "The SED document did not execute successfully:\n\n Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n \t`(model, errors) = validate_sbml_model(filename)`\n If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .", + "type": "SedmlExecutionError" + }, + "location": "tmp359632", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp359632:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp359632 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SKIPPED" + }, + { + "id": "c_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.216593, + "exception": null, + "id": "plot_1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mIllogicalVizWarning\u001b[0m: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mIllogicalVizWarning\u001b[0m: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mIllogicalVizWarning\u001b[0m: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mIllogicalVizWarning\u001b[0m: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SKIPPED" + }, + { + "id": "ds_S1_1", + "status": "SKIPPED" + }, + { + "id": "ds_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.066701, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.034642, + "exception": { + "message": "Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n\t`(model, errors) = validate_sbml_model(filename)`\nIf the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .", + "type": "MassSBMLError" + }, + "id": "task_1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33m- Variable `S2_1_c` has warnings.\r\n - XPath could not be validated.\r\n- Variable `S1_1_c` has warnings.\r\n - XPath could not be validated.\r\n- Variable `S1_1_s` has warnings.\r\n - XPath could not be validated.\r\n- Variable `S2_1_s` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mModel `model_1` may be invalid.\r\n - The model file `/tmp/tmp1y2zkv3f/./00001-sbml-l3v2.xml` has warnings.\r\n - 1 warning of type SBML unit consistency (99507). The following is the first warning at line 3, column 2:\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions.\r\n - 1 warning of type SBML unit consistency (99508). The following is the first warning at line 29, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20702). The following is the first warning at line 29, column 6:\r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n - 1 warning of type SBML unit consistency (99505). The following is the first warning at line 39, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type Modeling practice (80701). The following is the first warning at line 29, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mSBML model is written as Level 3 Version 2, will attempt to convert the SBML model from Level 3 Version 2 to Level 3 Version 1 before parsing\u001b[0m\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "netpyne": { + "exception_message": "Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1", + "log_yml": { + "duration": 0.140419, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "neuron": { + "exception_message": "Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1", + "log_yml": { + "duration": 0.034594, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "opencor": { + "exception_message": "Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1", + "log_yml": { + "duration": 0.020313, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pyneuroml": { + "exception_message": "Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1", + "log_yml": { + "duration": 0.077575, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pysces": { + "exception_message": "", + "log_yml": { + "duration": 2.169071, + "exception": null, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` has warnings.\r\n - The model file `00001-sbml-l3v2.xml` has warnings.\r\n - 1 warning of type SBML unit consistency (99507). The following is the first warning at line 3, column 2:\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions.\r\n - 1 warning of type SBML unit consistency (99508). The following is the first warning at line 29, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20702). The following is the first warning at line 29, column 6:\r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n - 1 warning of type SBML unit consistency (99505). The following is the first warning at line 39, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type Modeling practice (80701). The following is the first warning at line 29, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp704056` has warnings.\r\n - Model `model_1` has warnings.\r\n - The model file `00001-sbml-l3v2.xml` has warnings.\r\n - 1 warning of type SBML unit consistency (99507). The following is the first warning at line 3, column 2:\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions.\r\n - 1 warning of type SBML unit consistency (99508). The following is the first warning at line 29, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20702). The following is the first warning at line 29, column 6:\r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n - 1 warning of type SBML unit consistency (99505). The following is the first warning at line 39, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type Modeling practice (80701). The following is the first warning at line 29, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 1.429044, + "exception": null, + "location": "tmp704056", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp704056:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp704056 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L3V2\r\nInfo: single compartment model: locating \"reaction1\" in default compartment\r\nWriting file: /tmp/tmp3vl49w67.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmp0p253j1i.xml\r\nout: /tmp/tmp3vl49w67.psc\r\nUsing model directory: /Pysces/psc\r\n/tmp/tmp3vl49w67.psc loading ..... \r\nParsing file: /tmp/tmp3vl49w67.psc\r\nInfo: No reagents have been fixed\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . no flux conservation\r\n done.\r\n \r\nCVODE time for 51 points: 0.0020084381103515625\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SUCCEEDED" + }, + { + "id": "c_S2_1", + "status": "SUCCEEDED" + } + ], + "duration": 0.600432, + "exception": null, + "id": "plot_1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SUCCEEDED" + }, + { + "id": "ds_S1_1", + "status": "SUCCEEDED" + }, + { + "id": "ds_S2_1", + "status": "SUCCEEDED" + } + ], + "duration": 0.172397, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 0.169901, + "exception": null, + "id": "task_1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `S2_1_s` has warnings.\r\n - XPath could not be validated.\r\n- Variable `S1_1_s` has warnings.\r\n - XPath could not be validated.\r\n- Variable `S1_1_c` has warnings.\r\n - XPath could not be validated.\r\n- Variable `S2_1_c` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "simulatorDetails": [ + { + "key": "method", + "value": "pysces.PyscesModel.Simulate" + }, + { + "key": "arguments", + "value": { + "cvode_abstol": 1e-09, + "cvode_access_solver": true, + "cvode_h0": 0.0, + "cvode_hmax": 0.0, + "cvode_hmin": 0.0, + "cvode_mxord": 5, + "cvode_mxstep": 5000, + "cvode_reltol": 1e-09, + "cvode_return_event_timepoints": false, + "cvode_stats": false, + "cvode_track_assignment_rules": true + } + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "rbapy": { + "exception_message": "Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.66583, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Language for model `model_1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.|$)` such as `urn:sedml:language:rba`).", + "type": "CombineArchiveExecutionError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` may be invalid.\r\n - The model file `00001-sbml-l3v2.xml` may be invalid.\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions. \r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp708002` may be invalid.\r\n - Model `model_1` may be invalid.\r\n - The model file `00001-sbml-l3v2.xml` may be invalid.\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions. \r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 0.42883, + "exception": { + "message": "The SED document did not execute successfully:\n\n Language for model `model_1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.|$)` such as `urn:sedml:language:rba`).", + "type": "SedmlExecutionError" + }, + "location": "tmp708002", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp708002:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp708002 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SKIPPED" + }, + { + "id": "c_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.227427, + "exception": null, + "id": "plot_1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SKIPPED" + }, + { + "id": "ds_S1_1", + "status": "SKIPPED" + }, + { + "id": "ds_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.051989, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.024601, + "exception": { + "message": "Language for model `model_1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.|$)` such as `urn:sedml:language:rba`).", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "smoldyn": { + "exception_message": "Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1", + "log_yml": {}, + "detailed_error_log": {} + }, + "tellurium": { + "exception_message": "", + "log_yml": { + "duration": 1.342302, + "exception": null, + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` has warnings.\r\n - The model file `00001-sbml-l3v2.xml` has warnings.\r\n - 1 warning of type SBML unit consistency (99507). The following is the first warning at line 3, column 2:\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions.\r\n - 1 warning of type SBML unit consistency (99508). The following is the first warning at line 29, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20702). The following is the first warning at line 29, column 6:\r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n - 1 warning of type SBML unit consistency (99505). The following is the first warning at line 39, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type Modeling practice (80701). The following is the first warning at line 29, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp264702` has warnings.\r\n - Model `model_1` has warnings.\r\n - The model file `00001-sbml-l3v2.xml` has warnings.\r\n - 1 warning of type SBML unit consistency (99507). The following is the first warning at line 3, column 2:\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions.\r\n - 1 warning of type SBML unit consistency (99508). The following is the first warning at line 29, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20702). The following is the first warning at line 29, column 6:\r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n - 1 warning of type SBML unit consistency (99505). The following is the first warning at line 39, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type Modeling practice (80701). The following is the first warning at line 29, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\u001b[0m\r\n\r\n", + "sedDocuments": [ + { + "duration": 0.667745, + "exception": null, + "location": "tmp264702", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp264702:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp264702 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SUCCEEDED" + }, + { + "id": "c_S2_1", + "status": "SUCCEEDED" + } + ], + "duration": 0.331755, + "exception": null, + "id": "plot_1", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning:\r\n\r\n\u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n\r\n", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SUCCEEDED" + }, + { + "id": "ds_S1_1", + "status": "SUCCEEDED" + }, + { + "id": "ds_S2_1", + "status": "SUCCEEDED" + } + ], + "duration": 0.07227, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 0.073165, + "exception": null, + "id": "task_1", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33m- Variable `S1_1_s` has warnings.\r\n - XPath could not be validated.\r\n- Variable `S2_1_s` has warnings.\r\n - XPath could not be validated.\r\n- Variable `S1_1_c` has warnings.\r\n - XPath could not be validated.\r\n- Variable `S2_1_c` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mModel `model_1` may be invalid.\r\n - The model file `/tmp/tmpwzv1gbo7/./00001-sbml-l3v2.xml` has warnings.\r\n - 1 warning of type SBML unit consistency (99507). The following is the first warning at line 3, column 2:\r\n - In situations where a mathematical expression refers to extent, the units of extent should be consistent with the global extent units of the model. In models where the 'extentUnits' attribute has not been declared, libSBML does not yet have the functionality to verify accurately the consistency of the units in such expressions.\r\n - 1 warning of type SBML unit consistency (99508). The following is the first warning at line 29, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'k1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20702). The following is the first warning at line 29, column 6:\r\n - If the attribute 'units' on a given Parameter object has not been set, then the unit of measurement associated with that parameter's value is undefined.\r\n Reference: L3V2 Section 4.7.3\r\n The with id 'k1' does not have a 'units' attribute.\r\n - 1 warning of type SBML unit consistency (99505). The following is the first warning at line 39, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'compartment * k1 * S1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type Modeling practice (80701). The following is the first warning at line 29, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'k1' does not have a 'units' attribute.\u001b[0m\r\n\r\n", + "simulatorDetails": [ + { + "key": "method", + "value": "simulate" + }, + { + "key": "solver", + "value": "cvode" + }, + { + "key": "relative_tolerance", + "value": 1e-06 + }, + { + "key": "absolute_tolerance", + "value": 1e-12 + }, + { + "key": "stiff", + "value": true + }, + { + "key": "maximum_bdf_order", + "value": 5 + }, + { + "key": "maximum_adams_order", + "value": 12 + }, + { + "key": "maximum_num_steps", + "value": 20000 + }, + { + "key": "maximum_time_step", + "value": 0.0 + }, + { + "key": "minimum_time_step", + "value": 0.0 + }, + { + "key": "initial_time_step", + "value": 0.0 + }, + { + "key": "multiple_steps", + "value": false + }, + { + "key": "variable_step_size", + "value": false + }, + { + "key": "max_output_rows", + "value": 100000 + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "vcell": { + "exception_message": "Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1", + "log_yml": { + "duration": 3, + "exception": null, + "output": "Processing tmp190725. 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Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.|$)` such as `urn:sedml:language:bngl`).", + "type": "SedmlExecutionError" + }, + "location": "tmp317828", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp317828:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp317828 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SKIPPED" + }, + { + "id": "c_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.151124, + "exception": null, + "id": "plot_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SKIPPED" + }, + { + "id": "ds_S1_1", + "status": "SKIPPED" + }, + { + "id": "ds_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.057554, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.025411, + "exception": { + "message": "Language for model `model_1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. 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Simulation must be an instance of one of the following:\n - SteadyStateSimulation", + "type": "CombineArchiveExecutionError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. 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Simulation must be an instance of one of the following:\n - SteadyStateSimulation", + "type": "SedmlExecutionError" + }, + "location": "tmp125101", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp125101:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp125101 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SKIPPED" + }, + { + "id": "c_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.180071, + "exception": null, + "id": "plot_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SKIPPED" + }, + { + "id": "ds_S1_1", + "status": "SKIPPED" + }, + { + "id": "ds_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.054795, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.028423, + "exception": { + "message": "UniformTimeCourseSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. 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Simulation must be an instance of one of the following:\n - SteadyStateSimulation", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.34159, + "exception": { + "message": "The SED document did not execute successfully:\n\n UniformTimeCourseSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:\n - SteadyStateSimulation", + "type": "SedmlExecutionError" + }, + "location": "tmp129681", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp129681:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp129681 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SKIPPED" + }, + { + "id": "c_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.168312, + "exception": null, + "id": "plot_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SKIPPED" + }, + { + "id": "ds_S1_1", + "status": "SKIPPED" + }, + { + "id": "ds_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.060222, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.028816, + "exception": { + "message": "UniformTimeCourseSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. 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The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:\n Output start time: 0.0\n Output end time: 5.0\n Number of steps: 50", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.34216, + "exception": { + "message": "The SED document did not execute successfully:\n\n Simulation `simulation_1` is invalid.\n - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:\n Output start time: 0.0\n Output end time: 5.0\n Number of steps: 50", + "type": "SedmlExecutionError" + }, + "location": "tmp256142", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp256142:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp256142 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SKIPPED" + }, + { + "id": "c_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.178315, + "exception": null, + "id": "plot_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SKIPPED" + }, + { + "id": "ds_S1_1", + "status": "SKIPPED" + }, + { + "id": "ds_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.054549, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.029284, + "exception": { + "message": "Simulation `simulation_1` is invalid.\n - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:\n Output start time: 0.0\n Output end time: 5.0\n Number of steps: 50", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + } + }, + "libsbmlsim": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b6885a60072d20f48acb", + "download": "https://api.biosimulations.org/results/6728b6885a60072d20f48acb/download", + "logs": "https://api.biosimulations.org/logs/6728b6885a60072d20f48acb?includeOutput=true", + "log_yml": { + "duration": 0.697696, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 0.434444, + "exception": null, + "location": "tmp412874", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp412874:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp412874 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SUCCEEDED" + }, + { + "id": "c_S2_1", + "status": "SUCCEEDED" + } + ], + "duration": 0.196723, + "exception": null, + "id": "plot_1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SUCCEEDED" + }, + { + "id": "ds_S1_1", + "status": "SUCCEEDED" + }, + { + "id": "ds_S2_1", + "status": "SUCCEEDED" + } + ], + "duration": 0.061553, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000086", + "duration": 0.092233, + "exception": null, + "id": "task_1", + "output": "", + "simulatorDetails": [ + { + "key": "method", + "value": "simulateSBMLFromFile" + }, + { + "key": "arguments", + "value": { + "dt": 0.001, + "method": 51, + "print_amount": 0, + "print_interval": 100, + "sim_time": 5.0, + "use_lazy_method": 0 + } + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + }, + "masspy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b68a0d09353e8f0f89c3", + "download": "https://api.biosimulations.org/results/6728b68a0d09353e8f0f89c3/download", + "logs": "https://api.biosimulations.org/logs/6728b68a0d09353e8f0f89c3?includeOutput=true", + "log_yml": { + "duration": 1.120088, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n The following targets are not supported:\n - 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Python Simulator for Cellular Systems *\r\n* http://pysces.sourceforge.net *\r\n* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2024 *\r\n* Triple-J Group for Molecular Cell Physiology *\r\n* Stellenbosch University, ZA and VU University Amsterdam, NL *\r\n* PySCeS is distributed under the PySCeS (BSD style) licence, see *\r\n* LICENCE.txt (supplied with this release) for details *\r\n* Please cite PySCeS with: doi:10.1093/bioinformatics/bti046 *\r\n***********************************************************************\r\n", + "sedDocuments": [ + { + "duration": 0.622144, + "exception": null, + "location": "tmp384164", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp384164:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp384164 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L3V2\r\nInfo: single compartment model: locating \"reaction1\" in default compartment\r\nWriting file: /tmp/tmp4mj1xvmt.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpigr7u72o.xml\r\nout: /tmp/tmp4mj1xvmt.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmp4mj1xvmt.psc loading ..... \r\nParsing file: /tmp/tmp4mj1xvmt.psc\r\nInfo: No reagents have been fixed\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . no flux conservation\r\n done.\r\n \r\nCVODE time for 51 points: 0.007776975631713867\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SUCCEEDED" + }, + { + "id": "c_S2_1", + "status": "SUCCEEDED" + } + ], + "duration": 0.405717, + "exception": null, + "id": "plot_1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SUCCEEDED" + }, + { + "id": "ds_S1_1", + "status": "SUCCEEDED" + }, + { + "id": "ds_S2_1", + "status": "SUCCEEDED" + } + ], + "duration": 0.058856, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 0.080845, + "exception": null, + "id": "task_1", + "output": "", + "simulatorDetails": [ + { + "key": "method", + "value": "pysces.PyscesModel.Simulate" + }, + { + "key": "arguments", + "value": { + "cvode_abstol": 1e-09, + "cvode_access_solver": true, + "cvode_h0": 0.0, + "cvode_hmax": 0.0, + "cvode_hmin": 0.0, + "cvode_mxord": 5, + "cvode_mxstep": 5000, + "cvode_reltol": 1e-09, + "cvode_return_event_timepoints": false, + "cvode_stats": false, + "cvode_track_assignment_rules": true + } + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + }, + "rbapy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b693b678b3883bb5dedd", + "download": "https://api.biosimulations.org/results/6728b693b678b3883bb5dedd/download", + "logs": "https://api.biosimulations.org/logs/6728b693b678b3883bb5dedd?includeOutput=true", + "log_yml": { + "duration": 0.599051, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Language for model `model_1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.|$)` such as `urn:sedml:language:rba`).", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.3463, + "exception": { + "message": "The SED document did not execute successfully:\n\n Language for model `model_1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.|$)` such as `urn:sedml:language:rba`).", + "type": "SedmlExecutionError" + }, + "location": "tmp569097", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp569097:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp569097 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SKIPPED" + }, + { + "id": "c_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.166468, + "exception": null, + "id": "plot_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SKIPPED" + }, + { + "id": "ds_S1_1", + "status": "SKIPPED" + }, + { + "id": "ds_S2_1", + "status": "SKIPPED" + } + ], + "duration": 0.06125, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.027023, + "exception": { + "message": "Language for model `model_1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.|$)` such as `urn:sedml:language:rba`).", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + } + }, + "smoldyn": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b6955a60072d20f48b10", + "download": "https://api.biosimulations.org/results/6728b6955a60072d20f48b10/download", + "logs": "https://api.biosimulations.org/logs/6728b6955a60072d20f48b10?includeOutput=true", + "log_yml": { + "duration": 0.061281, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "tellurium": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b6970d09353e8f0f8a0b", + "download": "https://api.biosimulations.org/results/6728b6970d09353e8f0f8a0b/download", + "logs": "https://api.biosimulations.org/logs/6728b6970d09353e8f0f8a0b?includeOutput=true", + "log_yml": { + "duration": 1.176542, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 0.726483, + "exception": null, + "location": "tmp348905", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp348905:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n Plots (1):\r\n plot_1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp348905 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `plot_1`\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `plot_1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `report_1` ...", + "outputs": [ + { + "curves": [ + { + "id": "c_S1_1", + "status": "SUCCEEDED" + }, + { + "id": "c_S2_1", + "status": "SUCCEEDED" + } + ], + "duration": 0.39315, + "exception": null, + "id": "plot_1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "ds_time", + "status": "SUCCEEDED" + }, + { + "id": "ds_S1_1", + "status": "SUCCEEDED" + }, + { + "id": "ds_S2_1", + "status": "SUCCEEDED" + } + ], + "duration": 0.058473, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 0.182248, + "exception": null, + "id": "task_1", + "output": "", + "simulatorDetails": [ + { + "key": "method", + "value": "simulate" + }, + { + "key": "solver", + "value": "cvode" + }, + { + "key": "relative_tolerance", + "value": 1e-06 + }, + { + "key": "absolute_tolerance", + "value": 1e-12 + }, + { + "key": "stiff", + "value": true + }, + { + "key": "maximum_bdf_order", + "value": 5 + }, + { + "key": "maximum_adams_order", + "value": 12 + }, + { + "key": "maximum_num_steps", + "value": 20000 + }, + { + "key": "maximum_time_step", + "value": 0.0 + }, + { + "key": "minimum_time_step", + "value": 0.0 + }, + { + "key": "initial_time_step", + "value": 0.0 + }, + { + "key": "multiple_steps", + "value": false + }, + { + "key": "variable_step_size", + "value": false + }, + { + "key": "max_output_rows", + "value": 100000 + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + }, + "vcell": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b69a5a60072d20f48b21", + "download": "https://api.biosimulations.org/results/6728b69a5a60072d20f48b21/download", + "logs": "https://api.biosimulations.org/logs/6728b69a5a60072d20f48b21?includeOutput=true", + "log_yml": { + "duration": null, + "exception": null, + "output": null, + "sedDocuments": [], + "skipReason": null, + "status": "QUEUED" + } + }, + "xpp": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b69c5a60072d20f48b37", + "download": "https://api.biosimulations.org/results/6728b69c5a60072d20f48b37/download", + "logs": "https://api.biosimulations.org/logs/6728b69c5a60072d20f48b37?includeOutput=true", + "log_yml": { + "duration": 0.066845, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + } +} \ No newline at end of file diff --git a/test_suite/test_01186/tests/results_compatibility_biosimulators.md b/test_suite/test_01186/tests/results_compatibility_biosimulators.md new file mode 100644 index 00000000..a382fc23 --- /dev/null +++ b/test_suite/test_01186/tests/results_compatibility_biosimulators.md @@ -0,0 +1,75 @@ +| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------|:---------| +| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/

|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | +| | | | - The SED-ML file at location `./tmp267694` is invalid. | - The SED-ML file at location `./tmp640928` is invalid. | | | +| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | +| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | +| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | +| | | | - The SED-ML file at location `./tmp347049` is invalid. | - The SED-ML file at location `./tmp46347` is invalid. | | | +| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | +| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | +| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | +| | | | - The SED-ML file at location `./tmp838310` is invalid. | - The SED-ML file at location `./tmp433696` is invalid. | | | +| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | +| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | +| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | +| | | | - The SED-ML file at location `./tmp528257` is invalid. | - The SED-ML file at location `./tmp385050` is invalid. | | | +| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | +| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | +| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | +| | | | - The SED-ML file at location `./tmp171288` is invalid. | - The SED-ML file at location `./tmp413781` is invalid. | | | +| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | +| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | +| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | +| | | | - The SED-ML file at location `./tmp860188` is invalid. | - The SED-ML file at location `./tmp332181` is invalid. | | | +| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | +| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | +| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | +| | | | - The SED-ML file at location `./tmp595452` is invalid. | - The SED-ML file at location `./tmp697896` is invalid. | | | +| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | +| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | +| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | +| | | | - The SED-ML file at location `./tmp956508` is invalid. | - The SED-ML file at location `./tmp90777` is invalid. | | | +| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | +| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | +| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | +| | | | - The SED-ML file at location `./tmp385105` is invalid. | - The SED-ML file at location `./tmp39181` is invalid. | | | +| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | +| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | +| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
|
❌ FAILview
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logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | +| | | | - The SED-ML file at location `./tmp581425` is invalid. | - The SED-ML file at location `./tmp205834` is invalid. | | | +| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | +| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | +| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
|
⚠ XFAILEXPECTED FAIL

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logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
|
⚠ XFAILEXPECTED FAIL

view
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logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
|
⚠ XFAILEXPECTED FAIL

view
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logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
|
⚠ XFAILEXPECTED FAIL

view
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logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
|
❌ FAILview
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logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | +| | | | - The SED-ML file at location `./tmp956852` is invalid. | - The SED-ML file at location `./tmp186426` is invalid. | | | +| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | +| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | +| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | +| | | | - The SED-ML file at location `./tmp868261` is invalid. | - The SED-ML file at location `./tmp37134` is invalid. | | | +| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | +| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | +| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
|
⚠ XFAILEXPECTED FAIL

view
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logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
|
❌ FAILview
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logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | +| | | | - The SED-ML file at location `./tmp399285` is invalid. | - The SED-ML file at location `./tmp453545` is invalid. | | | +| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | +| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | +| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 19 |
vcellhttps://github.com/virtualcell/vcell
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
|
❌ FAILview
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logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/test_suite/test_01186/tests/results_local.json b/test_suite/test_01186/tests/results_local.json new file mode 100644 index 00000000..03405273 --- /dev/null +++ b/test_suite/test_01186/tests/results_local.json @@ -0,0 +1,307 @@ +{ + "amici": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/amici' returned non-zero exit status 1", + "log_yml": { + "duration": 0.445042, + "exception": { + "message": "`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp640928` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "brian2": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.051707, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "bionetgen": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1", + "log_yml": { + "duration": 0.316504, + "exception": { + "message": "`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp46347` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` has warnings.\r\n - The model file `01186-sbml-l3v2.xml` has warnings.\r\n - 24 warnings of type SBML unit consistency (99508). The following is the first warning at line 72, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20518). The following is the first warning at line 72, column 6:\r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n - 23 warnings of type SBML unit consistency (20616). The following is the first warning at line 75, column 6:\r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp46347` has warnings.\r\n - Model `model_1` has warnings.\r\n - The model file `01186-sbml-l3v2.xml` has warnings.\r\n - 24 warnings of type SBML unit consistency (99508). The following is the first warning at line 72, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20518). The following is the first warning at line 72, column 6:\r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n - 23 warnings of type SBML unit consistency (20616). The following is the first warning at line 75, column 6:\r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "boolnet": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1", + "log_yml": { + "duration": 0.178893, + "exception": { + "message": "`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp433696` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` may be invalid.\r\n - The model file `01186-sbml-l3v2.xml` may be invalid.\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'A' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'B' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'B' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'C' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'C' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'D' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'D' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'E' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'E' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'F' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'F' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'G' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'G' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'H' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'H' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'I' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'I' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'J' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'J' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'K' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'K' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'L' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'L' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'M' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'N' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'N' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'O' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'O' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'P' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'P' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Q' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'Q' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'R' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'R' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'S' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'S' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'T' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'T' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'U' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'U' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'X' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'X' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Y' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'Y' does not have a substanceUnits attribute, nor does its enclosing .\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp433696` may be invalid.\r\n - Model `model_1` may be invalid.\r\n - The model file `01186-sbml-l3v2.xml` may be invalid.\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'A' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'B' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'B' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'C' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'C' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'D' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'D' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'E' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'E' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'F' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'F' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'G' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'G' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'H' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'H' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'I' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'I' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'J' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'J' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'K' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'K' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'L' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'L' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'M' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'N' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'N' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'O' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'O' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'P' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'P' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Q' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'Q' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'R' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'R' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'S' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'S' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'T' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'T' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'U' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'U' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'X' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'X' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Y' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'Y' does not have a substanceUnits attribute, nor does its enclosing .\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cbmpy": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.224672, + "exception": { + "message": "`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp385050` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` has warnings.\r\n - The model file `01186-sbml-l3v2.xml` has warnings.\r\n - 24 warnings of type SBML unit consistency (99508). The following is the first warning at line 72, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20518). The following is the first warning at line 72, column 6:\r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n - 23 warnings of type SBML unit consistency (20616). The following is the first warning at line 75, column 6:\r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp385050` has warnings.\r\n - Model `model_1` has warnings.\r\n - The model file `01186-sbml-l3v2.xml` has warnings.\r\n - 24 warnings of type SBML unit consistency (99508). The following is the first warning at line 72, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20518). The following is the first warning at line 72, column 6:\r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n - 23 warnings of type SBML unit consistency (20616). The following is the first warning at line 75, column 6:\r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cobrapy": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.159565, + "exception": { + "message": "`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp413781` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` has warnings.\r\n - The model file `01186-sbml-l3v2.xml` has warnings.\r\n - 24 warnings of type SBML unit consistency (99508). The following is the first warning at line 72, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20518). The following is the first warning at line 72, column 6:\r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n - 23 warnings of type SBML unit consistency (20616). The following is the first warning at line 75, column 6:\r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp413781` has warnings.\r\n - Model `model_1` has warnings.\r\n - The model file `01186-sbml-l3v2.xml` has warnings.\r\n - 24 warnings of type SBML unit consistency (99508). The following is the first warning at line 72, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20518). The following is the first warning at line 72, column 6:\r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n - 23 warnings of type SBML unit consistency (20616). The following is the first warning at line 75, column 6:\r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "copasi": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1", + "log_yml": { + "duration": 0.332948, + "exception": { + "message": "`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp332181` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` has warnings.\r\n - The model file `01186-sbml-l3v2.xml` has warnings.\r\n - 24 warnings of type SBML unit consistency (99508). The following is the first warning at line 72, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20518). The following is the first warning at line 72, column 6:\r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n - 23 warnings of type SBML unit consistency (20616). The following is the first warning at line 75, column 6:\r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp332181` has warnings.\r\n - Model `model_1` has warnings.\r\n - The model file `01186-sbml-l3v2.xml` has warnings.\r\n - 24 warnings of type SBML unit consistency (99508). The following is the first warning at line 72, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20518). The following is the first warning at line 72, column 6:\r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n - 23 warnings of type SBML unit consistency (20616). The following is the first warning at line 75, column 6:\r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "gillespy2": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/gillespy2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.177558, + "exception": { + "message": "`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp697896` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` has warnings.\r\n - The model file `01186-sbml-l3v2.xml` has warnings.\r\n - 24 warnings of type SBML unit consistency (99508). The following is the first warning at line 72, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20518). The following is the first warning at line 72, column 6:\r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n - 23 warnings of type SBML unit consistency (20616). The following is the first warning at line 75, column 6:\r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp697896` has warnings.\r\n - Model `model_1` has warnings.\r\n - The model file `01186-sbml-l3v2.xml` has warnings.\r\n - 24 warnings of type SBML unit consistency (99508). The following is the first warning at line 72, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20518). The following is the first warning at line 72, column 6:\r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n - 23 warnings of type SBML unit consistency (20616). The following is the first warning at line 75, column 6:\r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "ginsim": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.313585, + "exception": { + "message": "`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp90777` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` may be invalid.\r\n - The model file `01186-sbml-l3v2.xml` may be invalid.\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'A' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'B' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'B' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'C' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'C' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'D' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'D' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'E' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'E' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'F' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'F' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'G' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'G' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'H' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'H' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'I' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'I' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'J' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'J' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'K' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'K' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'L' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'L' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'M' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'N' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'N' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'O' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'O' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'P' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'P' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Q' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'Q' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'R' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'R' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'S' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'S' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'T' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'T' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'U' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'U' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'X' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'X' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Y' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'Y' does not have a substanceUnits attribute, nor does its enclosing .\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp90777` may be invalid.\r\n - Model `model_1` may be invalid.\r\n - The model file `01186-sbml-l3v2.xml` may be invalid.\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'A' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'B' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'B' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'C' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'C' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'D' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'D' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'E' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'E' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'F' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'F' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'G' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'G' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'H' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'H' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'I' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'I' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'J' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'J' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'K' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'K' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'L' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'L' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'M' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'N' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'N' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'O' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'O' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'P' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'P' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Q' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'Q' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'R' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'R' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'S' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'S' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'T' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'T' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'U' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'U' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'X' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'X' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Y' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'Y' does not have a substanceUnits attribute, nor does its enclosing .\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "libsbmlsim": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/libsbmlsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.291287, + "exception": { + "message": "`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp39181` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` may be invalid.\r\n - The model file `01186-sbml-l3v2.xml` may be invalid.\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'A' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'B' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'B' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'C' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'C' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'D' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'D' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'E' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'E' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'F' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'F' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'G' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'G' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'H' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'H' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'I' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'I' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'J' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'J' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'K' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'K' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'L' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'L' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'M' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'N' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'N' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'O' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'O' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'P' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'P' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Q' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'Q' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'R' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'R' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'S' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'S' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'T' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'T' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'U' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'U' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'X' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'X' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Y' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'Y' does not have a substanceUnits attribute, nor does its enclosing .\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp39181` may be invalid.\r\n - Model `model_1` may be invalid.\r\n - The model file `01186-sbml-l3v2.xml` may be invalid.\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'A' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'B' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'B' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'C' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'C' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'D' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'D' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'E' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'E' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'F' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'F' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'G' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'G' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'H' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'H' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'I' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'I' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'J' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'J' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'K' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'K' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'L' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'L' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'M' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'N' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'N' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'O' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'O' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'P' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'P' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Q' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'Q' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'R' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'R' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'S' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'S' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'T' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'T' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'U' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'U' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'X' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'X' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Y' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'Y' does not have a substanceUnits attribute, nor does its enclosing .\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "masspy": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.197211, + "exception": { + "message": "`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp205834` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` has warnings.\r\n - The model file `01186-sbml-l3v2.xml` has warnings.\r\n - 24 warnings of type SBML unit consistency (99508). The following is the first warning at line 72, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20518). The following is the first warning at line 72, column 6:\r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n - 23 warnings of type SBML unit consistency (20616). The following is the first warning at line 75, column 6:\r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp205834` has warnings.\r\n - Model `model_1` has warnings.\r\n - The model file `01186-sbml-l3v2.xml` has warnings.\r\n - 24 warnings of type SBML unit consistency (99508). The following is the first warning at line 72, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20518). The following is the first warning at line 72, column 6:\r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n - 23 warnings of type SBML unit consistency (20616). The following is the first warning at line 75, column 6:\r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\u001b[0m\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "netpyne": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1", + "log_yml": { + "duration": 0.284652, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "neuron": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1", + "log_yml": { + "duration": 0.043271, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "opencor": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1", + "log_yml": { + "duration": 0.02603, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pyneuroml": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1", + "log_yml": { + "duration": 0.045681, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pysces": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1", + "log_yml": { + "duration": 0.324198, + "exception": { + "message": "`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp186426` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` has warnings.\r\n - The model file `01186-sbml-l3v2.xml` has warnings.\r\n - 24 warnings of type SBML unit consistency (99508). The following is the first warning at line 72, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20518). The following is the first warning at line 72, column 6:\r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n - 23 warnings of type SBML unit consistency (20616). The following is the first warning at line 75, column 6:\r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp186426` has warnings.\r\n - Model `model_1` has warnings.\r\n - The model file `01186-sbml-l3v2.xml` has warnings.\r\n - 24 warnings of type SBML unit consistency (99508). The following is the first warning at line 72, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20518). The following is the first warning at line 72, column 6:\r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n - 23 warnings of type SBML unit consistency (20616). The following is the first warning at line 75, column 6:\r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "rbapy": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.131336, + "exception": { + "message": "`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp37134` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` may be invalid.\r\n - The model file `01186-sbml-l3v2.xml` may be invalid.\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'A' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'B' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'B' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'C' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'C' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'D' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'D' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'E' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'E' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'F' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'F' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'G' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'G' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'H' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'H' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'I' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'I' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'J' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'J' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'K' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'K' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'L' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'L' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'M' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'N' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'N' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'O' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'O' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'P' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'P' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Q' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'Q' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'R' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'R' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'S' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'S' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'T' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'T' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'U' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'U' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'X' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'X' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Y' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'Y' does not have a substanceUnits attribute, nor does its enclosing .\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp37134` may be invalid.\r\n - Model `model_1` may be invalid.\r\n - The model file `01186-sbml-l3v2.xml` may be invalid.\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'A' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'B' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'B' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'C' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'C' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'D' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'D' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'E' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'E' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'F' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'F' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'G' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'G' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'H' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'H' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'I' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'I' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'J' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'J' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'K' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'K' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'L' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'L' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'M' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'N' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'N' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'O' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'O' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'P' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'P' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Q' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'Q' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'R' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'R' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'S' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'S' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'T' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'T' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'U' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'U' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'X' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'X' does not have a substanceUnits attribute, nor does its enclosing .\r\n \r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Y' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'Y' does not have a substanceUnits attribute, nor does its enclosing .\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "smoldyn": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1", + "log_yml": {}, + "detailed_error_log": {} + }, + "tellurium": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/tellurium' returned non-zero exit status 1", + "log_yml": { + "duration": 0.416693, + "exception": { + "message": "`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp453545` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe SED document is potentially incorrect.\r\n - Model `model_1` has warnings.\r\n - The model file `01186-sbml-l3v2.xml` has warnings.\r\n - 24 warnings of type SBML unit consistency (99508). The following is the first warning at line 72, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20518). The following is the first warning at line 72, column 6:\r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n - 23 warnings of type SBML unit consistency (20616). The following is the first warning at line 75, column 6:\r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./tmp453545` has warnings.\r\n - Model `model_1` has warnings.\r\n - The model file `01186-sbml-l3v2.xml` has warnings.\r\n - 24 warnings of type SBML unit consistency (99508). The following is the first warning at line 72, column 6:\r\n - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n The units of the 'Cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 1 warning of type SBML unit consistency (20518). The following is the first warning at line 72, column 6:\r\n - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n Reference: L3V2 Section 4.5.4\r\n The 'Cell' has no discernable units.\r\n - 23 warnings of type SBML unit consistency (20616). The following is the first warning at line 75, column 6:\r\n - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\r\n Reference: L3V2 Section 4.6.5\r\n The with id 'A' does not have a substanceUnits attribute, nor does its enclosing .\u001b[0m\r\n\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "vcell": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1", + "log_yml": { + "duration": 2, + "exception": null, + "output": "Processing tmp291036. Done", + "sedDocuments": [], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": { + "status": "FAIL", + "error_message": "Runtime Exception" + } + }, + "xpp": { + "exception_message": "Command '-i /root/in/01186-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1", + "log_yml": { + "duration": 0.340051, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + } +} \ No newline at end of file diff --git a/test_suite/test_01186/tests/results_remote.json b/test_suite/test_01186/tests/results_remote.json new file mode 100644 index 00000000..1d109f3c --- /dev/null +++ b/test_suite/test_01186/tests/results_remote.json @@ -0,0 +1,356 @@ +{ + "amici": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b7265a60072d20f48b96", + "download": "https://api.biosimulations.org/results/6728b7265a60072d20f48b96/download", + "logs": "https://api.biosimulations.org/logs/6728b7265a60072d20f48b96?includeOutput=true", + "log_yml": { + "duration": 0.299356, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp267694` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "brian2": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b72a0d09353e8f0f8a88", + "download": "https://api.biosimulations.org/results/6728b72a0d09353e8f0f8a88/download", + "logs": "https://api.biosimulations.org/logs/6728b72a0d09353e8f0f8a88?includeOutput=true", + "log_yml": { + "duration": 0.058261, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "bionetgen": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b72b0d09353e8f0f8a8c", + "download": "https://api.biosimulations.org/results/6728b72b0d09353e8f0f8a8c/download", + "logs": "https://api.biosimulations.org/logs/6728b72b0d09353e8f0f8a8c?includeOutput=true", + "log_yml": { + "duration": 0.202798, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp347049` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "boolnet": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b72d5a60072d20f48b99", + "download": "https://api.biosimulations.org/results/6728b72d5a60072d20f48b99/download", + "logs": "https://api.biosimulations.org/logs/6728b72d5a60072d20f48b99?includeOutput=true", + "log_yml": { + "duration": 0.207202, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp838310` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "cbmpy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b72f5a60072d20f48b9e", + "download": "https://api.biosimulations.org/results/6728b72f5a60072d20f48b9e/download", + "logs": "https://api.biosimulations.org/logs/6728b72f5a60072d20f48b9e?includeOutput=true", + "log_yml": { + "duration": 0.335865, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp528257` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "cobrapy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b730b678b3883bb5df8f", + "download": "https://api.biosimulations.org/results/6728b730b678b3883bb5df8f/download", + "logs": "https://api.biosimulations.org/logs/6728b730b678b3883bb5df8f?includeOutput=true", + "log_yml": { + "duration": 0.201831, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp171288` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "copasi": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b7335a60072d20f48ba3", + "download": "https://api.biosimulations.org/results/6728b7335a60072d20f48ba3/download", + "logs": "https://api.biosimulations.org/logs/6728b7335a60072d20f48ba3?includeOutput=true", + "log_yml": { + "duration": 0.186713, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp860188` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "gillespy2": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b7350d09353e8f0f8a96", + "download": "https://api.biosimulations.org/results/6728b7350d09353e8f0f8a96/download", + "logs": "https://api.biosimulations.org/logs/6728b7350d09353e8f0f8a96?includeOutput=true", + "log_yml": { + "duration": 0.207018, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp595452` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "ginsim": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b7365a60072d20f48ba8", + "download": "https://api.biosimulations.org/results/6728b7365a60072d20f48ba8/download", + "logs": "https://api.biosimulations.org/logs/6728b7365a60072d20f48ba8?includeOutput=true", + "log_yml": { + "duration": 0.171673, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp956508` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "libsbmlsim": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b738b678b3883bb5dfa0", + "download": "https://api.biosimulations.org/results/6728b738b678b3883bb5dfa0/download", + "logs": "https://api.biosimulations.org/logs/6728b738b678b3883bb5dfa0?includeOutput=true", + "log_yml": { + "duration": 0.159555, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp385105` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "masspy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b73ab678b3883bb5dfa5", + "download": "https://api.biosimulations.org/results/6728b73ab678b3883bb5dfa5/download", + "logs": "https://api.biosimulations.org/logs/6728b73ab678b3883bb5dfa5?includeOutput=true", + "log_yml": { + "duration": 0.413051, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp581425` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "netpyne": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b73cb678b3883bb5dfb0", + "download": "https://api.biosimulations.org/results/6728b73cb678b3883bb5dfb0/download", + "logs": "https://api.biosimulations.org/logs/6728b73cb678b3883bb5dfb0?includeOutput=true", + "log_yml": { + "duration": 0.066357, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "neuron": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b73d5a60072d20f48be0", + "download": "https://api.biosimulations.org/results/6728b73d5a60072d20f48be0/download", + "logs": "https://api.biosimulations.org/logs/6728b73d5a60072d20f48be0?includeOutput=true", + "log_yml": { + "duration": 0.038132, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "opencor": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b73fb678b3883bb5dfcb", + "download": "https://api.biosimulations.org/results/6728b73fb678b3883bb5dfcb/download", + "logs": "https://api.biosimulations.org/logs/6728b73fb678b3883bb5dfcb?includeOutput=true", + "log_yml": { + "duration": 0.039215, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "pyneuroml": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b7415a60072d20f48bfc", + "download": "https://api.biosimulations.org/results/6728b7415a60072d20f48bfc/download", + "logs": "https://api.biosimulations.org/logs/6728b7415a60072d20f48bfc?includeOutput=true", + "log_yml": { + "duration": 0.043981, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "pysces": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b7435a60072d20f48c09", + "download": "https://api.biosimulations.org/results/6728b7435a60072d20f48c09/download", + "logs": "https://api.biosimulations.org/logs/6728b7435a60072d20f48c09?includeOutput=true", + "log_yml": { + "duration": 0.180308, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp956852` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "libtk8.6.so: cannot open shared object file: No such file or directory\r\n\r\nPySCeS defaults to matplotlib's TKagg backend if not specified in the user configuration file, set \"matplotlib_backend = \" \r\nMatplotlib interface loaded (pysces.plt.m)\r\nPitcon routines available\r\nNLEQ2 routines available\r\nSBML support available\r\nYou are using NumPy (2.1.2) with SciPy (1.14.1)\r\nAssimulo CVode available\r\nRateChar is available\r\nParallel scanner is available\r\n\r\nPySCeS environment\r\n******************\r\npysces.model_dir = /home/FCAM/crbmapi/Pysces/psc\r\npysces.output_dir = /home/FCAM/crbmapi/Pysces\r\n\r\n\r\n***********************************************************************\r\n* Welcome to PySCeS (1.2.2) - Python Simulator for Cellular Systems *\r\n* http://pysces.sourceforge.net *\r\n* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2024 *\r\n* Triple-J Group for Molecular Cell Physiology *\r\n* Stellenbosch University, ZA and VU University Amsterdam, NL *\r\n* PySCeS is distributed under the PySCeS (BSD style) licence, see *\r\n* LICENCE.txt (supplied with this release) for details *\r\n* Please cite PySCeS with: doi:10.1093/bioinformatics/bti046 *\r\n***********************************************************************\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "rbapy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b744b678b3883bb5dfe8", + "download": "https://api.biosimulations.org/results/6728b744b678b3883bb5dfe8/download", + "logs": "https://api.biosimulations.org/logs/6728b744b678b3883bb5dfe8?includeOutput=true", + "log_yml": { + "duration": 0.214364, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp868261` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "smoldyn": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b746b678b3883bb5dfee", + "download": "https://api.biosimulations.org/results/6728b746b678b3883bb5dfee/download", + "logs": "https://api.biosimulations.org/logs/6728b746b678b3883bb5dfee?includeOutput=true", + "log_yml": { + "duration": 0.05399, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "tellurium": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b7480d09353e8f0f8b0e", + "download": "https://api.biosimulations.org/results/6728b7480d09353e8f0f8b0e/download", + "logs": "https://api.biosimulations.org/logs/6728b7480d09353e8f0f8b0e?includeOutput=true", + "log_yml": { + "duration": 0.374941, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp399285` is invalid.\n - Data generator `OBJF_1` is invalid.\n - Variable `OBJF` is invalid.\n - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "vcell": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b74cb678b3883bb5e023", + "download": "https://api.biosimulations.org/results/6728b74cb678b3883bb5e023/download", + "logs": "https://api.biosimulations.org/logs/6728b74cb678b3883bb5e023?includeOutput=true", + "log_yml": { + "duration": null, + "exception": null, + "output": null, + "sedDocuments": [], + "skipReason": null, + "status": "QUEUED" + } + }, + "xpp": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6728b74d0d09353e8f0f8b26", + "download": "https://api.biosimulations.org/results/6728b74d0d09353e8f0f8b26/download", + "logs": "https://api.biosimulations.org/logs/6728b74d0d09353e8f0f8b26?includeOutput=true", + "log_yml": { + "duration": 0.06467, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + } +} \ No newline at end of file diff --git a/test_suite/test_test_suite_compatibility_biosimulators.py b/test_suite/test_test_suite_compatibility_biosimulators.py index f7161680..6e8dbaa2 100644 --- a/test_suite/test_test_suite_compatibility_biosimulators.py +++ b/test_suite/test_test_suite_compatibility_biosimulators.py @@ -46,8 +46,9 @@ def parse_arguments(): parser.add_argument( "--cases", - action="store", - type=list, + action="extend", + nargs="+", + type=str, default=[], help="Limit to the cases listed in the file. Empty list means no limit", ) @@ -106,7 +107,7 @@ def process_cases(args): print(f"Processing {len(subfolders)} subfolders in {args.suite_path}") test_folder = 'tests' - for subfolder in subfolders: + for subfolder in args.cases: # create an equivalently named folder in the starting directory os.chdir(args.suite_path) print(f"Processing {subfolder}") @@ -139,9 +140,10 @@ def process_cases(args): os.chdir(new_directory) print(f"Changed to {new_directory}") - engines_list = list(engines.keys()) + engine_list = list(engines.keys()) - utils.run_biosimulators_remotely_and_locally(os.path.basename(sedml_file_path), + utils.run_biosimulators_remotely_and_locally(engine_list, + os.path.basename(sedml_file_path), os.path.basename(sbml_file_path), os.path.join(test_folder,'d1_plots_remote'), os.path.join(test_folder,'d1_plots_local'), @@ -149,7 +151,7 @@ def process_cases(args): if __name__ == "__main__": - args = parse_arguments() + args = parse_arguments() process_cases(args) diff --git a/utils/__init__.py b/utils/__init__.py index 6b41d690..1c1151c8 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -21,6 +21,7 @@ from pyneuroml import biosimulations import pandas as pd from requests.exceptions import HTTPError +import json ENGINES = { 'amici': { @@ -1233,6 +1234,15 @@ def create_combined_results_table(results_remote, suffix_remote = ' (R)' suffix_local = ' (L)' + + # save results_remote and results_local as json files with dicts + path_to_results_remote = os.path.join(test_folder, 'results_remote.json') + path_to_results_local = os.path.join(test_folder, 'results_local.json') + + with open(path_to_results_remote, 'w') as f: + json.dump(results_remote, f, indent=4) + with open(path_to_results_local, 'w') as f: + json.dump(results_local, f, indent=4) # Create results tables for remote and local results results_table_remote = create_results_table(results_remote, sbml_file_name, sedml_file_name, d1_plots_remote_dir) From a979a7ccd6268e4407b820d446b64b0174032dd9 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 4 Nov 2024 13:08:51 +0000 Subject: [PATCH 03/22] add sedml and sbml files of case 01186 --- .../test_01186/01186-sbml-l3v2-sedml.xml | 50 ++ test_suite/test_01186/01186-sbml-l3v2.xml | 633 ++++++++++++++++++ 2 files changed, 683 insertions(+) create mode 100644 test_suite/test_01186/01186-sbml-l3v2-sedml.xml create mode 100644 test_suite/test_01186/01186-sbml-l3v2.xml diff --git a/test_suite/test_01186/01186-sbml-l3v2-sedml.xml b/test_suite/test_01186/01186-sbml-l3v2-sedml.xml new file mode 100644 index 00000000..e966115b --- /dev/null +++ b/test_suite/test_01186/01186-sbml-l3v2-sedml.xml @@ -0,0 +1,50 @@ + + + + + + + + + + + + + + + + + + + + + R01 + + + + + + + + R26 + + + + + + + + OBJF + + + + + + + + + + + + + \ No newline at end of file diff --git a/test_suite/test_01186/01186-sbml-l3v2.xml b/test_suite/test_01186/01186-sbml-l3v2.xml new file mode 100644 index 00000000..69fee4af --- /dev/null +++ b/test_suite/test_01186/01186-sbml-l3v2.xml @@ -0,0 +1,633 @@ + + + + + +

+ Maximize single objective function, hard bounds. +

+ + + + + + + + + + Olivier + Brett + + bgoli@users.sourceforge.net + + VU university Amsterdam + + + + + + 2012-12-21T11:05:21Z + + + 2012-12-21T10:05:21Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

subsystem: C3

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subsystem: C3

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subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C2

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: C1

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

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+ + + + + + + + + + + + + + + + + +

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+ + + + + + + + + + + + + + + + + +

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+ + + + + + + + + + + + + + + + + +

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+ + + + + + + + + + + + + + + + + +

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+ + + + + + + + + + + + + + + + + +

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+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: C4

+ + + + + + + + + + + + + + + + + +

subsystem: L

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + +

subsystem: C3

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From 1959b391ec629d572656717c30dc7292bb3e3770 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 4 Nov 2024 14:53:03 +0000 Subject: [PATCH 04/22] update ansi_to_html --- .../results_compatibility_biosimulators.md | 46 ++++----- .../results_compatibility_biosimulators.md | 46 ++++----- .../results_compatibility_biosimulators.md | 98 +++++-------------- test_suite/test_test_suite_results_table.py | 68 +++++++++++++ utils/__init__.py | 15 +-- 5 files changed, 142 insertions(+), 131 deletions(-) create mode 100644 test_suite/test_test_suite_results_table.py diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md index e4cedfa3..2e280e3c 100644 --- a/SBML/tests/results_compatibility_biosimulators.md +++ b/SBML/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | -|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------| -| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
|
❌ FAILview
download
logs

ERROR MESSAGE:
Reached maximum number of steps

|
❌ FAILERROR MESSAGE:
Reached maximum number of steps

| plot | plot | -| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 19 |
vcellhttps://github.com/virtualcell/vcell
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | -| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------| +| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
|
❌ FAILview
download
logs

ERROR MESSAGE:
Reached maximum number of steps

|
❌ FAILERROR MESSAGE:
Reached maximum number of steps

| plot | plot | +| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 19 |
vcellhttps://github.com/virtualcell/vcell
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/test_suite/test_00001/tests/results_compatibility_biosimulators.md b/test_suite/test_00001/tests/results_compatibility_biosimulators.md index d36280a6..42a52340 100644 --- a/test_suite/test_00001/tests/results_compatibility_biosimulators.md +++ b/test_suite/test_00001/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | -|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------|:--------------------------------------------------------| -| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']

Only following targets are supported:
- M_S1
- M_S2
- R_reaction1
- S1
- S2
- k1
- reaction1

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 19 |
vcellhttps://github.com/virtualcell/vcell
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | -| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------| +| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with amici. ['SBML', 'SED-ML'] are compatible with amici
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with copasi. ['SBML', 'SED-ML'] are compatible with copasi
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with masspy. ['SBML', 'SED-ML'] are compatible with masspy
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']

Only following targets are supported:
- M_S1
- M_S2
- R_reaction1
- S1
- S2
- k1
- reaction1

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with pysces. ['SBML', 'SED-ML'] are compatible with pysces
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 19 |
vcellhttps://github.com/virtualcell/vcell
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/test_suite/test_01186/tests/results_compatibility_biosimulators.md b/test_suite/test_01186/tests/results_compatibility_biosimulators.md index a382fc23..be3b84fe 100644 --- a/test_suite/test_01186/tests/results_compatibility_biosimulators.md +++ b/test_suite/test_01186/tests/results_compatibility_biosimulators.md @@ -1,75 +1,23 @@ -| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | -|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------|:---------| -| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | -| | | | - The SED-ML file at location `./tmp267694` is invalid. | - The SED-ML file at location `./tmp640928` is invalid. | | | -| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | -| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | -| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | -| | | | - The SED-ML file at location `./tmp347049` is invalid. | - The SED-ML file at location `./tmp46347` is invalid. | | | -| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | -| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | -| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | -| | | | - The SED-ML file at location `./tmp838310` is invalid. | - The SED-ML file at location `./tmp433696` is invalid. | | | -| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | -| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | -| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | -| | | | - The SED-ML file at location `./tmp528257` is invalid. | - The SED-ML file at location `./tmp385050` is invalid. | | | -| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | -| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | -| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | -| | | | - The SED-ML file at location `./tmp171288` is invalid. | - The SED-ML file at location `./tmp413781` is invalid. | | | -| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | -| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | -| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | -| | | | - The SED-ML file at location `./tmp860188` is invalid. | - The SED-ML file at location `./tmp332181` is invalid. | | | -| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | -| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | -| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | -| | | | - The SED-ML file at location `./tmp595452` is invalid. | - The SED-ML file at location `./tmp697896` is invalid. | | | -| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | -| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | -| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | -| | | | - The SED-ML file at location `./tmp956508` is invalid. | - The SED-ML file at location `./tmp90777` is invalid. | | | -| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | -| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | -| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | -| | | | - The SED-ML file at location `./tmp385105` is invalid. | - The SED-ML file at location `./tmp39181` is invalid. | | | -| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | -| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | -| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | -| | | | - The SED-ML file at location `./tmp581425` is invalid. | - The SED-ML file at location `./tmp205834` is invalid. | | | -| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | -| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | -| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | -| | | | - The SED-ML file at location `./tmp956852` is invalid. | - The SED-ML file at location `./tmp186426` is invalid. | | | -| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | -| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | -| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | -| | | | - The SED-ML file at location `./tmp868261` is invalid. | - The SED-ML file at location `./tmp37134` is invalid. | | | -| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | -| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | -| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive. |
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive. | | | -| | | | - The SED-ML file at location `./tmp399285` is invalid. | - The SED-ML file at location `./tmp453545` is invalid. | | | -| | | | - Data generator `OBJF_1` is invalid. | - Data generator `OBJF_1` is invalid. | | | -| | | | - Variable `OBJF` is invalid. | - Variable `OBJF` is invalid. | | | -| | | | - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 19 |
vcellhttps://github.com/virtualcell/vcell
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | -| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------|:---------| +| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp267694` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp640928` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp347049` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp46347` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp838310` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp433696` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp528257` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp385050` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp171288` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp413781` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp860188` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp332181` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp595452` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp697896` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp956508` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp90777` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp385105` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp39181` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp581425` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp205834` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp956852` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp186426` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp868261` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp37134` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp399285` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp453545` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 19 |
vcellhttps://github.com/virtualcell/vcell
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/test_suite/test_test_suite_results_table.py b/test_suite/test_test_suite_results_table.py new file mode 100644 index 00000000..7a94e34c --- /dev/null +++ b/test_suite/test_test_suite_results_table.py @@ -0,0 +1,68 @@ +#!/usr/bin/env python3 + +""" +produce a markdown table of the results of running various tests on the SBML Test Suite + +get this version of the test suite that includes sedml versions or the sedml validation will fail: +https://github.com/sbmlteam/sbml-test-suite/releases/download/3.4.0/semantic_tests_with_sedml_and_graphs.v3.4.0.zip +""" + +import os +import sys +import json +sys.path.append("..") +import utils +engines = utils.ENGINES + + +def create_test_suite_results_tables(): + """ + Create a table of results for each test case in the test suite + + """ + starting_dir = os.getcwd() + print('Current working directory:', starting_dir) + subfolders = [f for f in os.listdir(starting_dir) if os.path.isdir(f) and f.startswith('test_')] + + print(subfolders) + + for subfolder in subfolders: + subfolder_path = os.path.join(starting_dir, subfolder) + os.chdir(subfolder_path) + print(f"Changed to {os.getcwd()}") + + test_folder = 'tests' + + results_paths = { + "local": os.path.join(subfolder_path, test_folder, 'results_local.json'), + "remote": os.path.join(subfolder_path, test_folder, 'results_remote.json') + } + + results = {} + for key, path in results_paths.items(): + with open(path, 'r') as f: + results[key] = json.load(f) + + d1_plot_paths = { + "local": os.path.join(subfolder_path, test_folder, 'd1_plots_local'), + "remote": os.path.join(subfolder_path, test_folder, 'd1_plots_remote') + } + + # get sbml filename with reg ex (it should contain sbml but not sedml) + sbml_file_name = [f for f in os.listdir(subfolder_path) if 'sbml' in f and 'sedml' not in f][0] + sedml_file_name = [f for f in os.listdir(subfolder_path) if 'sedml' in f][0] + + results_table = utils.create_combined_results_table(results["remote"], + results["local"], + sedml_file_name, + sbml_file_name, + d1_plot_paths["local"], + d1_plot_paths["remote"], + test_folder='tests') + + + print(results_table) + + +if __name__ == "__main__": + create_test_suite_results_tables() diff --git a/utils/__init__.py b/utils/__init__.py index 1c1151c8..a7592a85 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -398,11 +398,8 @@ def ansi_to_html(text): if len(text_message) > 0: text = text_message text = bytes(text[0], "utf-8").decode("unicode_escape") - elif 'The COMBINE/OMEX did not execute successfully:' in text: - text = text # to deal with remote error message - else: - text = text.replace('|', '') - return text + # elif 'The COMBINE/OMEX did not execute successfully:' in text: + # text = text # to deal with remote error message text = text.replace('|', '') @@ -410,8 +407,8 @@ def ansi_to_html(text): text = re.sub(r'<([^>]*)>', r'\1', text) # replace color codes with html color codes - text = text.replace("\x1b[33m",'') - text = text.replace("\x1b[31m",'') + text = text.replace("\x1b[33m","") + text = text.replace("\x1b[31m","") # # remove .\x1b[0m text = text.replace("\x1b[0m", "") @@ -430,9 +427,7 @@ def ansi_to_html(text): text = text.replace('BioSimulatorsWarning:', '

BioSimulatorsWarning:

') text = text.replace('warnings.warn(termcolor.colored(message, Colors.warning.value), category)', '
') - # if text includes The COMBINE/OMEX did not execute successfully: make everyhting from that point red - text = text.replace('The COMBINE/OMEX did not execute successfully:', 'The COMBINE/OMEX did not execute successfully:') - return text + return text def check_file_compatibility_test(engine, model_filepath, experiment_filepath): ''' From 228eace9df7c33f02930e61ecc4826b2133e1046 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 4 Nov 2024 14:57:54 +0000 Subject: [PATCH 05/22] remvoe test code for case handling --- test_suite/process_test_suite.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/test_suite/process_test_suite.py b/test_suite/process_test_suite.py index 0d3ca223..643175e4 100755 --- a/test_suite/process_test_suite.py +++ b/test_suite/process_test_suite.py @@ -125,9 +125,7 @@ def process_cases(args): # Suppress specific UserWarning caused by matplotlib (required to suppress interactive plots) warnings.filterwarnings("ignore", category=UserWarning, message="FigureCanvasAgg is non-interactive, and thus cannot be shown") subfolders = os.listdir(suite_path_abs) if args.limit == 0 else os.listdir(suite_path_abs)[:args.limit] - # do same for cases - subfolders = os.listdir(suite_path_abs) if args.cases == [] else os.listdir(suite_path_abs)cases - + for subfolder in subfolders: # if sbml_level_version is empty string (default), find the highest level and version in the folder if args.sbml_level_version == "highest": From 58917f97ffea08289979eec2d2acc1a7b61c5ca9 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 4 Nov 2024 15:04:17 +0000 Subject: [PATCH 06/22] enable processing of a given list of cases, or a limit of cases that are processed sequentially when an empty lissed is passed --- .../test_test_suite_compatibility_biosimulators.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/test_suite/test_test_suite_compatibility_biosimulators.py b/test_suite/test_test_suite_compatibility_biosimulators.py index 6e8dbaa2..f7221b39 100644 --- a/test_suite/test_test_suite_compatibility_biosimulators.py +++ b/test_suite/test_test_suite_compatibility_biosimulators.py @@ -102,12 +102,16 @@ def process_cases(args): os.chdir(args.suite_path) # change to test suite directory suite_path_abs = os.getcwd() # absolute path to test suite - subfolders = os.listdir(suite_path_abs) if args.limit == 0 else os.listdir(suite_path_abs)[:args.limit] - # subfolders = os.listdir(suite_path_abs) if args.cases == [] else os.listdir(suite_path_abs)[args.cases] + if args.cases != []: + subfolders = args.cases + else: + subfolders = os.listdir(suite_path_abs) if args.limit == 0 else os.listdir(suite_path_abs)[:args.limit] + print(f"Processing {len(subfolders)} subfolders in {args.suite_path}") test_folder = 'tests' - for subfolder in args.cases: + + for subfolder in subfolders: # create an equivalently named folder in the starting directory os.chdir(args.suite_path) print(f"Processing {subfolder}") From a6e7d65112d57c07488f53a4e5a77040cc40a4ee Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 4 Nov 2024 15:10:39 +0000 Subject: [PATCH 07/22] correct handling of cases in proces_test_suite script --- test_suite/process_test_suite.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/test_suite/process_test_suite.py b/test_suite/process_test_suite.py index 643175e4..9b211172 100755 --- a/test_suite/process_test_suite.py +++ b/test_suite/process_test_suite.py @@ -47,8 +47,9 @@ def parse_arguments(): parser.add_argument( "--cases", - action="store", - type=list, + action="extend", + nargs="+", + type=str, default=[], help="Limit to the cases listed in the file. Empty list means no limit", ) From 43e2d40bef78ae10732016286e6ccdabafa21a4d Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 4 Nov 2024 15:15:07 +0000 Subject: [PATCH 08/22] add full stop ad end of sentence in compatibility check messages in check_file_compatibility_test function --- utils/__init__.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/utils/__init__.py b/utils/__init__.py index a7592a85..cd74f0cf 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -442,11 +442,11 @@ def check_file_compatibility_test(engine, model_filepath, experiment_filepath): if input_filetypes_tuple in engine_filetypes_tuple_list: file_types = [TYPES[i] for i in input_filetypes_tuple] - return 'pass', (f"The file extensions {input_filetypes_tuple} suggest the input file types are '{file_types}'. {compatible_filetypes} are compatible with {engine}") + return 'pass', (f"The file extensions {input_filetypes_tuple} suggest the input file types are '{file_types}'. {compatible_filetypes} are compatible with {engine}.") if 'xml' in input_filetypes_tuple: - return 'unsure', (f"The file extensions of the input files are '{input_filetypes_tuple}'. These may be compatible with {engine}. {compatible_filetypes} are compatible with {engine}") + return 'unsure', (f"The file extensions of the input files are '{input_filetypes_tuple}'. These may be compatible with {engine}. {compatible_filetypes} are compatible with {engine}.") else: - return 'FAIL', (f"The file extensions {input_filetypes_tuple} suggest the input file types are not compatibe with {engine}. {compatible_filetypes} are compatible with {engine}") + return 'FAIL', (f"The file extensions {input_filetypes_tuple} suggest the input file types are not compatibe with {engine}. {compatible_filetypes} are compatible with {engine}.") def collapsible_content(content, title='Details'): From 5cd032878d8661f8125624aa210095511023cda2 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 4 Nov 2024 15:28:52 +0000 Subject: [PATCH 09/22] exclude files ending with 'omex' in test suite results table --- .../results_compatibility_biosimulators.md | 46 +++++++++--------- .../test_00001/00001-sbml-l3v2-sedml.omex | Bin 1989 -> 0 bytes .../results_compatibility_biosimulators.md | 46 +++++++++--------- .../results_compatibility_biosimulators.md | 46 +++++++++--------- test_suite/test_test_suite_results_table.py | 4 +- 5 files changed, 72 insertions(+), 70 deletions(-) delete mode 100644 test_suite/test_00001/00001-sbml-l3v2-sedml.omex diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md index 2e280e3c..1e52472d 100644 --- a/SBML/tests/results_compatibility_biosimulators.md +++ b/SBML/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | -|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------| -| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
|
❌ FAILview
download
logs

ERROR MESSAGE:
Reached maximum number of steps

|
❌ FAILERROR MESSAGE:
Reached maximum number of steps

| plot | plot | -| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 19 |
vcellhttps://github.com/virtualcell/vcell
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | -| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------| +| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici.
|
❌ FAILview
download
logs

ERROR MESSAGE:
Reached maximum number of steps

|
❌ FAILERROR MESSAGE:
Reached maximum number of steps

| plot | plot | +| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 19 |
vcellhttps://github.com/virtualcell/vcell
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/test_suite/test_00001/00001-sbml-l3v2-sedml.omex b/test_suite/test_00001/00001-sbml-l3v2-sedml.omex deleted file mode 100644 index ec0894cacfe5ae5324b2024f3020fb40a845b0c2..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 1989 zcmZ`)XH*jg7Y)m@2^#@RAZ!Q?1ft9`+d?owmh4qo3CIZ3f;ROBq$7pAWU+kC z;+X*e?sE+Eyy@@bjSW+a3Jj>kcOzM(fyp%aP8Nc0{e0#?VP!`&;}M@BnQYP1b>UHw zL8oSIQwrMaRSuMLHpYFrVQ4g3n2wq-tP%%`xr)auT#SnQB?ndSNTKYf(&^}jQVsP) ztp>3}kJ8e{1C}2S9@YW#_mFL-&QjO%Ib1s;3RK#*z($j}_z|J*LqwRgtML&ajHcE9(#wVhk@&K1NF(KeBF?QQn8yRKqj#U^~(NI}k;%jeUu zkQnn^;nst|X!c2kBi&71O3wP0S1znx#@O1e4@yT#gUm)?PO3jUJW0BoD7qO$F{SD8 z#faJ}S;rrVKy^?*!CRQBy7*4I|L|B#xw9M$kdOXCqwXWx@Uj3qO7DHi;Q7ahY27*<3#;wNGOqE1gnI&dyJyYOe97QhTeN`|c9!|qP zqV1HKF(b{hQVI{R7JZ6SYaXKcA=RSgWSKP6%L3rzVWCb|X6mqCyokap`N}H!imKCY zyEZv3LjYX)$fl{KsJk{KZv%cMNsE}=A28fl{7F0NfdFHtO6+zE(f~R5ctbP;WT>0G z#cy_9K*z<#^?jmmqL$r;kB`bTu#He}KdA>X)+o?F7lCe1CyyI~w4Bf*usl6M#vEDs z<7FTIeTT3mG;^ebf##tFO11r>SQuipK=nUwBEXlNYW7NIZtEToL6AH#Ny48kIc4fs z%008gA7-V!ovKi&_b()bAFo=+_TpBw!6e5wh$@{q*@Q0JnX)z&>zfR1U)KcJ8@r{( z5J{b6(RGL4Xf5-_dHaO$NT@i^glSMiT&~2N+`UPxM|RjP{eT9`kpUNd*R1q>)*4%L zI(L~Rj-aQUZ-79Qd-nQ*uKBnqDXChF0ho~%1P zn^zQL!oNvET~R!tfdcXLAYM-QKBG2ezV=s`mzLDn`SwM`fL)Y#+l}O!nb8_TYr3m@ zxgr0P_>R}#YST#qRh_5Sf(_bJK%^09C04o9BUL}F<@A)Q=JC~nz->bkJ?Vi_Hg zFCx7S##cU$@}|0M{)AJ|NKDa4{Ed5An(328Mz+n<&9%36{3J@(W*p#eW6c{&IwtWz z=lst93xOQ~5Ii>)^t{v|Sg*hUNB}HCC7_o_wK3m~iY!BNLuA%v_}6 z8BBo)GoN(v1?5Ug3X<`9SRc={mlw@X^zJDanD7P5q$tQqPJZaMkV5D6w5DXf@or3+uwqIBICb4p=4ytgn}q_WQdbmH zX8x2qRf!7IeKl8r*(qEJQYgV3-M=zuejL~;(rizr$V+}_0J(Q>D|4L7$0bWuCaK+| zDvi1kI5v=geEE!q?6lj2F;vGX}xjC%Ij_1(Qa+~O*p z-trRMG1gonoTSHVn0Ts=-c}m#w_5-XiRDb#wUI9_qiqW(ZQx4#ya!&I0;zfMeNE!* zZP#**Ga#LoLC@~$=CeXDF$)3yfBc&7@CCjO!+$FOnHK-m0RT-2TufhO$Jerd b^TOY<8?6883@ZfNg)c)a=S@1t)4$lCR#txD diff --git a/test_suite/test_00001/tests/results_compatibility_biosimulators.md b/test_suite/test_00001/tests/results_compatibility_biosimulators.md index 42a52340..90fe7e21 100644 --- a/test_suite/test_00001/tests/results_compatibility_biosimulators.md +++ b/test_suite/test_00001/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | -|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------| -| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with amici. ['SBML', 'SED-ML'] are compatible with amici
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with copasi. ['SBML', 'SED-ML'] are compatible with copasi
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with masspy. ['SBML', 'SED-ML'] are compatible with masspy
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']

Only following targets are supported:
- M_S1
- M_S2
- R_reaction1
- S1
- S2
- k1
- reaction1

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with pysces. ['SBML', 'SED-ML'] are compatible with pysces
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 19 |
vcellhttps://github.com/virtualcell/vcell
|
❌ FAILThe file extensions other suggest the input file types are not compatibe with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | -| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions other suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------| +| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']

Only following targets are supported:
- M_S1
- M_S2
- R_reaction1
- S1
- S2
- k1
- reaction1

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 19 |
vcellhttps://github.com/virtualcell/vcell
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/test_suite/test_01186/tests/results_compatibility_biosimulators.md b/test_suite/test_01186/tests/results_compatibility_biosimulators.md index be3b84fe..0964ba94 100644 --- a/test_suite/test_01186/tests/results_compatibility_biosimulators.md +++ b/test_suite/test_01186/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | -|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------|:---------| -| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp267694` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp640928` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp347049` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp46347` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp838310` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp433696` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp528257` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp385050` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp171288` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp413781` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp860188` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp332181` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp595452` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp697896` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp956508` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp90777` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp385105` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp39181` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp581425` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp205834` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp956852` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp186426` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp868261` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp37134` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp399285` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp453545` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 19 |
vcellhttps://github.com/virtualcell/vcell
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | -| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------|:---------| +| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp267694` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp640928` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp347049` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp46347` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp838310` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp433696` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp528257` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp385050` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp171288` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp413781` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp860188` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp332181` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp595452` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp697896` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp956508` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp90777` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp385105` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp39181` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp581425` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp205834` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp956852` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp186426` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp868261` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp37134` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp399285` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp453545` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 19 |
vcellhttps://github.com/virtualcell/vcell
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/test_suite/test_test_suite_results_table.py b/test_suite/test_test_suite_results_table.py index 7a94e34c..b849257e 100644 --- a/test_suite/test_test_suite_results_table.py +++ b/test_suite/test_test_suite_results_table.py @@ -50,7 +50,9 @@ def create_test_suite_results_tables(): # get sbml filename with reg ex (it should contain sbml but not sedml) sbml_file_name = [f for f in os.listdir(subfolder_path) if 'sbml' in f and 'sedml' not in f][0] - sedml_file_name = [f for f in os.listdir(subfolder_path) if 'sedml' in f][0] + # also sbml file does not end with omex + sbml_file_name = [f for f in os.listdir(subfolder_path) if 'sbml' in f and 'sedml' not in f and not f.endswith('omex')][0] + sedml_file_name = [f for f in os.listdir(subfolder_path) if 'sedml' in f and not f.endswith('omex')][0] results_table = utils.create_combined_results_table(results["remote"], results["local"], From 744a15ec9cbcd54d84d8d40507eac78561e2d59b Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 4 Nov 2024 16:46:12 +0000 Subject: [PATCH 10/22] Improve compatibility messages. When files have an .xml extension but 'sbml' or 'sbml' and 'sedml' in the filename they can be labeled as SBML and SEDML (test suite) --- .../results_compatibility_biosimulators.md | 46 +++++++------- .../results_compatibility_biosimulators.md | 46 +++++++------- .../results_compatibility_biosimulators.md | 46 +++++++------- utils/__init__.py | 63 ++++++++++++------- 4 files changed, 110 insertions(+), 91 deletions(-) diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md index 1e52472d..3092d5e7 100644 --- a/SBML/tests/results_compatibility_biosimulators.md +++ b/SBML/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | -|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------| -| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici.
|
❌ FAILview
download
logs

ERROR MESSAGE:
Reached maximum number of steps

|
❌ FAILERROR MESSAGE:
Reached maximum number of steps

| plot | plot | -| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 19 |
vcellhttps://github.com/virtualcell/vcell
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | -| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------| +| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici.
|
❌ FAILview
download
logs

ERROR MESSAGE:
Reached maximum number of steps

|
❌ FAILERROR MESSAGE:
Reached maximum number of steps

| plot | plot | +| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatibe with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatibe with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatibe with brian2.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatibe with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatibe with netpyne.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatibe with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatibe with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatibe with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatibe with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatibe with smoldyn.

['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 19 |
vcellhttps://github.com/virtualcell/vcell
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatibe with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/test_suite/test_00001/tests/results_compatibility_biosimulators.md b/test_suite/test_00001/tests/results_compatibility_biosimulators.md index 90fe7e21..60056dcf 100644 --- a/test_suite/test_00001/tests/results_compatibility_biosimulators.md +++ b/test_suite/test_00001/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | -|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------| -| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']

Only following targets are supported:
- M_S1
- M_S2
- R_reaction1
- S1
- S2
- k1
- reaction1

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 19 |
vcellhttps://github.com/virtualcell/vcell
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | -| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------| +| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with amici.

['SBML', 'SED-ML'] are compatible with amici.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with brian2.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with cbmpy.

['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with cobrapy.

['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with copasi.

['SBML', 'SED-ML'] are compatible with copasi.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with gillespy2.

['SBML', 'SED-ML'] are compatible with gillespy2.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with libsbmlsim.

['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with masspy.

['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']

Only following targets are supported:
- M_S1
- M_S2
- R_reaction1
- S1
- S2
- k1
- reaction1

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with netpyne.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with pysces.

['SBML', 'SED-ML'] are compatible with pysces.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with smoldyn.

['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with tellurium.

['SBML', 'SED-ML'] are compatible with tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 19 |
vcellhttps://github.com/virtualcell/vcell
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with vcell.

['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
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logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/test_suite/test_01186/tests/results_compatibility_biosimulators.md b/test_suite/test_01186/tests/results_compatibility_biosimulators.md index 0964ba94..b6f70c9c 100644 --- a/test_suite/test_01186/tests/results_compatibility_biosimulators.md +++ b/test_suite/test_01186/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | -|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------|:---------| -| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp267694` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp640928` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp347049` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp46347` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp838310` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp433696` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp528257` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp385050` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp171288` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp413781` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp860188` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp332181` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp595452` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp697896` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp956508` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp90777` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp385105` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp39181` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp581425` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp205834` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp956852` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp186426` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp868261` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp37134` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp399285` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp453545` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 19 |
vcellhttps://github.com/virtualcell/vcell
|
⚠ WARNINGThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | -| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------|:---------| +| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with amici.

['SBML', 'SED-ML'] are compatible with amici.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp267694` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp640928` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp347049` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp46347` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp838310` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp433696` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with brian2.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with cbmpy.

['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp528257` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp385050` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with cobrapy.

['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp171288` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp413781` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with copasi.

['SBML', 'SED-ML'] are compatible with copasi.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp860188` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp332181` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with gillespy2.

['SBML', 'SED-ML'] are compatible with gillespy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp595452` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp697896` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp956508` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp90777` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with libsbmlsim.

['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp385105` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp39181` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with masspy.

['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp581425` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp205834` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with netpyne.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with pysces.

['SBML', 'SED-ML'] are compatible with pysces.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp956852` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp186426` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp868261` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp37134` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with smoldyn.

['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with tellurium.

['SBML', 'SED-ML'] are compatible with tellurium.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp399285` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp453545` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 19 |
vcellhttps://github.com/virtualcell/vcell
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with vcell.

['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/utils/__init__.py b/utils/__init__.py index cd74f0cf..5a23c134 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -432,21 +432,27 @@ def ansi_to_html(text): def check_file_compatibility_test(engine, model_filepath, experiment_filepath): ''' Check if the file extensions suggest the file types are compatible with the engine. - This is done by comparing the file extensions of the model and experiment files with the file types supported by the engine. - For SED-ML files, the expected file extension is '.sedml'. For SBML files, the expected file extension is '.sbml'. + Only .sedml and .sbml files, and .xml files with 'sedml' and/or 'sbml' in their filename + are considered at this moment. It can be extended to other cases if needed in the future. ''' - input_filetypes_tuple = get_filetypes(model_filepath, experiment_filepath) + file_extensions = get_filetypes(model_filepath, experiment_filepath) engine_filetypes_tuple_list = ENGINES[engine]['formats'] flat_engine_filetypes_tuple_list = [item for sublist in engine_filetypes_tuple_list for item in sublist if sublist != 'unclear'] compatible_filetypes = [TYPES[i] for i in flat_engine_filetypes_tuple_list if i in list(TYPES.keys())] - if input_filetypes_tuple in engine_filetypes_tuple_list: - file_types = [TYPES[i] for i in input_filetypes_tuple] - return 'pass', (f"The file extensions {input_filetypes_tuple} suggest the input file types are '{file_types}'. {compatible_filetypes} are compatible with {engine}.") - if 'xml' in input_filetypes_tuple: - return 'unsure', (f"The file extensions of the input files are '{input_filetypes_tuple}'. These may be compatible with {engine}. {compatible_filetypes} are compatible with {engine}.") + if file_extensions in engine_filetypes_tuple_list: + file_types = [TYPES[i] for i in file_extensions] + return 'pass', (f"The file extensions {file_extensions} suggest the input file types are '{file_types}'. {compatible_filetypes} are compatible with {engine}.") + if 'xml' in file_extensions: + if 'sbml' in model_filepath and 'sedml' not in model_filepath: + if 'sbml' in experiment_filepath and 'sedml' in experiment_filepath: + file_types = ('sbml', 'sedml') + if file_types in engine_filetypes_tuple_list: + return 'pass', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {[TYPES[i] for i in file_types]} which is compatible with {engine}.

{compatible_filetypes} are compatible with {engine}.") + else: + return 'unsure', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {[TYPES[i] for i in file_types]} which is not compatible with {engine}.

{compatible_filetypes} are compatible with {engine}.") else: - return 'FAIL', (f"The file extensions {input_filetypes_tuple} suggest the input file types are not compatibe with {engine}. {compatible_filetypes} are compatible with {engine}.") + return 'unsure', (f"The file extensions {file_extensions} suggest the input file types may not be compatibe with {engine}.

{compatible_filetypes} are compatible with {engine}.") def collapsible_content(content, title='Details'): @@ -459,7 +465,7 @@ def collapsible_content(content, title='Details'): return f'
{title}{content}
' else: return f'{title}' - + def get_filetypes(model_filepath, simulation_filepath): """ Get the filetypes of the model and simulation files @@ -467,17 +473,29 @@ def get_filetypes(model_filepath, simulation_filepath): Input: model_filepath, simulation_filepath Output: tuple of filetypes """ - if model_filepath.endswith(".sbml") and simulation_filepath.endswith(".sedml"): - filetypes = ('sbml', 'sedml') - elif model_filepath.endswith(".xml") and simulation_filepath.endswith(".xml"): - filetypes = ('xml', 'xml') - elif model_filepath.endswith(".xml") and simulation_filepath.endswith(".sedml"): - filetypes = ('xml', 'sedml') - elif model_filepath.endswith(".sbml") and simulation_filepath.endswith(".xml"): - filetypes = ('sbml', 'xml') - else: - filetypes = "other" - return filetypes + model_ext = os.path.splitext(model_filepath)[-1].lstrip('.') + simulation_ext = os.path.splitext(simulation_filepath)[-1].lstrip('.') + + return (model_ext, simulation_ext) + +# def get_filetypes(model_filepath, simulation_filepath): +# """ +# Get the filetypes of the model and simulation files + +# Input: model_filepath, simulation_filepath +# Output: tuple of filetypes +# """ +# if model_filepath.endswith(".sbml") and simulation_filepath.endswith(".sedml"): +# filetypes = ('sbml', 'sedml') +# elif model_filepath.endswith(".xml") and simulation_filepath.endswith(".xml"): +# filetypes = ('xml', 'xml') +# elif model_filepath.endswith(".xml") and simulation_filepath.endswith(".sedml"): +# filetypes = ('xml', 'sedml') +# elif model_filepath.endswith(".sbml") and simulation_filepath.endswith(".xml"): +# filetypes = ('sbml', 'xml') +# else: +# filetypes = "other" +# return filetypes def delete_output_folder(output_dir): ''' @@ -1034,6 +1052,7 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir): pass_html = "✅ PASS" fail_html = "❌ FAIL" warning_html = "⚠ WARNING" + unsure_html = "❓ UNSURE" xfail_html = "⚠ XFAIL" for e in results.keys(): @@ -1072,7 +1091,7 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir): if compatibility_content[0] == 'pass': results_table.loc[results_table[ENGINE] == e, COMPAT] = collapsible_content(compatibility_content[1], title=f'{pass_html}') elif compatibility_content[0] == 'unsure': - results_table.loc[results_table[ENGINE] == e, COMPAT] = collapsible_content(compatibility_content[1], title=f'{warning_html}') + results_table.loc[results_table[ENGINE] == e, COMPAT] = collapsible_content(compatibility_content[1], title=f'{unsure_html}') else: results_table.loc[results_table[ENGINE] == e, COMPAT] = collapsible_content(compatibility_content[1], title=f'{fail_html}') From ccf8305284f1e67c8d2fee51e4aa9b7afe8eee40 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 5 Nov 2024 11:07:58 +0000 Subject: [PATCH 11/22] draft BioModels compatibility table --- ...t_biomodels_compatibility_biosimulators.py | 247 ++++++++++++++++++ 1 file changed, 247 insertions(+) create mode 100644 BioModels/test_biomodels_compatibility_biosimulators.py diff --git a/BioModels/test_biomodels_compatibility_biosimulators.py b/BioModels/test_biomodels_compatibility_biosimulators.py new file mode 100644 index 00000000..4f50b5bc --- /dev/null +++ b/BioModels/test_biomodels_compatibility_biosimulators.py @@ -0,0 +1,247 @@ +#!/usr/bin/env python3 + +md_description = \ +''' +Download and run validation tests on all the curated models from BioModels https://www.ebi.ac.uk/biomodels. +The final step is to run the model in tellurium, +only models specified in SBML with a matching SEDML file are run in tellurium. +Errors or validation failures are reported at each step. +Outputs to the Markdown Table below. + +'valid-sbml-units' enforces strict unit checking, 'broken-ref' indicates that the SEDML file contained +a broken source='model.xml' reference which was corrected to the name of the model's provided SBML file. +''' + +import pyneuroml.sbml #for validate_sbml_files +import pyneuroml.sedml #for validate_sedml_files + +import re +import os +import urllib +import sys + +sys.path.append("..") +import utils + +API_URL: str = "https://www.ebi.ac.uk/biomodels" + +out_format="json" +max_count = 0 #0 for unlimited + +#local temporary storage of the model files +#this is independent of caching, and still happens when caching is turned off +#this allows the model to be executed and the files manually examined etc +tmp_dir = "tmplocalfiles" + +#suppress stdout/err output from validation functions to make progress counter readable +suppress_stdout = True +suppress_stderr = True + +#whether to replace "model.xml" in the sedml file with the name of the actual sbml file +fix_broken_ref = True + +#skip tests that cause the script to be killed due to lack of RAM +#needs at least 8GB +skip = {} + +def download_file(model_id,filename,output_file,cache): + ''' + request the given file and save it to disk + ''' + + qfilename = urllib.parse.quote_plus(filename) + + response = cache.do_request(f'{API_URL}/model/download/{model_id}?filename={qfilename}').content + + with open(output_file,"wb") as fout: + fout.write(response) + +def replace_model_xml(sedml_path,sbml_filename): + ''' + if the SEDML refers to a generic "model.xml" file + and the SBML file is not called this + replace the SEDML reference with the actual SBML filename + + method used assumes 'source="model.xml"' will only + occur in the SBML file reference + which was true at time of testing on current BioModels release + + returns True if the SBML reference already seemed valid + ''' + + if sbml_filename == "model.xml": return True + + with open(sedml_path,encoding='utf-8') as f: + data = f.read() + + if not 'source="model.xml"' in data: return True + + data = data.replace('source="model.xml"',f'source="{sbml_filename}"') + + with open(f'{sedml_path}',"w",encoding="utf-8") as fout: + fout.write(data) + + return False + +def validate_sbml_file(model_id,mtab,info,cache,sup): + ''' + tasks relating to validating the SBML file + return None to indicate aborting any further tests on this model + otherwise return the SBML filename + ''' + + #handle only single SBML files + if not info['format']['name'] == "SBML": + mtab['valid_sbml'] = ['NonSBML', f"{info['format']['name']}:{info['files']['main']}"] + return None + + if len(info['files']['main']) > 1: + mtab['valid_sbml'] = ['MultipleSBMLs',f"{info['files']['main']}"] + return None + + if len(info['files']['main']) < 1: + mtab['valid_sbml'] = ['NoSBMLs',f"{info['files']['main']}"] + return None + + #download the sbml file + sbml_file = info['files']['main'][0]['name'] + try: + download_file(model_id,sbml_file,sbml_file,cache) + except Exception as e: + mtab['valid_sbml'] = ['DownloadFail',f"{sbml_file} {e}"] + return None + + #validate the sbml file + sup.suppress() #suppress validation warning/error messages + valid_sbml = pyneuroml.sbml.validate_sbml_files([sbml_file], strict_units=False) + valid_sbml_units = pyneuroml.sbml.validate_sbml_files([sbml_file], strict_units=True) + sup.restore() + + mtab['valid_sbml'] = ['pass' if valid_sbml else 'FAIL', f'[{sbml_file}]({API_URL}/{model_id}#Files)'] + mtab['valid_sbml_units'] = 'pass' if valid_sbml_units else 'FAIL' + + return sbml_file + +def validate_sedml_file(model_id,mtab,info,cache,sup,sbml_file): + ''' + tasks relating to validating the SEDML file + return None to indicate aborting any further tests on this model + otherwise return the SEDML filename + ''' + + #must have a SEDML file as well in order to be executed + if not 'additional' in info['files']: + mtab['valid_sedml'] = f"NoSEDML" + return None + + sedml_file = [] + for file_info in info['files']['additional']: + pattern = 'SED[-]?ML' + target = f"{file_info['name']}|{file_info['description']}".upper() + if re.search(pattern,target): + sedml_file.append(file_info['name']) + + #require exactly one SEDML file + if len(sedml_file) == 0: + mtab['valid_sedml'] = "NoSEDML" + return None + + if len(sedml_file) > 1: + mtab['valid_sedml'] = ["MultipleSEDMLs",f"{sedml_file}"] + return None + + #download sedml file + sedml_file = sedml_file[0] + try: + download_file(model_id,sedml_file,sedml_file,cache) + except: + mtab['valid_sedml'] = ["DownloadFail",f"{sedml_file}"] + return None + + #if the sedml file contains a generic 'source="model.xml"' replace it with the sbml filename + if fix_broken_ref: + broken_ref = replace_model_xml(sedml_file,sbml_file) + mtab['broken_ref'] = 'pass' if broken_ref else 'FAIL' + else: + mtab['broken_ref'] = 'NA' + + sup.suppress() + valid_sedml = pyneuroml.sedml.validate_sedml_files([sedml_file]) + sup.restore() + mtab['valid_sedml'] = ['pass' if valid_sedml else 'FAIL', f'[{sedml_file}]({API_URL}/{model_id}#Files)'] + + return sedml_file + +def main(): + ''' + download the BioModel model files, run various validation steps + report the results as a markdown table README file with a summary row at the top + ''' + + #caching is used to prevent the need to download the same responses from the remote server multiple times during testing + #mode="off" to disable caching, "store" to wipe and store fresh results, "reuse" to use the stored cache + cache = utils.RequestCache(mode="auto",direc="cache") + + #accumulate results in columns defined by keys which correspond to the local variable names to be used below + #to allow automated loading into the columns + column_labels = "Model |valid-sbml|valid-sbml-units|valid-sedml|broken-ref|tellurium" + column_keys = "model_desc|valid_sbml|valid_sbml_units|valid_sedml|broken_ref|tellurium_outcome" + mtab = utils.MarkdownTable(column_labels,column_keys) + + #allow stdout/stderr from validation tests to be suppressed to improve progress count visibility + sup = utils.SuppressOutput(stdout=suppress_stdout,stderr=suppress_stderr) + + #get list of all available models + model_ids = cache.do_request(f"{API_URL}/model/identifiers?format={out_format}").json()['models'] + count = 0 + starting_dir = os.getcwd() + + for model_id in model_ids[0:1]: + #allow testing on a small sample of models + if max_count > 0 and count >= max_count: break + count += 1 + print(f"\r{model_id} {count}/{len(model_ids)} ",end='') + + #only process curated models + #BIOMD ids should be the curated models + if not 'BIOMD' in model_id: + continue + + #skip if on the list to be skipped + if count in skip or model_id in skip: + continue + + #from this point the model will create an output row even if not all tests are run + mtab.new_row() #append empty placeholder row + info = cache.do_request(f"{API_URL}/{model_id}?format={out_format}").json() + + if len(info['name']) > 36: + model_summary = f"[{model_id}]({API_URL}/{model_id})
{info['name'][:30]}" + model_details = f"{info['name']}" + mtab['model_desc'] = mtab.make_fold(model_summary,model_details) + else: + mtab['model_desc'] = f"[{model_id}]({API_URL}/{model_id})
{info['name']}" + + #make temporary downloads of the sbml and sedml files + model_dir = os.path.join(starting_dir,tmp_dir,model_id) + os.makedirs(model_dir,exist_ok=True) + os.chdir(model_dir) + + #sbml file validation tasks, includes downloading a local copy + sbml_file = validate_sbml_file(model_id,mtab,info,cache,sup) + if not sbml_file: continue # no further tests possible + + sedml_file = validate_sedml_file(model_id,mtab,info,cache,sup,sbml_file) + if not sedml_file: continue # no further tests possible + + test_folder = 'tests' + engine_list = list(utils.ENGINES.keys()) + utils.run_biosimulators_remotely_and_locally(engine_list, + os.path.basename(sedml_file), + os.path.basename(sbml_file), + os.path.join(test_folder,'d1_plots_remote'), + os.path.join(test_folder,'d1_plots_local'), + test_folder=test_folder) + +if __name__ == "__main__": + main() \ No newline at end of file From 88ce0f4c44d23a575a99cfe5e4fb7db6ff0cc5d4 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 5 Nov 2024 11:49:37 +0000 Subject: [PATCH 12/22] store cache and sett Agg for matplotlib to prevent matplotlib windows opening --- BioModels/parse_biomodels.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/BioModels/parse_biomodels.py b/BioModels/parse_biomodels.py index d5b0a6dd..b14bf041 100755 --- a/BioModels/parse_biomodels.py +++ b/BioModels/parse_biomodels.py @@ -24,6 +24,8 @@ sys.path.append("..") import utils +matplotlib.use('Agg') #prevent matplotlib from trying to open a window + API_URL: str = "https://www.ebi.ac.uk/biomodels" out_format="json" @@ -181,7 +183,7 @@ def main(): #caching is used to prevent the need to download the same responses from the remote server multiple times during testing #mode="off" to disable caching, "store" to wipe and store fresh results, "reuse" to use the stored cache - cache = utils.RequestCache(mode="auto",direc="cache") + cache = utils.RequestCache(mode="store",direc="cache") #accumulate results in columns defined by keys which correspond to the local variable names to be used below #to allow automated loading into the columns From dbe378b0067c107de0cfb62f15475305c23c19b1 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Wed, 6 Nov 2024 10:44:11 +0000 Subject: [PATCH 13/22] add BIOMD0000000001 results table --- .../BIOMD0000000001/BIOMD0000000001_url.omex | Bin 0 -> 8231 bytes .../BIOMD0000000001/BIOMD0000000001_url.sedml | 634 ++++ .../BIOMD0000000001/BIOMD0000000001_url.xml | 1343 +++++++++ .../amici_autogen_plot_for_task1.pdf | Bin 0 -> 11104 bytes .../copasi_autogen_plot_for_task1.pdf | Bin 0 -> 11133 bytes .../pysces_autogen_plot_for_task1.pdf | Bin 0 -> 11174 bytes .../tellurium_autogen_plot_for_task1.pdf | Bin 0 -> 11134 bytes .../vcell_autogen_plot_for_task1.pdf | Bin 0 -> 15029 bytes .../amici_autogen_plot_for_task1.pdf | Bin 0 -> 11110 bytes .../copasi_autogen_plot_for_task1.pdf | Bin 0 -> 11139 bytes .../masspy_autogen_plot_for_task1.pdf | Bin 0 -> 5954 bytes .../pysces_autogen_plot_for_task1.pdf | Bin 0 -> 11180 bytes .../tellurium_autogen_plot_for_task1.pdf | Bin 0 -> 11113 bytes .../results_compatibility_biosimulators.md | 23 + .../BIOMD0000000001/tests/results_local.json | 2167 ++++++++++++++ .../BIOMD0000000001/tests/results_remote.json | 2580 +++++++++++++++++ ...t_biomodels_compatibility_biosimulators.py | 19 +- BioModels/test_biomodels_results_table.py | 68 + 18 files changed, 6823 insertions(+), 11 deletions(-) create mode 100644 BioModels/BIOMD0000000001/BIOMD0000000001_url.omex create mode 100644 BioModels/BIOMD0000000001/BIOMD0000000001_url.sedml create mode 100644 BioModels/BIOMD0000000001/BIOMD0000000001_url.xml create mode 100644 BioModels/BIOMD0000000001/tests/d1_plots_local/amici_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000001/tests/d1_plots_local/copasi_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000001/tests/d1_plots_local/pysces_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000001/tests/d1_plots_local/tellurium_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000001/tests/d1_plots_local/vcell_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000001/tests/d1_plots_remote/amici_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000001/tests/d1_plots_remote/copasi_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000001/tests/d1_plots_remote/masspy_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000001/tests/d1_plots_remote/pysces_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000001/tests/d1_plots_remote/tellurium_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000001/tests/results_compatibility_biosimulators.md create mode 100644 BioModels/BIOMD0000000001/tests/results_local.json create mode 100644 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auto_dg_for_task1_kr_0__x + + + + + + + + auto_dg_for_task1_kf_1__x + + + + + + + + auto_dg_for_task1_kr_1__x + + + + + + + + auto_dg_for_task1_kf_2__x + + + + + + + + auto_dg_for_task1_kr_2__x + + + + + + + + auto_dg_for_task1_kf_3__x + + + + + + + + auto_dg_for_task1_kr_3__x + + + + + + + + auto_dg_for_task1_kf_4__x + + + + + + + + auto_dg_for_task1_kr_4__x + + + + + + + + auto_dg_for_task1_kf_5__x + + + + + + + + auto_dg_for_task1_kr_5__x + + + + + + + + auto_dg_for_task1_kf_6__x + + + + + + + + auto_dg_for_task1_kr_6__x + + + + + + + + auto_dg_for_task1_kf_7__x + + + + + + + + auto_dg_for_task1_kr_7__x + + + + + + + + auto_dg_for_task1_kf_8__x + + + + + + + + auto_dg_for_task1_kr_8__x + + + + + + + + auto_dg_for_task1_kf_9__x + + + + + + + + auto_dg_for_task1_kr_9__x + + + + + + + + auto_dg_for_task1_kf_10__x + + + + + + + + auto_dg_for_task1_kr_10__x + + + + + + + + auto_dg_for_task1_kf_11__x + + + + + + + + auto_dg_for_task1_kr_11__x + + + + + + + + auto_dg_for_task1_kf_12__x + + + + + + + + auto_dg_for_task1_kr_12__x + + + + + + + + auto_dg_for_task1_kf_13__x + + + + + + + + auto_dg_for_task1_kr_13__x + + + + + + + + auto_dg_for_task1_kf_14__x + + + + + + + + auto_dg_for_task1_kr_14__x + + + + + + + + auto_dg_for_task1_kf_15__x + + + + + + + + auto_dg_for_task1_kr_15__x + + + + + + + + auto_dg_for_task1_kf_16__x + + + + + + + + auto_dg_for_task1_kr_16__x + + + + + + + + auto_dg_for_task1_t2__x + + + + + + + + auto_dg_for_task1_comp1__x + + + + + + + + auto_dg_for_task1_React0__x + + + + + + + + auto_dg_for_task1_React1__x + + + + + + + + auto_dg_for_task1_React2__x + + + + + + + + auto_dg_for_task1_React3__x + + + + + + + + auto_dg_for_task1_React4__x + + + + + + + + auto_dg_for_task1_React5__x + + + + + + + + auto_dg_for_task1_React6__x + + + + + + + + auto_dg_for_task1_React7__x + + + + + + + + auto_dg_for_task1_React8__x + + + + + + + + auto_dg_for_task1_React9__x + + + + + + + + auto_dg_for_task1_React10__x + + + + + + + + auto_dg_for_task1_React11__x + + + + + + + + auto_dg_for_task1_React12__x + + + + + + + + auto_dg_for_task1_React13__x + + + + + + + + auto_dg_for_task1_React14__x + + + + + + + + auto_dg_for_task1_React15__x + + + + + + + + auto_dg_for_task1_React16__x + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/BioModels/BIOMD0000000001/BIOMD0000000001_url.xml b/BioModels/BIOMD0000000001/BIOMD0000000001_url.xml new file mode 100644 index 00000000..411e0c65 --- /dev/null +++ b/BioModels/BIOMD0000000001/BIOMD0000000001_url.xml @@ -0,0 +1,1343 @@ + + + + + +
Edelstein1996 - EPSP ACh event
+
+

Model of a nicotinic Excitatory Post-Synaptic Potential in a + Torpedo electric organ. Acetylcholine is not represented + explicitely, but by an event that changes the constants of + transition from unliganded to liganded.  +

+
+
+

This model has initially been encoded using StochSim.

+
+
+

This model is described in the article:

+
+ A kinetic mechanism for + nicotinic acetylcholine receptors based on multiple allosteric + transitions. +
+
Edelstein SJ, Schaad O, Henry E, + Bertrand D, Changeux JP.
+
Biol Cybern 1996 Nov; 75(5): + 361-379
+

Abstract:

+
+

Nicotinic acetylcholine receptors are transmembrane + oligomeric proteins that mediate interconversions between open + and closed channel states under the control of + neurotransmitters. Fast in vitro chemical kinetics and in vivo + electrophysiological recordings are consistent with the + following multi-step scheme. Upon binding of agonists, receptor + molecules in the closed but activatable resting state (the + Basal state, B) undergo rapid transitions to states of higher + affinities with either open channels (the Active state, A) or + closed channels (the initial Inactivatable and fully + Desensitized states, I and D). In order to represent the + functional properties of such receptors, we have developed a + kinetic model that links conformational interconversion rates + to agonist binding and extends the general principles of the + Monod-Wyman-Changeux model of allosteric transitions. The + crucial assumption is that the linkage is controlled by the + position of the interconversion transition states on a + hypothetical linear reaction coordinate. Application of the + model to the peripheral nicotine acetylcholine receptor (nAChR) + accounts for the main properties of ligand-gating, including + single-channel events, and several new relationships are + predicted. Kinetic simulations reveal errors inherent in using + the dose-response analysis, but justify its application under + defined conditions. The model predicts that (in order to + overcome the intrinsic stability of the B state and to produce + the appropriate cooperativity) channel activation is driven by + an A state with a Kd in the 50 nM range, hence some 140-fold + stronger than the apparent affinity of the open state deduced + previously. According to the model, recovery from the + desensitized states may occur via rapid transit through the A + state with minimal channel opening, thus without necessarily + undergoing a distinct recovery pathway, as assumed in the + standard 'cycle' model. Transitions to the desensitized states + by low concentration 'pre-pulses' are predicted to occur + without significant channel opening, but equilibrium values of + IC50 can be obtained only with long pre-pulse times. + Predictions are also made concerning allosteric effectors and + their possible role in coincidence detection. In terms of + future developments, the analysis presented here provides a + physical basis for constructing more biologically realistic + models of synaptic modulation that may be applied to artificial + neural networks.

+
+
+
+

This model is hosted on + BioModels Database + and identified by: + BIOMD0000000001.

+

To cite BioModels Database, please use: + BioModels Database: + An enhanced, curated and annotated resource for published + quantitative kinetic models.

+
+
+

To the extent possible under law, all copyright and related or + neighbouring rights to this encoded model have been dedicated to + the public domain worldwide. Please refer to + CC0 + Public Domain Dedication for more information.

+
+ + + + + + + + + + Le Novère + Nicolas + + lenov@ebi.ac.uk + + EMBL-EBI + + + + + + 2005-02-02T14:56:11Z + + + 2017-05-19T14:33:51Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

biliganded basal state

+ + + + + + + + + + + + + + + + + + + +

monoliganded intermediate

+ + + + + + + + + + + + + + + + + + + +

monoliganded active state

+ + + + + + + + + + + + + + + + + + + +

unkiganded active state

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monoliganded basal state

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unliganded basal state

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biliganded desensitised state

+ + + + + + + + + + + + + + + + + + + +

fully desensitised state

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biliganded intermediate

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monoliganded desensitised state

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unliganted intermediate

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biliganted active state

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first ligand on basal

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kf_0 * B - kr_0 * BL

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second ligand on basal

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kf_1 * BL - kr_1 * BLL

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opening of biliganded

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kf_2 * BLL - kr_2 * ALL

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first ligand on active

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kf_3 * A - kr_3 * AL

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second ligand on active

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kf_4 * AL - kr_4 * ALL

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opening of unliganded

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kf_5 * B - kr_5 * A

+ + + + + + comp1 + + + + + kf_5 + B + + + + kr_5 + A + + + + + + + + + +

opening of monoliganded

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kf_6 * BL - kr_6 * AL

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first ligand on intermediate

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kf_7 * I - kr_7 * IL

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second ligand on intermediate

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kf_8 * IL - kr_8 * ILL

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unliganded active <=> unliganded intermediate

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kf_9 * A - kr_9 * I

+ + + + + + comp1 + + + + + kf_9 + A + + + + kr_9 + I + + + + + + + + + +

monoliganded active <=> monoliganded intermediate

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kf_10 * AL - kr_10 * IL

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biliganded active <=> biliganded intermediate

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kf_11 * ALL - kr_11 * ILL

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first ligand on desensitised

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kf_12 * D - kr_12 * DL

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second ligand on desensitised

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kf_13 * DL - kr_13 * DLL

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unliganded intermediate <=> unliganded desensitised

+ + + + + + + + + + + +

kf_14 * I - kr_14 * D

+ + + + + + comp1 + + + + + kf_14 + I + + + + kr_14 + D + + + + + + + + + +

monoliganded intermediate <=> monoliganded desensitised

+ + + + + + + + + + + +

kf_15 * IL - kr_15 * DL

+ + + + + + comp1 + + + + + kf_15 + IL + + + + kr_15 + DL + + + + + + + + + +

biliganded intermediate <=> biliganded desensitised

+ + + + + + + + + + + +

kf_16 * ILL - kr_16 * DLL

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zjOGks7DjUi5}xk`_5@&}7%dmv1dt`;ao!Dp)zthG@C<-UMj7@TfJ0D5%sUjI?(mCW zw*99qg#D8yP^fuqzuqqn%T>^e-PphP!H{Yypi`us4T$hzH==_1pVfft`Be@3KdZr4 zx8RC!uB5aG?V`Bh7sN#~_KUc9e?${4_bZN&b9bg50^SIA-irmXcp*0Lh+|OLhqOBnGbw2V%go{)%VRz8{_iV!51OM40tuo9`$Kl%dfDPup7suqt&N>47-gXcP?OQUvj+6T$J_QW^;%%8jwNx(5LsYk|x)zA_e76X5<@b4ENSnQwuVTsGsTSitm z6zPxta2VLg{5}Q_iwEXm2@MY)#V(yA`J literal 0 HcmV?d00001 diff --git a/BioModels/BIOMD0000000001/tests/results_compatibility_biosimulators.md b/BioModels/BIOMD0000000001/tests/results_compatibility_biosimulators.md new file mode 100644 index 00000000..4ece4606 --- /dev/null +++ b/BioModels/BIOMD0000000001/tests/results_compatibility_biosimulators.md @@ -0,0 +1,23 @@ +| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------|:-----------------------------------------------------------------------| +| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with amici.

['SBML', 'SED-ML'] are compatible with amici.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with brian2.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with cbmpy.

['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with cobrapy.

['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with copasi.

['SBML', 'SED-ML'] are compatible with copasi.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with gillespy2.

['SBML', 'SED-ML'] are compatible with gillespy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with libsbmlsim.

['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with masspy.

['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Could not load MassModel 'BIOMD0000000001'

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| plot | | +| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with netpyne.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with pysces.

['SBML', 'SED-ML'] are compatible with pysces.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with smoldyn.

['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with tellurium.

['SBML', 'SED-ML'] are compatible with tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 19 |
vcellhttps://github.com/virtualcell/vcell
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with vcell.

['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

| ✅ PASS | | plot | +| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/BioModels/BIOMD0000000001/tests/results_local.json b/BioModels/BIOMD0000000001/tests/results_local.json new file mode 100644 index 00000000..0dfb32c8 --- /dev/null +++ b/BioModels/BIOMD0000000001/tests/results_local.json @@ -0,0 +1,2167 @@ +{ + "amici": { + "exception_message": "", + "log_yml": { + "duration": 16.878883, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 16.395254, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ALL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_t2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_comp1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React16", + "status": "SUCCEEDED" + } + ], + "duration": 0.267185, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ALL", + "status": "SUCCEEDED" + } + ], + "duration": 0.432204, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000496", + "duration": 15.522015, + "exception": null, + "id": "task1", + "output": "", + "simulatorDetails": [ + { + "key": "solver", + "value": "amici.amici.CVodeSolver" + }, + { + "key": "method", + "value": "amici.swig_wrappers.runAmiciSimulation" + }, + { + "key": "arguments", + "value": {} + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "brian2": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.081759, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpzxessd2h/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n [py.warnings]\r\npyNeuroML >>> WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpzxessd2h/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "bionetgen": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1", + "log_yml": { + "duration": 0.160269, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp64y_xz8l/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "boolnet": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1", + "log_yml": { + "duration": 0.144054, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp5f1k93po/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cbmpy": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.233937, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpllsy0tzm/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cobrapy": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.145853, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpcnif1fxb/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "copasi": { + "exception_message": "", + "log_yml": { + "duration": 1.406639, + "exception": null, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmplq5f15uj/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmplq5f15uj/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 1.081246, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ALL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_t2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_comp1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React16", + "status": "SUCCEEDED" + } + ], + "duration": 0.257525, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ALL", + "status": "SUCCEEDED" + } + ], + "duration": 0.499548, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000560", + "duration": 0.146259, + "exception": null, + "id": "task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task1_React9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_D__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_AL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_B__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_I__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_t2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_IL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_A__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_comp1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ILL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ALL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React10__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `BIOMD0000000001_url` may be invalid.\r\n - The model file `/tmp/tmplq5f15uj/./BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'LSODA/LSODAR hybrid method' (KISAO_0000560) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "simulatorDetails": [ + { + "key": "methodName", + "value": "lsoda" + }, + { + "key": "parameters", + "value": null + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "gillespy2": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/gillespy2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.14306, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp1cm368ul/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "ginsim": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.156454, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmppsbjd98y/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "libsbmlsim": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/libsbmlsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.158375, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpev59pj1u/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "masspy": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.165867, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mSedmlFeatureNotSupportedWarning\u001b[0m: \u001b[33m`/tmp/tmpv87m0uvc/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "netpyne": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1", + "log_yml": { + "duration": 0.051762, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "neuron": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1", + "log_yml": { + "duration": 0.12182, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpcvkt9vjo/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "opencor": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1", + "log_yml": { + "duration": 0.083156, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmphs4vnr76/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pyneuroml": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1", + "log_yml": { + "duration": 0.047416, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp_rolss6v/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pysces": { + "exception_message": "", + "log_yml": { + "duration": 1.484589, + "exception": null, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpbh50myyf/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpbh50myyf/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 1.14505, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V4\r\nINFO: Rescaling compartment with size 1e-16 to 1.0\r\ncsymbol time defined as \"time\" in event \r\nInfo: single compartment model: locating \"React0\" in default compartment\r\nInfo: single compartment model: locating \"React1\" in default compartment\r\nInfo: single compartment model: locating \"React2\" in default compartment\r\nInfo: single compartment model: locating \"React3\" in default compartment\r\nInfo: single compartment model: locating \"React4\" in default compartment\r\nInfo: single compartment model: locating \"React5\" in default compartment\r\nInfo: single compartment model: locating \"React6\" in default compartment\r\nInfo: single compartment model: locating \"React7\" in default compartment\r\nInfo: single compartment model: locating \"React8\" in default compartment\r\nInfo: single compartment model: locating \"React9\" in default compartment\r\nInfo: single compartment model: locating \"React10\" in default compartment\r\nInfo: single compartment model: locating \"React11\" in default compartment\r\nInfo: single compartment model: locating \"React12\" in default compartment\r\nInfo: single compartment model: locating \"React13\" in default compartment\r\nInfo: single compartment model: locating \"React14\" in default compartment\r\nInfo: single compartment model: locating \"React15\" in default compartment\r\nInfo: single compartment model: locating \"React16\" in default compartment\r\nWriting file: /tmp/tmpc7l_eyuc.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpn2ifuf74.xml\r\nout: /tmp/tmpc7l_eyuc.psc\r\nUsing model directory: /Pysces/psc\r\n/tmp/tmpc7l_eyuc.psc loading ..... \r\nParsing file: /tmp/tmpc7l_eyuc.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"t2\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . done.\r\n \r\nEvent(s) detected.\r\n\r\nINFO: events detected and we have Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\nCVODE time for 1001 points: 0.045973777770996094\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ALL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_t2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_comp1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React16", + "status": "SUCCEEDED" + } + ], + "duration": 0.298217, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ALL", + "status": "SUCCEEDED" + } + ], + "duration": 0.473628, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 0.178782, + "exception": null, + "id": "task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task1_React3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ALL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ILL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_t2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_I__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_IL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_D__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_comp1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_AL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_A__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_B__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_3__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "simulatorDetails": [ + { + "key": "method", + "value": "pysces.PyscesModel.Simulate" + }, + { + "key": "arguments", + "value": { + "cvode_abstol": 1e-09, + "cvode_access_solver": true, + "cvode_h0": 0.0, + "cvode_hmax": 0.0, + "cvode_hmin": 0.0, + "cvode_mxord": 5, + "cvode_mxstep": 5000, + "cvode_reltol": 1e-09, + "cvode_return_event_timepoints": false, + "cvode_stats": false, + "cvode_track_assignment_rules": true + } + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "rbapy": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.141643, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpqlaao665/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "smoldyn": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1", + "log_yml": {}, + "detailed_error_log": {} + }, + "tellurium": { + "exception_message": "", + "log_yml": { + "duration": 1.493313, + "exception": null, + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmpygc_3b8y/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmpygc_3b8y/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n", + "sedDocuments": [ + { + "duration": 1.032751, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ALL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_t2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_comp1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React16", + "status": "SUCCEEDED" + } + ], + "duration": 0.261701, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ALL", + "status": "SUCCEEDED" + } + ], + "duration": 0.453212, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning:\r\n\r\n\u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n\r\n", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 0.134319, + "exception": null, + "id": "task1", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33m- Variable `auto_dg_for_task1_React13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_t2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_D__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_I__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_IL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ALL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ILL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_AL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_B__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_A__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_comp1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DLL__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mModel `BIOMD0000000001_url` may be invalid.\r\n - The model file `/tmp/tmpygc_3b8y/./BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning:\r\n\r\n\u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n\r\n", + "simulatorDetails": [ + { + "key": "method", + "value": "simulate" + }, + { + "key": "solver", + "value": "cvode" + }, + { + "key": "relative_tolerance", + "value": 1e-06 + }, + { + "key": "absolute_tolerance", + "value": 1e-12 + }, + { + "key": "stiff", + "value": true + }, + { + "key": "maximum_bdf_order", + "value": 5 + }, + { + "key": "maximum_adams_order", + "value": 12 + }, + { + "key": "maximum_num_steps", + "value": 20000 + }, + { + "key": "maximum_time_step", + "value": 0.0 + }, + { + "key": "minimum_time_step", + "value": 0.0 + }, + { + "key": "initial_time_step", + "value": 0.0 + }, + { + "key": "multiple_steps", + "value": false + }, + { + "key": "variable_step_size", + "value": false + }, + { + "key": "max_output_rows", + "value": 100000 + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "vcell": { + "exception_message": "", + "log_yml": { + "duration": 13, + "exception": null, + "output": "Processing BIOMD0000000001_url.sedml. Done", + "sedDocuments": [ + { + "duration": null, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Initializing SED-ML document... done. Successful translation of SED-ML file. Building solvers and starting simulation of all tasks... Generating outputs... Generating CSV file... Done. 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Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + } +} \ No newline at end of file diff --git a/BioModels/BIOMD0000000001/tests/results_remote.json b/BioModels/BIOMD0000000001/tests/results_remote.json new file mode 100644 index 00000000..6f4be9b3 --- /dev/null +++ b/BioModels/BIOMD0000000001/tests/results_remote.json @@ -0,0 +1,2580 @@ +{ + "amici": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17a10d09353e8f0fc0b3", + "download": "https://api.biosimulations.org/results/672a17a10d09353e8f0fc0b3/download", + "logs": "https://api.biosimulations.org/logs/672a17a10d09353e8f0fc0b3?includeOutput=true", + "log_yml": { + "duration": 31.095497, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 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"exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "cobrapy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17ab0d09353e8f0fc0b9", + "download": "https://api.biosimulations.org/results/672a17ab0d09353e8f0fc0b9/download", + "logs": "https://api.biosimulations.org/logs/672a17ab0d09353e8f0fc0b9?includeOutput=true", + "log_yml": { + "duration": 0.18803, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "copasi": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17ad0d09353e8f0fc0bc", + "download": "https://api.biosimulations.org/results/672a17ad0d09353e8f0fc0bc/download", + "logs": "https://api.biosimulations.org/logs/672a17ad0d09353e8f0fc0bc?includeOutput=true", + "log_yml": { + "duration": 1.726035, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 1.387954, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml 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"SUCCEEDED" + }, + { + "id": "autogen_curve_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ALL", + "status": "SUCCEEDED" + } + ], + "duration": 0.596057, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000560", + "duration": 0.250485, + "exception": null, + "id": "task1", + "output": "", + "simulatorDetails": [ + { + "key": "methodName", + "value": "lsoda" + }, + { + "key": "parameters", + "value": null + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + }, + "gillespy2": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17b05a60072d20f4c211", + "download": "https://api.biosimulations.org/results/672a17b05a60072d20f4c211/download", + "logs": "https://api.biosimulations.org/logs/672a17b05a60072d20f4c211?includeOutput=true", + "log_yml": { + "duration": 0.198661, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "ginsim": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17b2b678b3883bb61539", + "download": "https://api.biosimulations.org/results/672a17b2b678b3883bb61539/download", + "logs": "https://api.biosimulations.org/logs/672a17b2b678b3883bb61539?includeOutput=true", + "log_yml": { + "duration": 0.184712, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "libsbmlsim": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17b35a60072d20f4c218", + "download": "https://api.biosimulations.org/results/672a17b35a60072d20f4c218/download", + "logs": "https://api.biosimulations.org/logs/672a17b35a60072d20f4c218?includeOutput=true", + "log_yml": { + "duration": 0.188246, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "masspy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17b5b678b3883bb6154b", + "download": "https://api.biosimulations.org/results/672a17b5b678b3883bb6154b/download", + "logs": "https://api.biosimulations.org/logs/672a17b5b678b3883bb6154b?includeOutput=true", + "log_yml": { + "duration": 1.428032, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Could not load MassModel 'BIOMD0000000001'", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.89302, + "exception": { + "message": "The SED document did not execute successfully:\n\n Could not load MassModel 'BIOMD0000000001'", + "type": "SedmlExecutionError" + }, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_BLL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_IL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_AL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_A", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_BL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_B", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_DLL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_D", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ILL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_DL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_I", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ALL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SKIPPED" 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}, + { + "id": "autogen_task1_React16", + "status": "SKIPPED" + } + ], + "duration": 0.056867, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_BLL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_IL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_AL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_A", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_BL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_B", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_DLL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_D", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_ILL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_DL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_I", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_ALL", + "status": "SKIPPED" + } + ], + "duration": 0.293776, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.322784, + "exception": { + "message": "Could not load MassModel 'BIOMD0000000001'", + "type": "MassSimulationError" + }, + "id": "task1", + "output": "\u001b[93mWARNING:\u001b[0m \u001b[93mModel does not contain SBML fbc package\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mModel does not contain SBML groups package\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'BIOMD0000000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'BIOMD0000000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'BIOMD0000000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'BIOMD0000000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'BIOMD0000000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'BLL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'BLL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'IL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'IL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'AL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'AL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'A' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'A'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'BL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'BL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'B' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'B'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'DLL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'DLL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'D' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'D'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'ILL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'ILL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'DL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'DL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'I' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'I'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'ALL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'ALL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React0'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React1'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React2'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React3'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React4'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React5'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React6'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React7'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React8'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React9'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React10'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React11'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React12'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React13'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React14'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React15'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React16'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React0'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React1'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React2'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React3'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React4'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React5'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React6'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React7'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React8'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React9'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React10'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React11'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React12'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React13'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React14'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React15'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React16'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + } + }, + "netpyne": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17b70d09353e8f0fc0d6", + "download": "https://api.biosimulations.org/results/672a17b70d09353e8f0fc0d6/download", + "logs": "https://api.biosimulations.org/logs/672a17b70d09353e8f0fc0d6?includeOutput=true", + "log_yml": { + "duration": 0.069968, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "neuron": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17b95a60072d20f4c227", + "download": "https://api.biosimulations.org/results/672a17b95a60072d20f4c227/download", + "logs": "https://api.biosimulations.org/logs/672a17b95a60072d20f4c227?includeOutput=true", + "log_yml": { + "duration": 0.047913, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "opencor": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17ba5a60072d20f4c231", + "download": "https://api.biosimulations.org/results/672a17ba5a60072d20f4c231/download", + "logs": "https://api.biosimulations.org/logs/672a17ba5a60072d20f4c231?includeOutput=true", + "log_yml": { + "duration": 0.039026, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpzlgtc159/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "pyneuroml": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17bc0d09353e8f0fc0e5", + "download": "https://api.biosimulations.org/results/672a17bc0d09353e8f0fc0e5/download", + "logs": "https://api.biosimulations.org/logs/672a17bc0d09353e8f0fc0e5?includeOutput=true", + "log_yml": { + "duration": 0.065451, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "pysces": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17be0d09353e8f0fc0ea", + "download": "https://api.biosimulations.org/results/672a17be0d09353e8f0fc0ea/download", + "logs": "https://api.biosimulations.org/logs/672a17be0d09353e8f0fc0ea?includeOutput=true", + "log_yml": { + "duration": 1.795554, + "exception": null, + "output": "libtk8.6.so: cannot open shared object file: No such file or directory\r\n\r\nPySCeS defaults to matplotlib's TKagg backend if not specified in the user configuration file, set \"matplotlib_backend = \" \r\nMatplotlib interface loaded (pysces.plt.m)\r\nPitcon routines available\r\nNLEQ2 routines available\r\nSBML support available\r\nYou are using NumPy (2.1.2) with SciPy (1.14.1)\r\nAssimulo CVode available\r\nRateChar is available\r\nParallel scanner is available\r\n\r\nPySCeS environment\r\n******************\r\npysces.model_dir = /home/FCAM/crbmapi/Pysces/psc\r\npysces.output_dir = /home/FCAM/crbmapi/Pysces\r\n\r\n\r\n***********************************************************************\r\n* Welcome to PySCeS (1.2.2) - Python Simulator for Cellular Systems *\r\n* http://pysces.sourceforge.net *\r\n* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2024 *\r\n* Triple-J Group for Molecular Cell Physiology *\r\n* Stellenbosch University, ZA and VU University Amsterdam, NL *\r\n* PySCeS is distributed under the PySCeS (BSD style) licence, see *\r\n* LICENCE.txt (supplied with this release) for details *\r\n* Please cite PySCeS with: doi:10.1093/bioinformatics/bti046 *\r\n***********************************************************************\r\n", + "sedDocuments": [ + { + "duration": 1.425644, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V4\r\nINFO: Rescaling compartment with size 1e-16 to 1.0\r\ncsymbol time defined as \"time\" in event \r\nInfo: single compartment model: locating \"React0\" in default compartment\r\nInfo: single compartment model: locating \"React1\" in default compartment\r\nInfo: single compartment model: locating \"React2\" in default compartment\r\nInfo: single compartment model: locating \"React3\" in default compartment\r\nInfo: single compartment model: locating \"React4\" in default compartment\r\nInfo: single compartment model: locating \"React5\" in default compartment\r\nInfo: single compartment model: locating \"React6\" in default compartment\r\nInfo: single compartment model: locating \"React7\" in default compartment\r\nInfo: single compartment model: locating \"React8\" in default compartment\r\nInfo: single compartment model: locating \"React9\" in default compartment\r\nInfo: single compartment model: locating \"React10\" in default compartment\r\nInfo: single compartment model: locating \"React11\" in default compartment\r\nInfo: single compartment model: locating \"React12\" in default compartment\r\nInfo: single compartment model: locating \"React13\" in default compartment\r\nInfo: single compartment model: locating \"React14\" in default compartment\r\nInfo: single compartment model: locating \"React15\" in default compartment\r\nInfo: single compartment model: locating \"React16\" in default compartment\r\nWriting file: /tmp/tmpusbz_uk4.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmprqun8mcy.xml\r\nout: /tmp/tmpusbz_uk4.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmpusbz_uk4.psc loading ..... \r\nParsing file: /tmp/tmpusbz_uk4.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"t2\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . done.\r\n \r\nEvent(s) detected.\r\n\r\nINFO: events detected and we have Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\nCVODE time for 1001 points: 0.06746697425842285\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ALL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_5", + "status": "SUCCEEDED" + }, + { + "id": 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file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "smoldyn": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17c15a60072d20f4c24d", + "download": "https://api.biosimulations.org/results/672a17c15a60072d20f4c24d/download", + "logs": "https://api.biosimulations.org/logs/672a17c15a60072d20f4c24d?includeOutput=true", + "log_yml": { + "duration": 0.053493, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "tellurium": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17c35a60072d20f4c25e", + "download": "https://api.biosimulations.org/results/672a17c35a60072d20f4c25e/download", + 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`autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ALL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SUCCEEDED" + }, + { + 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"QUEUED" + }, + { + "id": "autogen_task1_kr_2", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kf_3", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kr_3", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kf_4", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kr_4", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kf_5", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kr_5", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kf_6", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kr_6", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kf_7", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kr_7", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kf_8", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kr_8", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kf_9", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kr_9", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kf_10", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kr_10", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kf_11", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kr_11", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kf_12", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kr_12", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kf_13", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kr_13", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kf_14", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kr_14", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kf_15", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kr_15", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kf_16", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kr_16", + "status": "QUEUED" + }, + { + "id": "autogen_task1_t2", + "status": "QUEUED" + }, + { + "id": "autogen_task1_comp1", + "status": "QUEUED" + }, + { + "id": "autogen_task1_React0", + "status": "QUEUED" + }, + { + "id": "autogen_task1_React1", + "status": "QUEUED" + }, + { + "id": "autogen_task1_React2", + "status": "QUEUED" + }, + { + "id": "autogen_task1_React3", + "status": "QUEUED" + }, + { + "id": "autogen_task1_React4", + "status": "QUEUED" + }, + { + "id": "autogen_task1_React5", + "status": "QUEUED" + }, + { + "id": "autogen_task1_React6", + "status": "QUEUED" + }, + { + "id": "autogen_task1_React7", + "status": "QUEUED" + }, + { + "id": "autogen_task1_React8", + "status": "QUEUED" + }, + { + "id": "autogen_task1_React9", + "status": "QUEUED" + }, + { + "id": "autogen_task1_React10", + "status": "QUEUED" + }, + { + "id": "autogen_task1_React11", + "status": "QUEUED" + }, + { + "id": "autogen_task1_React12", + "status": "QUEUED" + }, + { + "id": "autogen_task1_React13", + "status": "QUEUED" + }, + { + "id": "autogen_task1_React14", + "status": "QUEUED" + }, + { + "id": "autogen_task1_React15", + "status": "QUEUED" + }, + { + "id": "autogen_task1_React16", + "status": "QUEUED" + } + ], + "duration": null, + "exception": null, + "id": "autogen_report_for_task1", + "output": null, + "skipReason": null, + "status": "QUEUED" + } + ], + "skipReason": null, + "status": "QUEUED", + "tasks": [ + { + "algorithm": null, + "duration": null, + "exception": null, + "id": "task1", + "output": null, + "simulatorDetails": null, + "skipReason": null, + "status": "QUEUED" + } + ] + } + ], + "skipReason": null, + "status": "QUEUED" + } + }, + "xpp": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672a17c80d09353e8f0fc122", + "download": "https://api.biosimulations.org/results/672a17c80d09353e8f0fc122/download", + "logs": "https://api.biosimulations.org/logs/672a17c80d09353e8f0fc122?includeOutput=true", + "log_yml": { + "duration": 0.047101, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + } +} \ No newline at end of file diff --git a/BioModels/test_biomodels_compatibility_biosimulators.py b/BioModels/test_biomodels_compatibility_biosimulators.py index 4f50b5bc..bd914f08 100644 --- a/BioModels/test_biomodels_compatibility_biosimulators.py +++ b/BioModels/test_biomodels_compatibility_biosimulators.py @@ -2,14 +2,8 @@ md_description = \ ''' -Download and run validation tests on all the curated models from BioModels https://www.ebi.ac.uk/biomodels. -The final step is to run the model in tellurium, -only models specified in SBML with a matching SEDML file are run in tellurium. -Errors or validation failures are reported at each step. -Outputs to the Markdown Table below. - -'valid-sbml-units' enforces strict unit checking, 'broken-ref' indicates that the SEDML file contained -a broken source='model.xml' reference which was corrected to the name of the model's provided SBML file. +Download and and create results table for curated models from BioModels https://www.ebi.ac.uk/biomodels. + ''' import pyneuroml.sbml #for validate_sbml_files @@ -19,10 +13,13 @@ import os import urllib import sys +import matplotlib sys.path.append("..") import utils +matplotlib.use('Agg') #prevent plotting from trying to open a window + API_URL: str = "https://www.ebi.ac.uk/biomodels" out_format="json" @@ -180,7 +177,7 @@ def main(): #caching is used to prevent the need to download the same responses from the remote server multiple times during testing #mode="off" to disable caching, "store" to wipe and store fresh results, "reuse" to use the stored cache - cache = utils.RequestCache(mode="auto",direc="cache") + cache = utils.RequestCache(mode="store",direc="cache") #accumulate results in columns defined by keys which correspond to the local variable names to be used below #to allow automated loading into the columns @@ -198,7 +195,7 @@ def main(): for model_id in model_ids[0:1]: #allow testing on a small sample of models - if max_count > 0 and count >= max_count: break + if max_count > 0 and count >= max_count:reak count += 1 print(f"\r{model_id} {count}/{len(model_ids)} ",end='') @@ -223,7 +220,7 @@ def main(): mtab['model_desc'] = f"[{model_id}]({API_URL}/{model_id})
{info['name']}" #make temporary downloads of the sbml and sedml files - model_dir = os.path.join(starting_dir,tmp_dir,model_id) + model_dir = os.path.join(starting_dir,model_id) os.makedirs(model_dir,exist_ok=True) os.chdir(model_dir) diff --git a/BioModels/test_biomodels_results_table.py b/BioModels/test_biomodels_results_table.py new file mode 100644 index 00000000..ad9d814d --- /dev/null +++ b/BioModels/test_biomodels_results_table.py @@ -0,0 +1,68 @@ +#!/usr/bin/env python3 + +""" +produce a markdown table of the results of running various tests on the SBML Test Suite + +get this version of the test suite that includes sedml versions or the sedml validation will fail: +https://github.com/sbmlteam/sbml-test-suite/releases/download/3.4.0/semantic_tests_with_sedml_and_graphs.v3.4.0.zip +""" + +import os +import sys +import json +sys.path.append("..") +import utils +engines = utils.ENGINES + + +def create_test_suite_results_tables(): + """ + Create a table of results for each test case in the test suite + + """ + starting_dir = os.getcwd() + print('Current working directory:', starting_dir) + subfolders = [f for f in os.listdir(starting_dir) if os.path.isdir(f) and f.startswith('BIOMD')] + + print(subfolders) + + for subfolder in subfolders: + subfolder_path = os.path.join(starting_dir, subfolder) + os.chdir(subfolder_path) + print(f"Changed to {os.getcwd()}") + + test_folder = 'tests' + + results_paths = { + "local": os.path.join(subfolder_path, test_folder, 'results_local.json'), + "remote": os.path.join(subfolder_path, test_folder, 'results_remote.json') + } + + results = {} + for key, path in results_paths.items(): + with open(path, 'r') as f: + results[key] = json.load(f) + + d1_plot_paths = { + "local": os.path.join(subfolder_path, test_folder, 'd1_plots_local'), + "remote": os.path.join(subfolder_path, test_folder, 'd1_plots_remote') + } + + # get sbml filename ends with .xml + sbml_file_name = [f for f in os.listdir(subfolder_path) if f.endswith('.xml')][0] + sedml_file_name = [f for f in os.listdir(subfolder_path) if 'sedml' in f and not f.endswith('omex')][0] + + results_table = utils.create_combined_results_table(results["remote"], + results["local"], + sedml_file_name, + sbml_file_name, + d1_plot_paths["local"], + d1_plot_paths["remote"], + test_folder='tests') + + + print(results_table) + + +if __name__ == "__main__": + create_test_suite_results_tables() From 5acc4e0304ef4a14c6c190eb8a14dbc9ec3ebaad Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Wed, 6 Nov 2024 10:44:25 +0000 Subject: [PATCH 14/22] simplify check_file_compatibility --- utils/__init__.py | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/utils/__init__.py b/utils/__init__.py index 5a23c134..e0463bf2 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -443,14 +443,18 @@ def check_file_compatibility_test(engine, model_filepath, experiment_filepath): if file_extensions in engine_filetypes_tuple_list: file_types = [TYPES[i] for i in file_extensions] return 'pass', (f"The file extensions {file_extensions} suggest the input file types are '{file_types}'. {compatible_filetypes} are compatible with {engine}.") + if 'xml' in file_extensions: - if 'sbml' in model_filepath and 'sedml' not in model_filepath: - if 'sbml' in experiment_filepath and 'sedml' in experiment_filepath: - file_types = ('sbml', 'sedml') - if file_types in engine_filetypes_tuple_list: - return 'pass', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {[TYPES[i] for i in file_types]} which is compatible with {engine}.

{compatible_filetypes} are compatible with {engine}.") - else: - return 'unsure', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {[TYPES[i] for i in file_types]} which is not compatible with {engine}.

{compatible_filetypes} are compatible with {engine}.") + model_sbml = 'sbml' in model_filepath + model_sedml = 'sedml' in model_filepath + experiment_sbml = 'sbml' in experiment_filepath + experiment_sedml = 'sedml' in experiment_filepath + + if model_sbml and experiment_sbml and experiment_sedml and not model_sedml: + file_types = [TYPES[i] for i in ('sbml', 'sedml') ] + return 'pass', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {file_types} which is compatible with {engine}.

{compatible_filetypes} are compatible with {engine}.") + else: + return 'unsure', (f"The file extensions {file_extensions} suggest the input file types may be compatibe with {engine}.

{compatible_filetypes} are compatible with {engine}.") else: return 'unsure', (f"The file extensions {file_extensions} suggest the input file types may not be compatibe with {engine}.

{compatible_filetypes} are compatible with {engine}.") From c4f8a6bea1c11cbaadccf0321814cd5c04bf499a Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Wed, 6 Nov 2024 11:12:41 +0000 Subject: [PATCH 15/22] fix broken plot links --- .../results_compatibility_biosimulators.md | 46 +++++++++---------- .../results_compatibility_biosimulators.md | 42 ++++++++--------- 2 files changed, 44 insertions(+), 44 deletions(-) diff --git a/test_suite/test_00001/tests/results_compatibility_biosimulators.md b/test_suite/test_00001/tests/results_compatibility_biosimulators.md index 60056dcf..0cf5a26e 100644 --- a/test_suite/test_00001/tests/results_compatibility_biosimulators.md +++ b/test_suite/test_00001/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | -|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------| -| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with amici.

['SBML', 'SED-ML'] are compatible with amici.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with brian2.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with cbmpy.

['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with cobrapy.

['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with copasi.

['SBML', 'SED-ML'] are compatible with copasi.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with gillespy2.

['SBML', 'SED-ML'] are compatible with gillespy2.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with libsbmlsim.

['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with masspy.

['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']

Only following targets are supported:
- M_S1
- M_S2
- R_reaction1
- S1
- S2
- k1
- reaction1

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with netpyne.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with pysces.

['SBML', 'SED-ML'] are compatible with pysces.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with smoldyn.

['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with tellurium.

['SBML', 'SED-ML'] are compatible with tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 19 |
vcellhttps://github.com/virtualcell/vcell
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with vcell.

['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | -| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------|:--------------------------------------------------------| +| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with amici.

['SBML', 'SED-ML'] are compatible with amici.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with brian2.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with cbmpy.

['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with cobrapy.

['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with copasi.

['SBML', 'SED-ML'] are compatible with copasi.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with gillespy2.

['SBML', 'SED-ML'] are compatible with gillespy2.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with libsbmlsim.

['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with masspy.

['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']

Only following targets are supported:
- M_S1
- M_S2
- R_reaction1
- S1
- S2
- k1
- reaction1

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with netpyne.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with pysces.

['SBML', 'SED-ML'] are compatible with pysces.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with smoldyn.

['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with tellurium.

['SBML', 'SED-ML'] are compatible with tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +| 19 |
vcellhttps://github.com/virtualcell/vcell
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with vcell.

['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/test_suite/test_01186/tests/results_compatibility_biosimulators.md b/test_suite/test_01186/tests/results_compatibility_biosimulators.md index b6f70c9c..449ed4a6 100644 --- a/test_suite/test_01186/tests/results_compatibility_biosimulators.md +++ b/test_suite/test_01186/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ | | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | |---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------|:---------| -| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with amici.

['SBML', 'SED-ML'] are compatible with amici.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp267694` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp640928` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp347049` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp46347` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp838310` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp433696` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with brian2.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with cbmpy.

['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp528257` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp385050` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with cobrapy.

['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp171288` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp413781` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with copasi.

['SBML', 'SED-ML'] are compatible with copasi.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp860188` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp332181` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with gillespy2.

['SBML', 'SED-ML'] are compatible with gillespy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp595452` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp697896` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp956508` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp90777` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with libsbmlsim.

['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp385105` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp39181` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with masspy.

['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp581425` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp205834` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with netpyne.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with pysces.

['SBML', 'SED-ML'] are compatible with pysces.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp956852` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp186426` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp868261` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp37134` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with smoldyn.

['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with tellurium.

['SBML', 'SED-ML'] are compatible with tellurium.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp399285` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp453545` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | -| 19 |
vcellhttps://github.com/virtualcell/vcell
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with vcell.

['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | -| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with amici.

['SBML', 'SED-ML'] are compatible with amici.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp393956` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp974378` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp202273` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp828624` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp319206` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp366959` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with brian2.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with cbmpy.

['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp770846` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp65202` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with cobrapy.

['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp714067` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp139256` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with copasi.

['SBML', 'SED-ML'] are compatible with copasi.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp639165` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp11739` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with gillespy2.

['SBML', 'SED-ML'] are compatible with gillespy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp554887` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp616620` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp462163` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp738082` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with libsbmlsim.

['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp814016` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp562557` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with masspy.

['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp15290` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp597394` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with netpyne.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with pysces.

['SBML', 'SED-ML'] are compatible with pysces.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp40497` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp858457` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp958607` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp300081` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with smoldyn.

['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with tellurium.

['SBML', 'SED-ML'] are compatible with tellurium.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp60106` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/01186-sbml-l3v2-sedml.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp366317` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.

ERROR TYPE:
ValueError
| | | +| 19 |
vcellhttps://github.com/virtualcell/vcell
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with vcell.

['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file From a3aa8886e8c31d77afacba4c6123667b6ff35744 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Wed, 6 Nov 2024 11:24:33 +0000 Subject: [PATCH 16/22] Add usage instructions for specific test cases in compatibility test script --- test_suite/test_test_suite_compatibility_biosimulators.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/test_suite/test_test_suite_compatibility_biosimulators.py b/test_suite/test_test_suite_compatibility_biosimulators.py index f7221b39..6bbfd5da 100644 --- a/test_suite/test_test_suite_compatibility_biosimulators.py +++ b/test_suite/test_test_suite_compatibility_biosimulators.py @@ -95,6 +95,9 @@ def process_cases(args): To test the highest level and version of SBML of the first 5 cases in the test suite: python test_test_suite_compatibility_biosimulators.py --limit 5 --suite-path /path/to/sbml-test-suite/cases/semantic --sbml-level_version highest + + To test cases 00001 and 01186 in the test suite: + python test_test_suite_compatibility_biosimulators.py --cases 00001 01186 --suite-path /path/to/sbml-test-suite/cases/semantic --sbml-level_version highest """ starting_dir = os.getcwd() # where results will be written From a7d2de062d3860f79e681ca986d33f948c500144 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Wed, 6 Nov 2024 11:25:31 +0000 Subject: [PATCH 17/22] Remove obsolete test suite results table script --- test_suite/test_test_suite_results_table.py | 70 --------------------- 1 file changed, 70 deletions(-) delete mode 100644 test_suite/test_test_suite_results_table.py diff --git a/test_suite/test_test_suite_results_table.py b/test_suite/test_test_suite_results_table.py deleted file mode 100644 index b849257e..00000000 --- a/test_suite/test_test_suite_results_table.py +++ /dev/null @@ -1,70 +0,0 @@ -#!/usr/bin/env python3 - -""" -produce a markdown table of the results of running various tests on the SBML Test Suite - -get this version of the test suite that includes sedml versions or the sedml validation will fail: -https://github.com/sbmlteam/sbml-test-suite/releases/download/3.4.0/semantic_tests_with_sedml_and_graphs.v3.4.0.zip -""" - -import os -import sys -import json -sys.path.append("..") -import utils -engines = utils.ENGINES - - -def create_test_suite_results_tables(): - """ - Create a table of results for each test case in the test suite - - """ - starting_dir = os.getcwd() - print('Current working directory:', starting_dir) - subfolders = [f for f in os.listdir(starting_dir) if os.path.isdir(f) and f.startswith('test_')] - - print(subfolders) - - for subfolder in subfolders: - subfolder_path = os.path.join(starting_dir, subfolder) - os.chdir(subfolder_path) - print(f"Changed to {os.getcwd()}") - - test_folder = 'tests' - - results_paths = { - "local": os.path.join(subfolder_path, test_folder, 'results_local.json'), - "remote": os.path.join(subfolder_path, test_folder, 'results_remote.json') - } - - results = {} - for key, path in results_paths.items(): - with open(path, 'r') as f: - results[key] = json.load(f) - - d1_plot_paths = { - "local": os.path.join(subfolder_path, test_folder, 'd1_plots_local'), - "remote": os.path.join(subfolder_path, test_folder, 'd1_plots_remote') - } - - # get sbml filename with reg ex (it should contain sbml but not sedml) - sbml_file_name = [f for f in os.listdir(subfolder_path) if 'sbml' in f and 'sedml' not in f][0] - # also sbml file does not end with omex - sbml_file_name = [f for f in os.listdir(subfolder_path) if 'sbml' in f and 'sedml' not in f and not f.endswith('omex')][0] - sedml_file_name = [f for f in os.listdir(subfolder_path) if 'sedml' in f and not f.endswith('omex')][0] - - results_table = utils.create_combined_results_table(results["remote"], - results["local"], - sedml_file_name, - sbml_file_name, - d1_plot_paths["local"], - d1_plot_paths["remote"], - test_folder='tests') - - - print(results_table) - - -if __name__ == "__main__": - create_test_suite_results_tables() From c1aa779206258ced0afe06de175c0744da1a1f0b Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Wed, 6 Nov 2024 11:36:35 +0000 Subject: [PATCH 18/22] Remove test results table script --- BioModels/test_biomodels_results_table.py | 68 ----------------------- 1 file changed, 68 deletions(-) delete mode 100644 BioModels/test_biomodels_results_table.py diff --git a/BioModels/test_biomodels_results_table.py b/BioModels/test_biomodels_results_table.py deleted file mode 100644 index ad9d814d..00000000 --- a/BioModels/test_biomodels_results_table.py +++ /dev/null @@ -1,68 +0,0 @@ -#!/usr/bin/env python3 - -""" -produce a markdown table of the results of running various tests on the SBML Test Suite - -get this version of the test suite that includes sedml versions or the sedml validation will fail: -https://github.com/sbmlteam/sbml-test-suite/releases/download/3.4.0/semantic_tests_with_sedml_and_graphs.v3.4.0.zip -""" - -import os -import sys -import json -sys.path.append("..") -import utils -engines = utils.ENGINES - - -def create_test_suite_results_tables(): - """ - Create a table of results for each test case in the test suite - - """ - starting_dir = os.getcwd() - print('Current working directory:', starting_dir) - subfolders = [f for f in os.listdir(starting_dir) if os.path.isdir(f) and f.startswith('BIOMD')] - - print(subfolders) - - for subfolder in subfolders: - subfolder_path = os.path.join(starting_dir, subfolder) - os.chdir(subfolder_path) - print(f"Changed to {os.getcwd()}") - - test_folder = 'tests' - - results_paths = { - "local": os.path.join(subfolder_path, test_folder, 'results_local.json'), - "remote": os.path.join(subfolder_path, test_folder, 'results_remote.json') - } - - results = {} - for key, path in results_paths.items(): - with open(path, 'r') as f: - results[key] = json.load(f) - - d1_plot_paths = { - "local": os.path.join(subfolder_path, test_folder, 'd1_plots_local'), - "remote": os.path.join(subfolder_path, test_folder, 'd1_plots_remote') - } - - # get sbml filename ends with .xml - sbml_file_name = [f for f in os.listdir(subfolder_path) if f.endswith('.xml')][0] - sedml_file_name = [f for f in os.listdir(subfolder_path) if 'sedml' in f and not f.endswith('omex')][0] - - results_table = utils.create_combined_results_table(results["remote"], - results["local"], - sedml_file_name, - sbml_file_name, - d1_plot_paths["local"], - d1_plot_paths["remote"], - test_folder='tests') - - - print(results_table) - - -if __name__ == "__main__": - create_test_suite_results_tables() From 934a69a0b7667a4ed16dacbad9b479f3074b79ff Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 11 Nov 2024 15:09:37 +0000 Subject: [PATCH 19/22] correct mistake reak ->break --- BioModels/test_biomodels_compatibility_biosimulators.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/BioModels/test_biomodels_compatibility_biosimulators.py b/BioModels/test_biomodels_compatibility_biosimulators.py index bd914f08..575d0feb 100644 --- a/BioModels/test_biomodels_compatibility_biosimulators.py +++ b/BioModels/test_biomodels_compatibility_biosimulators.py @@ -195,9 +195,10 @@ def main(): for model_id in model_ids[0:1]: #allow testing on a small sample of models - if max_count > 0 and count >= max_count:reak + if max_count > 0 and count >= max_count: + break count += 1 - print(f"\r{model_id} {count}/{len(model_ids)} ",end='') + print(f"\r{model_id} {count}/{len(model_ids)}",end='') #only process curated models #BIOMD ids should be the curated models @@ -233,6 +234,7 @@ def main(): test_folder = 'tests' engine_list = list(utils.ENGINES.keys()) + engine_list = ['copasi'] utils.run_biosimulators_remotely_and_locally(engine_list, os.path.basename(sedml_file), os.path.basename(sbml_file), From 0a74c4b26fd5335d6b042d6a9ef64496b1296e0f Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 11 Nov 2024 17:10:47 +0000 Subject: [PATCH 20/22] improve check_file_compatibility_test function --- utils/__init__.py | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/utils/__init__.py b/utils/__init__.py index 1b7e4eaf..5d36c788 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -461,17 +461,20 @@ def check_file_compatibility_test(engine, model_filepath, experiment_filepath): if file_extensions in engine_filetypes_tuple_list: file_types = [TYPES[i] for i in file_extensions] return 'pass', (f"The file extensions {file_extensions} suggest the input file types are '{file_types}'. {compatible_filetypes} are compatible with {engine}.") + if 'xml' in file_extensions: - if 'sbml' in model_filepath and 'sedml' not in model_filepath: - if 'sbml' in experiment_filepath and 'sedml' in experiment_filepath: - file_types = ('sbml', 'sedml') - if file_types in engine_filetypes_tuple_list: - return 'pass', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {[TYPES[i] for i in file_types]} which is compatible with {engine}.

{compatible_filetypes} are compatible with {engine}.") - else: - return 'unsure', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {[TYPES[i] for i in file_types]} which is not compatible with {engine}.

{compatible_filetypes} are compatible with {engine}.") + model_sbml = 'sbml' in model_filepath + model_sedml = 'sedml' in model_filepath + experiment_sbml = 'sbml' in experiment_filepath + experiment_sedml = 'sedml' in experiment_filepath + + if model_sbml and experiment_sbml and experiment_sedml and not model_sedml: + file_types = [TYPES[i] for i in ('sbml', 'sedml') ] + return 'pass', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {file_types} which is compatible with {engine}.

{compatible_filetypes} are compatible with {engine}.") + else: + return 'unsure', (f"The file extensions {file_extensions} suggest the input file types may be compatibe with {engine}.

{compatible_filetypes} are compatible with {engine}.") else: return 'unsure', (f"The file extensions {file_extensions} suggest the input file types may not be compatibe with {engine}.

{compatible_filetypes} are compatible with {engine}.") - def collapsible_content(content, title='Details'): """ From 7f0a1dad58f649cede598db1f41d81cbb6f6974d Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 11 Nov 2024 17:28:39 +0000 Subject: [PATCH 21/22] Add BIOMD0000000138 resutls table --- .../results_compatibility_biosimulators.md | 46 +- .../BIOMD0000000138/BIOMD0000000138_url.sedml | 425 ++++ .../BIOMD0000000138/BIOMD0000000138_url.xml | 539 +++++ .../amici_autogen_plot_for_task1.pdf | Bin 0 -> 5948 bytes .../copasi_autogen_plot_for_task1.pdf | Bin 0 -> 8709 bytes .../pysces_autogen_plot_for_task1.pdf | Bin 0 -> 5948 bytes .../tellurium_autogen_plot_for_task1.pdf | Bin 0 -> 8708 bytes .../vcell_autogen_plot_for_task1.pdf | Bin 0 -> 12268 bytes .../amici_autogen_plot_for_task1.pdf | Bin 0 -> 5954 bytes .../copasi_autogen_plot_for_task1.pdf | Bin 0 -> 8715 bytes .../masspy_autogen_plot_for_task1.pdf | Bin 0 -> 5954 bytes .../pysces_autogen_plot_for_task1.pdf | Bin 0 -> 5954 bytes .../tellurium_autogen_plot_for_task1.pdf | Bin 0 -> 8714 bytes .../results_compatibility_biosimulators.md | 23 + .../BIOMD0000000138/tests/results_local.json | 1491 ++++++++++++++ .../BIOMD0000000138/tests/results_remote.json | 1772 +++++++++++++++++ ...t_biomodels_compatibility_biosimulators.py | 8 +- 17 files changed, 4279 insertions(+), 25 deletions(-) create mode 100644 BioModels/BIOMD0000000138/BIOMD0000000138_url.sedml create mode 100644 BioModels/BIOMD0000000138/BIOMD0000000138_url.xml create mode 100644 BioModels/BIOMD0000000138/tests/d1_plots_local/amici_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000138/tests/d1_plots_local/copasi_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000138/tests/d1_plots_local/pysces_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000138/tests/d1_plots_local/tellurium_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000138/tests/d1_plots_local/vcell_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000138/tests/d1_plots_remote/amici_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000138/tests/d1_plots_remote/copasi_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000138/tests/d1_plots_remote/masspy_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000138/tests/d1_plots_remote/pysces_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000138/tests/d1_plots_remote/tellurium_autogen_plot_for_task1.pdf create mode 100644 BioModels/BIOMD0000000138/tests/results_compatibility_biosimulators.md create mode 100644 BioModels/BIOMD0000000138/tests/results_local.json create mode 100644 BioModels/BIOMD0000000138/tests/results_remote.json diff --git a/BioModels/BIOMD0000000001/tests/results_compatibility_biosimulators.md b/BioModels/BIOMD0000000001/tests/results_compatibility_biosimulators.md index 4ece4606..08c5e99f 100644 --- a/BioModels/BIOMD0000000001/tests/results_compatibility_biosimulators.md +++ b/BioModels/BIOMD0000000001/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | -|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------|:-----------------------------------------------------------------------| -| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with amici.

['SBML', 'SED-ML'] are compatible with amici.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with brian2.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with cbmpy.

['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with cobrapy.

['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with copasi.

['SBML', 'SED-ML'] are compatible with copasi.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with gillespy2.

['SBML', 'SED-ML'] are compatible with gillespy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with libsbmlsim.

['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with masspy.

['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Could not load MassModel 'BIOMD0000000001'

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| plot | | -| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with netpyne.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with pysces.

['SBML', 'SED-ML'] are compatible with pysces.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | -| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with smoldyn.

['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with tellurium.

['SBML', 'SED-ML'] are compatible with tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -| 19 |
vcellhttps://github.com/virtualcell/vcell
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with vcell.

['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

| ✅ PASS | | plot | -| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------|:-----------------------------------------------------------------------| +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with amici.

['SBML', 'SED-ML'] are compatible with amici.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with brian2.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with cbmpy.

['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with cobrapy.

['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with copasi.

['SBML', 'SED-ML'] are compatible with copasi.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with gillespy2.

['SBML', 'SED-ML'] are compatible with gillespy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with libsbmlsim.

['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with masspy.

['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Could not load MassModel 'BIOMD0000000001'

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| plot | | +|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with netpyne.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with pysces.

['SBML', 'SED-ML'] are compatible with pysces.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with smoldyn.

['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with tellurium.

['SBML', 'SED-ML'] are compatible with tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
VCellhttps://github.com/virtualcell/vcell
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with vcell.

['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

| ✅ PASS | | plot | +|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/BioModels/BIOMD0000000138/BIOMD0000000138_url.sedml b/BioModels/BIOMD0000000138/BIOMD0000000138_url.sedml new file mode 100644 index 00000000..13802d13 --- /dev/null +++ b/BioModels/BIOMD0000000138/BIOMD0000000138_url.sedml @@ -0,0 +1,425 @@ + + + + + + + + + + + + + + + + + auto_time_for_task1_var + + + + + + + + auto_dg_for_task1_c__x + + + + + + + + auto_dg_for_task1_vca__x + + + + + + + + auto_dg_for_task1_vk__x + + + + + + + + auto_dg_for_task1_Cm__x + + + + + + + + auto_dg_for_task1_gk__x + + + + + + + + auto_dg_for_task1_gcal__x + + + + + + + + auto_dg_for_task1_gsk__x + + + + + + + + auto_dg_for_task1_ga__x + + + + + + + + auto_dg_for_task1_gf__x + + + + + + + + auto_dg_for_task1_vn__x + + + + + + + + auto_dg_for_task1_va__x + + + + + + + + auto_dg_for_task1_vm__x + + + + + + + + auto_dg_for_task1_vh__x + + + + + + + + auto_dg_for_task1_vf__x + + + + + + + + auto_dg_for_task1_sn__x + + + + + + + + auto_dg_for_task1_sa__x + + + + + + + + auto_dg_for_task1_sm__x + + + + + + + + auto_dg_for_task1_sh__x + + + + + + + + auto_dg_for_task1_sf__x + + + + + + + + auto_dg_for_task1_taun__x + + + + + + + + auto_dg_for_task1_tauh__x + + + + + + + + auto_dg_for_task1_lambda__x + + + + + + + + auto_dg_for_task1_kc__x + + + + + + + + auto_dg_for_task1_ks__x + + + + + + + + auto_dg_for_task1_ff__x + + + + + + + + auto_dg_for_task1_alpha__x + + + + + + + + auto_dg_for_task1_phik__x + + + + + + + + auto_dg_for_task1_phia__x + + + + + + + + auto_dg_for_task1_phih__x + + + + + + + + auto_dg_for_task1_phif__x + + + + + + + + auto_dg_for_task1_phical__x + + + + + + + + auto_dg_for_task1_cinf__x + + + + + + + + auto_dg_for_task1_ica__x + + + + + + + + auto_dg_for_task1_isk__x + + + + + + + + auto_dg_for_task1_ibk__x + + + + + + + + auto_dg_for_task1_ikdr__x + + + + + + + + auto_dg_for_task1_ia__x + + + + + + + + auto_dg_for_task1_ik__x + + + + + + + + auto_dg_for_task1_n__x + + + + + + + + auto_dg_for_task1_h__x + + + + + + + + auto_dg_for_task1_V__x + + + + + + + + auto_dg_for_task1_cell__x + + + + + + + + auto_dg_for_task1_reaction_0000004__x + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/BioModels/BIOMD0000000138/BIOMD0000000138_url.xml b/BioModels/BIOMD0000000138/BIOMD0000000138_url.xml new file mode 100644 index 00000000..c1212c7c --- /dev/null +++ b/BioModels/BIOMD0000000138/BIOMD0000000138_url.xml @@ -0,0 +1,539 @@ + + + + + +

The model is encoded according to the paper Low dose of dopamine may stimulate prolactin secretion by increasing fast potassium currents + Figure5 has been reproduced by MathSBML. One need to change the value of ga in order to get the three correct results.

+

the xppaut file of the model is avaiable on the following address offered by the author , http://www.math.fsu.edu/%7Ebertram/software/pituitary/JCNS_07.ode

+
+

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication + for more information.

+

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.

+
+

To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92. +

+ + + + + + + + + + + He + Enuo + + enuo@caltech.edu + + BNMC + + + + + + 2007-08-02T10:34:59Z + + + 2014-04-01T18:01:13Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ The concentration of Ca range can change from 0.1 to 0.3

+ + + + + + + + + + + + + + + + + + + + + + + + + + +

+ For figure 5A, ga=0, figure5B, ga=8, figure5C, ga=25

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b/BioModels/BIOMD0000000138/tests/results_compatibility_biosimulators.md new file mode 100644 index 00000000..3550c29d --- /dev/null +++ b/BioModels/BIOMD0000000138/tests/results_compatibility_biosimulators.md @@ -0,0 +1,23 @@ +| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------|:-----------------------------------------------------------------------| +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with amici.

['SBML', 'SED-ML'] are compatible with amici.
|
❌ FAILview
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ERROR MESSAGE:
lambda * (phik - n) / taun

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
lambda * (phik - n) / taun

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

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logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
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logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with brian2.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

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logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with cbmpy.

['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with cobrapy.

['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with copasi.

['SBML', 'SED-ML'] are compatible with copasi.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with gillespy2.

['SBML', 'SED-ML'] are compatible with gillespy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with libsbmlsim.

['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with masspy.

['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| plot | | +|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with netpyne.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with pysces.

['SBML', 'SED-ML'] are compatible with pysces.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AttributeError':'PysMod' object has no attribute 'lambda'

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AttributeError':'PysMod' object has no attribute 'lambda'

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with smoldyn.

['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with tellurium.

['SBML', 'SED-ML'] are compatible with tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
VCellhttps://github.com/virtualcell/vcell
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatibe with vcell.

['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

| ✅ PASS | | plot | +|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatibe with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/BioModels/BIOMD0000000138/tests/results_local.json b/BioModels/BIOMD0000000138/tests/results_local.json new file mode 100644 index 00000000..a8ec0304 --- /dev/null +++ b/BioModels/BIOMD0000000138/tests/results_local.json @@ -0,0 +1,1491 @@ +{ + "amici": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/amici' returned non-zero exit status 1", + "log_yml": { + "duration": 0.850246, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n rateRule \"lambda * (phik - n) / taun\" contains an unsupported expression: Sympify of expression 'could not parse 'lambda * (phik - n) / taun'' failed, because of exception being raised:\n TokenError: Starred arguments in lambda not supported.", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.52011, + "exception": { + "message": "The SED document did not execute successfully:\n\n rateRule \"lambda * (phik - n) / taun\" contains an unsupported expression: Sympify of expression 'could not parse 'lambda * (phik - n) / taun'' failed, because of exception being raised:\n TokenError: Starred arguments in lambda not supported.", + "type": "SedmlExecutionError" + }, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_c", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vca", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_Cm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gcal", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gsk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ga", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_va", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sa", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_taun", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_tauh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_lambda", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kc", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ks", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ff", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_alpha", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phih", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phif", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phical", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cinf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ica", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_isk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ibk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_n", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_h", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_V", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cell", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SKIPPED" + } + ], + "duration": 0.058425, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SKIPPED" + } + ], + "duration": 0.276489, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.091858, + "exception": { + "message": "rateRule \"lambda * (phik - n) / taun\" contains an unsupported expression: Sympify of expression 'could not parse 'lambda * (phik - n) / taun'' failed, because of exception being raised:\nTokenError: Starred arguments in lambda not supported.", + "type": "SBMLException" + }, + "id": "task1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "brian2": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.056218, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpu6r4hu1y/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n [py.warnings]\r\npyNeuroML >>> WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpu6r4hu1y/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "bionetgen": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1", + "log_yml": { + "duration": 0.180791, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpeshio693/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "boolnet": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1", + "log_yml": { + "duration": 0.164126, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpgkng3_hy/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cbmpy": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.24882, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp8l4hbgu5/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cobrapy": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.127481, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpjxguzzyz/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "copasi": { + "exception_message": "", + "log_yml": { + "duration": 1.22201, + "exception": null, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpiylro8bg/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpiylro8bg/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 0.921278, + "exception": null, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_c", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vca", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_Cm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gcal", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gsk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ga", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_va", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_taun", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_tauh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_lambda", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ks", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ff", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_alpha", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phih", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phif", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phical", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cinf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ica", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_isk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ibk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_n", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_h", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_V", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cell", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SUCCEEDED" + } + ], + "duration": 0.258751, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SUCCEEDED" + } + ], + "duration": 0.42799, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000560", + "duration": 0.107382, + "exception": null, + "id": "task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task1_phif__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cinf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sa__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ibk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ica__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_alpha__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_reaction_0000004__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cell__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_tauh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ikdr__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ff__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_lambda__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ks__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_Cm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_V__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_c__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vca__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ga__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kc__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_va__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gsk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phih__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gcal__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_h__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_taun__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_n__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phical__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_isk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vf__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `BIOMD0000000138_url` may be invalid.\r\n - The model file `/tmp/tmpiylro8bg/./BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'LSODA/LSODAR hybrid method' (KISAO_0000560) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "simulatorDetails": [ + { + "key": "methodName", + "value": "lsoda" + }, + { + "key": "parameters", + "value": null + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "gillespy2": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/gillespy2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.14345, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpfzgeabsg/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "ginsim": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.130563, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp_hz6rgwd/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "libsbmlsim": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/libsbmlsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.153092, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpxa6bvyzf/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "masspy": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.142051, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mSedmlFeatureNotSupportedWarning\u001b[0m: \u001b[33m`/tmp/tmpl5_adwtl/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "netpyne": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1", + "log_yml": { + "duration": 0.041781, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "neuron": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1", + "log_yml": { + "duration": 0.045526, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpodjpnvas/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "opencor": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1", + "log_yml": { + "duration": 0.062107, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpimbuyk1m/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pyneuroml": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1", + "log_yml": { + "duration": 0.05475, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpmsah6p4v/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pysces": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1", + "log_yml": { + "duration": 2.142324, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n :'PysMod' object has no attribute 'lambda'", + "type": "CombineArchiveExecutionError" + }, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp7egu9upf/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp7egu9upf/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 1.820202, + "exception": { + "message": "The SED document did not execute successfully:\n\n :'PysMod' object has no attribute 'lambda'", + "type": "SedmlExecutionError" + }, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V1\r\nlambda is a reserved symbol, replacing with Lambda\r\n\r\n*******************************************************************\r\nIssues encountered in SBML translation (model processed anyway)\r\nSBML source: /tmp/tmph6bvy05t.xml\r\n*******************************************************************\r\n\r\nReserved symbol lambda replaced with Lambda \r\n\r\n*******************************************************************\r\n\r\nInfo: single compartment model: locating \"reaction_0000004\" in default compartment\r\nWriting file: /tmp/tmp7kw5rkpa.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmph6bvy05t.xml\r\nout: /tmp/tmp7kw5rkpa.psc\r\nUsing model directory: /Pysces/psc\r\n/tmp/tmp7kw5rkpa.psc loading ..... \r\nParsing file: /tmp/tmp7kw5rkpa.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"vca\" has been initialised but does not occur in a rate equation\r\nInfo: \"vk\" has been initialised but does not occur in a rate equation\r\nInfo: \"Cm\" has been initialised but does not occur in a rate equation\r\nInfo: \"gk\" has been initialised but does not occur in a rate equation\r\nInfo: \"gcal\" has been initialised but does not occur in a rate equation\r\nInfo: \"gsk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ga\" has been initialised but does not occur in a rate equation\r\nInfo: \"gf\" has been initialised but does not occur in a rate equation\r\nInfo: \"vn\" has been initialised but does not occur in a rate equation\r\nInfo: \"va\" has been initialised but does not occur in a rate equation\r\nInfo: \"vm\" has been initialised but does not occur in a rate equation\r\nInfo: \"vh\" has been initialised but does not occur in a rate equation\r\nInfo: \"vf\" has been initialised but does not occur in a rate equation\r\nInfo: \"sn\" has been initialised but does not occur in a rate equation\r\nInfo: \"sa\" has been initialised but does not occur in a rate equation\r\nInfo: \"sm\" has been initialised but does not occur in a rate equation\r\nInfo: \"sh\" has been initialised but does not occur in a rate equation\r\nInfo: \"sf\" has been initialised but does not occur in a rate equation\r\nInfo: \"taun\" has been initialised but does not occur in a rate equation\r\nInfo: \"tauh\" has been initialised but does not occur in a rate equation\r\nInfo: \"Lambda\" has been initialised but does not occur in a rate equation\r\nInfo: \"ks\" has been initialised but does not occur in a rate equation\r\nInfo: \"phik\" has been initialised but does not occur in a rate equation\r\nInfo: \"phia\" has been initialised but does not occur in a rate equation\r\nInfo: \"phih\" has been initialised but does not occur in a rate equation\r\nInfo: \"phif\" has been initialised but does not occur in a rate equation\r\nInfo: \"phical\" has been initialised but does not occur in a rate equation\r\nInfo: \"cinf\" has been initialised but does not occur in a rate equation\r\nInfo: \"isk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ibk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ikdr\" has been initialised but does not occur in a rate equation\r\nInfo: \"ia\" has been initialised but does not occur in a rate equation\r\nInfo: \"ik\" has been initialised but does not occur in a rate equation\r\nInfo: \"n\" has been initialised but does not occur in a rate equation\r\nInfo: \"h\" has been initialised but does not occur in a rate equation\r\nInfo: \"V\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . no flux conservation\r\n done.\r\n \r\n\r\nAssignment rule(s) detected.\r\nRate rule(s) detected.\r\nINFO: RateRules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nINFO: Assignment Rules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nCVODE time for 1001 points: 0.02880549430847168\r\nRateRules evaluated and added to mod.data_sim.\r\n \u001b[31mfailed - 'PysMod' object has no attribute 'lambda'\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_c", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vca", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_Cm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gcal", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gsk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ga", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_va", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sa", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_taun", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_tauh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_lambda", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kc", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ks", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ff", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_alpha", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phih", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phif", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phical", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cinf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ica", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_isk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ibk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_n", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_h", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_V", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cell", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SKIPPED" + } + ], + "duration": 0.116927, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SKIPPED" + } + ], + "duration": 0.371212, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 1.134029, + "exception": { + "message": "'PysMod' object has no attribute 'lambda'", + "type": "AttributeError" + }, + "id": "task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task1_h__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_va__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sa__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phih__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_taun__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_c__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_alpha__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vca__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_n__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ga__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gsk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gcal__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_tauh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phical__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ff__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cinf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_lambda__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_Cm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ks__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ibk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_V__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cell__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kc__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ica__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phif__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ikdr__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_isk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_reaction_0000004__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "rbapy": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.18608, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpt51vbuiz/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "smoldyn": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1", + "log_yml": {}, + "detailed_error_log": {} + }, + "tellurium": { + "exception_message": "", + "log_yml": { + "duration": 1.193888, + "exception": null, + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmp370xud5o/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmp370xud5o/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n", + "sedDocuments": [ + { + "duration": 0.791637, + "exception": null, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_c", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vca", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_Cm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gcal", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gsk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ga", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_va", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_taun", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_tauh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_lambda", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ks", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ff", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_alpha", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phih", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phif", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phical", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cinf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ica", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_isk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ibk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_n", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_h", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_V", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cell", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SUCCEEDED" + } + ], + "duration": 0.207648, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SUCCEEDED" + } + ], + "duration": 0.312604, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 0.124152, + "exception": null, + "id": "task1", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33m- Variable `auto_dg_for_task1_gcal__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vca__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ikdr__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ibk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_va__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_V__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gsk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ga__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phical__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kc__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ff__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_alpha__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_Cm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sa__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cell__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_c__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cinf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_lambda__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_reaction_0000004__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_h__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phih__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ks__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_n__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_isk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_tauh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phif__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_taun__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ica__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mModel `BIOMD0000000138_url` may be invalid.\r\n - The model file `/tmp/tmp370xud5o/./BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning:\r\n\r\n\u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n\r\n", + "simulatorDetails": [ + { + "key": "method", + "value": "simulate" + }, + { + "key": "solver", + "value": "cvode" + }, + { + "key": "relative_tolerance", + "value": 1e-06 + }, + { + "key": "absolute_tolerance", + "value": 1e-12 + }, + { + "key": "stiff", + "value": true + }, + { + "key": "maximum_bdf_order", + "value": 5 + }, + { + "key": "maximum_adams_order", + "value": 12 + }, + { + "key": "maximum_num_steps", + "value": 20000 + }, + { + "key": "maximum_time_step", + "value": 0.0 + }, + { + "key": "minimum_time_step", + "value": 0.0 + }, + { + "key": "initial_time_step", + "value": 0.0 + }, + { + "key": "multiple_steps", + "value": false + }, + { + "key": "variable_step_size", + "value": false + }, + { + "key": "max_output_rows", + "value": 100000 + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "vcell": { + "exception_message": "", + "log_yml": { + "duration": 9, + "exception": null, + "output": "Processing BIOMD0000000138_url.sedml. Done", + "sedDocuments": [ + { + "duration": null, + "exception": null, + "location": "BIOMD0000000138_url.sedml", + "output": "Initializing SED-ML document... done. Successful translation of SED-ML file. Building solvers and starting simulation of all tasks... Generating outputs... Generating CSV file... Done. Generating HDF5 file...", + "outputs": [ + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SUCCEEDED" + } + ], + "duration": null, + "exception": null, + "id": "autogen_plot_for_task1", + "output": null, + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_c", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vca", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_Cm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gcal", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gsk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ga", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_va", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_taun", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_tauh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_lambda", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ks", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ff", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_alpha", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phih", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phif", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phical", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cinf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ica", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_isk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ibk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_n", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_h", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_V", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cell", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SUCCEEDED" + } + ], + "duration": null, + "exception": null, + "id": "autogen_report_for_task1", + "output": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 1, + "exception": null, + "id": "task1", + "output": "Initializing simulation job 0 ... done. Starting simulation... done.", + "simulatorDetails": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "xpp": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1", + "log_yml": { + "duration": 0.049408, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp1k_stn43/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + } +} \ No newline at end of file diff --git a/BioModels/BIOMD0000000138/tests/results_remote.json b/BioModels/BIOMD0000000138/tests/results_remote.json new file mode 100644 index 00000000..2268395c --- /dev/null +++ b/BioModels/BIOMD0000000138/tests/results_remote.json @@ -0,0 +1,1772 @@ +{ + "amici": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c8c0d09353e8f106b51", + "download": "https://api.biosimulations.org/results/67323c8c0d09353e8f106b51/download", + "logs": "https://api.biosimulations.org/logs/67323c8c0d09353e8f106b51?includeOutput=true", + "log_yml": { + "duration": 1.059903, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n rateRule \"lambda * (phik - n) / taun\" contains an unsupported expression: Sympify of expression 'could not parse 'lambda * (phik - n) / taun'' failed, because of exception being raised:\n TokenError: Starred arguments in lambda not supported.", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.629425, + "exception": { + "message": "The SED document did not execute successfully:\n\n rateRule \"lambda * (phik - n) / taun\" contains an unsupported expression: Sympify of expression 'could not parse 'lambda * (phik - n) / taun'' failed, because of exception being raised:\n TokenError: Starred arguments in lambda not supported.", + "type": "SedmlExecutionError" + }, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_c", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vca", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_Cm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gcal", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gsk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ga", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_va", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sa", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_taun", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_tauh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_lambda", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kc", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ks", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ff", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_alpha", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phih", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phif", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phical", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cinf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ica", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_isk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ibk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_n", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_h", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_V", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cell", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SKIPPED" + } + ], + "duration": 0.060745, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SKIPPED" + } + ], + "duration": 0.341835, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.104082, + "exception": { + "message": "rateRule \"lambda * (phik - n) / taun\" contains an unsupported expression: Sympify of expression 'could not parse 'lambda * (phik - n) / taun'' failed, because of exception being raised:\nTokenError: Starred arguments in lambda not supported.", + "type": "SBMLException" + }, + "id": "task1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + } + }, + "brian2": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c8eb678b3883bb6c1d2", + "download": "https://api.biosimulations.org/results/67323c8eb678b3883bb6c1d2/download", + "logs": "https://api.biosimulations.org/logs/67323c8eb678b3883bb6c1d2?includeOutput=true", + "log_yml": { + "duration": 0.048472, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "bionetgen": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c900d09353e8f106b54", + "download": "https://api.biosimulations.org/results/67323c900d09353e8f106b54/download", + "logs": "https://api.biosimulations.org/logs/67323c900d09353e8f106b54?includeOutput=true", + "log_yml": { + "duration": 0.19821, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "boolnet": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c92b678b3883bb6c1d6", + "download": "https://api.biosimulations.org/results/67323c92b678b3883bb6c1d6/download", + "logs": "https://api.biosimulations.org/logs/67323c92b678b3883bb6c1d6?includeOutput=true", + "log_yml": { + "duration": 0.182139, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "cbmpy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c930d09353e8f106b57", + "download": "https://api.biosimulations.org/results/67323c930d09353e8f106b57/download", + "logs": "https://api.biosimulations.org/logs/67323c930d09353e8f106b57?includeOutput=true", + "log_yml": { + "duration": 0.31853, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "cobrapy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c95b678b3883bb6c1dc", + "download": "https://api.biosimulations.org/results/67323c95b678b3883bb6c1dc/download", + "logs": "https://api.biosimulations.org/logs/67323c95b678b3883bb6c1dc?includeOutput=true", + "log_yml": { + "duration": 0.176861, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "copasi": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c980d09353e8f106b5b", + "download": "https://api.biosimulations.org/results/67323c980d09353e8f106b5b/download", + "logs": "https://api.biosimulations.org/logs/67323c980d09353e8f106b5b?includeOutput=true", + "log_yml": { + "duration": 1.265494, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 0.950286, + "exception": null, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml 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"autogen_task1_ff", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_alpha", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phih", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phif", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phical", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cinf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ica", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_isk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ibk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_n", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_h", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_V", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cell", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SUCCEEDED" + } + ], + "duration": 0.24725, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SUCCEEDED" + } + ], + "duration": 0.395308, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000560", + "duration": 0.17546, + "exception": null, + "id": "task1", + "output": "", + "simulatorDetails": [ + { + "key": "methodName", + "value": "lsoda" + }, + { + "key": "parameters", + "value": null + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + }, + "gillespy2": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c9a5a60072d20f56d8d", + "download": "https://api.biosimulations.org/results/67323c9a5a60072d20f56d8d/download", + "logs": "https://api.biosimulations.org/logs/67323c9a5a60072d20f56d8d?includeOutput=true", + "log_yml": { + "duration": 0.211598, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "ginsim": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c9c5a60072d20f56d90", + "download": "https://api.biosimulations.org/results/67323c9c5a60072d20f56d90/download", + "logs": "https://api.biosimulations.org/logs/67323c9c5a60072d20f56d90?includeOutput=true", + "log_yml": { + "duration": 0.185889, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "libsbmlsim": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323c9eb678b3883bb6c1ec", + "download": "https://api.biosimulations.org/results/67323c9eb678b3883bb6c1ec/download", + "logs": "https://api.biosimulations.org/logs/67323c9eb678b3883bb6c1ec?includeOutput=true", + "log_yml": { + "duration": 0.193056, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "masspy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323ca05a60072d20f56da2", + "download": "https://api.biosimulations.org/results/67323ca05a60072d20f56da2/download", + "logs": "https://api.biosimulations.org/logs/67323ca05a60072d20f56da2?includeOutput=true", + "log_yml": { + "duration": 1.181274, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n \t`(model, errors) = validate_sbml_model(filename)`\n If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.612617, + "exception": { + "message": "The SED document did not execute successfully:\n\n Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n \t`(model, errors) = validate_sbml_model(filename)`\n If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .", + "type": "SedmlExecutionError" + }, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_c", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vca", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_Cm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gcal", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gsk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ga", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_va", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sa", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_taun", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_tauh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_lambda", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kc", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ks", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ff", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_alpha", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phih", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phif", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phical", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cinf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ica", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_isk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ibk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_n", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_h", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_V", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cell", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SKIPPED" + } + ], + "duration": 0.061385, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SKIPPED" + } + ], + "duration": 0.319179, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.083462, + "exception": { + "message": "Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n\t`(model, errors) = validate_sbml_model(filename)`\nIf the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .", + "type": "MassSBMLError" + }, + "id": "task1", + "output": "\u001b[93mWARNING:\u001b[0m \u001b[93mModel does not contain SBML fbc package\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mModel does not contain SBML groups package\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'model_0000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'model_0000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + } + }, + "netpyne": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323ca1b678b3883bb6c200", + "download": "https://api.biosimulations.org/results/67323ca1b678b3883bb6c200/download", + "logs": "https://api.biosimulations.org/logs/67323ca1b678b3883bb6c200?includeOutput=true", + "log_yml": { + "duration": 0.05409, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "neuron": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323ca30d09353e8f106b76", + "download": "https://api.biosimulations.org/results/67323ca30d09353e8f106b76/download", + "logs": "https://api.biosimulations.org/logs/67323ca30d09353e8f106b76?includeOutput=true", + "log_yml": { + "duration": 0.049106, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "opencor": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323ca40d09353e8f106b7d", + "download": "https://api.biosimulations.org/results/67323ca40d09353e8f106b7d/download", + "logs": "https://api.biosimulations.org/logs/67323ca40d09353e8f106b7d?includeOutput=true", + "log_yml": { + "duration": 0.02749, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpnh9ii2_u/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "pyneuroml": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323ca60d09353e8f106b82", + "download": "https://api.biosimulations.org/results/67323ca60d09353e8f106b82/download", + "logs": "https://api.biosimulations.org/logs/67323ca60d09353e8f106b82?includeOutput=true", + "log_yml": { + "duration": 0.050187, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "pysces": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323ca80d09353e8f106b87", + "download": "https://api.biosimulations.org/results/67323ca80d09353e8f106b87/download", + "logs": "https://api.biosimulations.org/logs/67323ca80d09353e8f106b87?includeOutput=true", + "log_yml": { + "duration": 2.233287, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n :'PysMod' object has no attribute 'lambda'", + "type": "CombineArchiveExecutionError" + }, + "output": "libtk8.6.so: cannot open shared object file: No such file or directory\r\n\r\nPySCeS defaults to matplotlib's TKagg backend if not specified in the user configuration file, set \"matplotlib_backend = \" \r\nMatplotlib interface loaded (pysces.plt.m)\r\nPitcon routines available\r\nNLEQ2 routines available\r\nSBML support available\r\nYou are using NumPy (2.1.2) with SciPy (1.14.1)\r\nAssimulo CVode available\r\nRateChar is available\r\nParallel scanner is available\r\n\r\nPySCeS environment\r\n******************\r\npysces.model_dir = /home/FCAM/crbmapi/Pysces/psc\r\npysces.output_dir = /home/FCAM/crbmapi/Pysces\r\n\r\n\r\n***********************************************************************\r\n* Welcome to PySCeS (1.2.2) - Python Simulator for Cellular Systems *\r\n* http://pysces.sourceforge.net *\r\n* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2024 *\r\n* Triple-J Group for Molecular Cell Physiology *\r\n* Stellenbosch University, ZA and VU University Amsterdam, NL *\r\n* PySCeS is distributed under the PySCeS (BSD style) licence, see *\r\n* LICENCE.txt (supplied with this release) for details *\r\n* Please cite PySCeS with: doi:10.1093/bioinformatics/bti046 *\r\n***********************************************************************\r\n", + "sedDocuments": [ + { + "duration": 1.882373, + "exception": { + "message": "The SED document did not execute successfully:\n\n :'PysMod' object has no attribute 'lambda'", + "type": "SedmlExecutionError" + }, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V1\r\nlambda is a reserved symbol, replacing with Lambda\r\n\r\n*******************************************************************\r\nIssues encountered in SBML translation (model processed anyway)\r\nSBML source: /tmp/tmpzhjj07jb.xml\r\n*******************************************************************\r\n\r\nReserved symbol lambda replaced with Lambda \r\n\r\n*******************************************************************\r\n\r\nInfo: single compartment model: locating \"reaction_0000004\" in default compartment\r\nWriting file: /tmp/tmpdr5eja8y.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpzhjj07jb.xml\r\nout: /tmp/tmpdr5eja8y.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmpdr5eja8y.psc loading ..... \r\nParsing file: /tmp/tmpdr5eja8y.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"vca\" has been initialised but does not occur in a rate equation\r\nInfo: \"vk\" has been initialised but does not occur in a rate equation\r\nInfo: \"Cm\" has been initialised but does not occur in a rate equation\r\nInfo: \"gk\" has been initialised but does not occur in a rate equation\r\nInfo: \"gcal\" has been initialised but does not occur in a rate equation\r\nInfo: \"gsk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ga\" has been initialised but does not occur in a rate equation\r\nInfo: \"gf\" has been initialised but does not occur in a rate equation\r\nInfo: \"vn\" has been initialised but does not occur in a rate equation\r\nInfo: \"va\" has been initialised but does not occur in a rate equation\r\nInfo: \"vm\" has been initialised but does not occur in a rate equation\r\nInfo: \"vh\" has been initialised but does not occur in a rate equation\r\nInfo: \"vf\" has been initialised but does not occur in a rate equation\r\nInfo: \"sn\" has been initialised but does not occur in a rate equation\r\nInfo: \"sa\" has been initialised but does not occur in a rate equation\r\nInfo: \"sm\" has been initialised but does not occur in a rate equation\r\nInfo: \"sh\" has been initialised but does not occur in a rate equation\r\nInfo: \"sf\" has been initialised but does not occur in a rate equation\r\nInfo: \"taun\" has been initialised but does not occur in a rate equation\r\nInfo: \"tauh\" has been initialised but does not occur in a rate equation\r\nInfo: \"Lambda\" has been initialised but does not occur in a rate equation\r\nInfo: \"ks\" has been initialised but does not occur in a rate equation\r\nInfo: \"phik\" has been initialised but does not occur in a rate equation\r\nInfo: \"phia\" has been initialised but does not occur in a rate equation\r\nInfo: \"phih\" has been initialised but does not occur in a rate equation\r\nInfo: \"phif\" has been initialised but does not occur in a rate equation\r\nInfo: \"phical\" has been initialised but does not occur in a rate equation\r\nInfo: \"cinf\" has been initialised but does not occur in a rate equation\r\nInfo: \"isk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ibk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ikdr\" has been initialised but does not occur in a rate equation\r\nInfo: \"ia\" has been initialised but does not occur in a rate equation\r\nInfo: \"ik\" has been initialised but does not occur in a rate equation\r\nInfo: \"n\" has been initialised but does not occur in a rate equation\r\nInfo: \"h\" has been initialised but does not occur in a rate equation\r\nInfo: \"V\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . no flux conservation\r\n done.\r\n \r\n\r\nAssignment rule(s) detected.\r\nRate rule(s) detected.\r\nINFO: RateRules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nINFO: Assignment Rules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nCVODE time for 1001 points: 0.048134565353393555\r\nRateRules evaluated and added to mod.data_sim.\r\n \u001b[31mfailed - 'PysMod' object has no attribute 'lambda'\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_c", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vca", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_Cm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gk", + "status": "SKIPPED" + }, + { + "id": 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}, + { + "id": "autogen_task1_kc", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ks", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ff", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_alpha", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phih", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phif", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phical", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cinf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ica", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_isk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ibk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_n", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_h", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_V", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cell", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SKIPPED" + } + ], + "duration": 0.059516, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SKIPPED" + } + ], + "duration": 0.4909, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 1.188505, + "exception": { + "message": "'PysMod' object has no attribute 'lambda'", + "type": "AttributeError" + }, + "id": "task1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + } + }, + "rbapy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323ca9b678b3883bb6c229", + "download": "https://api.biosimulations.org/results/67323ca9b678b3883bb6c229/download", + "logs": "https://api.biosimulations.org/logs/67323ca9b678b3883bb6c229?includeOutput=true", + "log_yml": { + "duration": 0.191135, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "smoldyn": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323cab0d09353e8f106b90", + "download": "https://api.biosimulations.org/results/67323cab0d09353e8f106b90/download", + "logs": "https://api.biosimulations.org/logs/67323cab0d09353e8f106b90?includeOutput=true", + "log_yml": { + "duration": 0.05373, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "tellurium": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323cad5a60072d20f56dd1", + "download": "https://api.biosimulations.org/results/67323cad5a60072d20f56dd1/download", + "logs": "https://api.biosimulations.org/logs/67323cad5a60072d20f56dd1?includeOutput=true", + "log_yml": { + "duration": 1.527764, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 1.025925, + "exception": null, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_c", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vca", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_Cm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gcal", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gsk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ga", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_va", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_taun", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_tauh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_lambda", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ks", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ff", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_alpha", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phih", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phif", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phical", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cinf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ica", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_isk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ibk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_n", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_h", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_V", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cell", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SUCCEEDED" + } + ], + "duration": 0.279603, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SUCCEEDED" + } + ], + "duration": 0.347925, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 0.23826, + "exception": null, + "id": "task1", + "output": "", + "simulatorDetails": [ + { + "key": "method", + "value": "simulate" + }, + { + "key": "solver", + "value": "cvode" + }, + { + "key": "relative_tolerance", + "value": 1e-06 + }, + { + "key": "absolute_tolerance", + "value": 1e-12 + }, + { + "key": "stiff", + "value": true + }, + { + "key": "maximum_bdf_order", + "value": 5 + }, + { + "key": "maximum_adams_order", + "value": 12 + }, + { + "key": "maximum_num_steps", + "value": 20000 + }, + { + "key": "maximum_time_step", + "value": 0.0 + }, + { + "key": "minimum_time_step", + "value": 0.0 + }, + { + "key": "initial_time_step", + "value": 0.0 + }, + { + "key": "multiple_steps", + "value": false + }, + { + "key": "variable_step_size", + "value": false + }, + { + "key": "max_output_rows", + "value": 100000 + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + }, + "vcell": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323caf5a60072d20f56dd9", + "download": "https://api.biosimulations.org/results/67323caf5a60072d20f56dd9/download", + "logs": "https://api.biosimulations.org/logs/67323caf5a60072d20f56dd9?includeOutput=true", + "log_yml": { + "duration": null, + "exception": null, + "output": null, + "sedDocuments": [ + { + "duration": null, + "exception": null, + "location": "BIOMD0000000138_url.sedml", + "output": null, + "outputs": [ + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "QUEUED" + } + ], + "duration": null, + "exception": null, + "id": "autogen_plot_for_task1", + "output": null, + "skipReason": null, + "status": "QUEUED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "QUEUED" + }, + { + "id": "autogen_task1_c", + "status": "QUEUED" + }, + { + "id": "autogen_task1_vca", + "status": "QUEUED" + }, + { + "id": "autogen_task1_vk", + "status": "QUEUED" + }, + { + "id": "autogen_task1_Cm", + "status": "QUEUED" + }, + { + "id": "autogen_task1_gk", + "status": "QUEUED" + }, + { + "id": "autogen_task1_gcal", + "status": "QUEUED" + }, + { + "id": "autogen_task1_gsk", + "status": "QUEUED" + }, + { + "id": "autogen_task1_ga", + "status": "QUEUED" + }, + { + "id": "autogen_task1_gf", + "status": "QUEUED" + }, + { + "id": "autogen_task1_vn", + "status": "QUEUED" + }, + { + "id": "autogen_task1_va", + "status": "QUEUED" + }, + { + "id": "autogen_task1_vm", + "status": "QUEUED" + }, + { + "id": "autogen_task1_vh", + "status": "QUEUED" + }, + { + "id": "autogen_task1_vf", + "status": "QUEUED" + }, + { + "id": "autogen_task1_sn", + "status": "QUEUED" + }, + { + "id": "autogen_task1_sa", + "status": "QUEUED" + }, + { + "id": "autogen_task1_sm", + "status": "QUEUED" + }, + { + "id": "autogen_task1_sh", + "status": "QUEUED" + }, + { + "id": "autogen_task1_sf", + "status": "QUEUED" + }, + { + "id": "autogen_task1_taun", + "status": "QUEUED" + }, + { + "id": "autogen_task1_tauh", + "status": "QUEUED" + }, + { + "id": "autogen_task1_lambda", + "status": "QUEUED" + }, + { + "id": "autogen_task1_kc", + "status": "QUEUED" + }, + { + "id": "autogen_task1_ks", + "status": "QUEUED" + }, + { + "id": "autogen_task1_ff", + "status": "QUEUED" + }, + { + "id": "autogen_task1_alpha", + "status": "QUEUED" + }, + { + "id": "autogen_task1_phik", + "status": "QUEUED" + }, + { + "id": "autogen_task1_phia", + "status": "QUEUED" + }, + { + "id": "autogen_task1_phih", + "status": "QUEUED" + }, + { + "id": "autogen_task1_phif", + "status": "QUEUED" + }, + { + "id": "autogen_task1_phical", + "status": "QUEUED" + }, + { + "id": "autogen_task1_cinf", + "status": "QUEUED" + }, + { + "id": "autogen_task1_ica", + "status": "QUEUED" + }, + { + "id": "autogen_task1_isk", + "status": "QUEUED" + }, + { + "id": "autogen_task1_ibk", + "status": "QUEUED" + }, + { + "id": "autogen_task1_ikdr", + "status": "QUEUED" + }, + { + "id": "autogen_task1_ia", + "status": "QUEUED" + }, + { + "id": "autogen_task1_ik", + "status": "QUEUED" + }, + { + "id": "autogen_task1_n", + "status": "QUEUED" + }, + { + "id": "autogen_task1_h", + "status": "QUEUED" + }, + { + "id": "autogen_task1_V", + "status": "QUEUED" + }, + { + "id": "autogen_task1_cell", + "status": "QUEUED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "QUEUED" + } + ], + "duration": null, + "exception": null, + "id": "autogen_report_for_task1", + "output": null, + "skipReason": null, + "status": "QUEUED" + } + ], + "skipReason": null, + "status": "QUEUED", + "tasks": [ + { + "algorithm": null, + "duration": null, + "exception": null, + "id": "task1", + "output": null, + "simulatorDetails": null, + "skipReason": null, + "status": "QUEUED" + } + ] + } + ], + "skipReason": null, + "status": "QUEUED" + } + }, + "xpp": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67323cb15a60072d20f56ddf", + "download": "https://api.biosimulations.org/results/67323cb15a60072d20f56ddf/download", + "logs": "https://api.biosimulations.org/logs/67323cb15a60072d20f56ddf?includeOutput=true", + "log_yml": { + "duration": 0.048852, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + } +} \ No newline at end of file diff --git a/BioModels/test_biomodels_compatibility_biosimulators.py b/BioModels/test_biomodels_compatibility_biosimulators.py index 575d0feb..89bb5ecb 100644 --- a/BioModels/test_biomodels_compatibility_biosimulators.py +++ b/BioModels/test_biomodels_compatibility_biosimulators.py @@ -193,7 +193,10 @@ def main(): count = 0 starting_dir = os.getcwd() - for model_id in model_ids[0:1]: + if cases != None: + model_ids = cases + + for model_id in model_ids: #allow testing on a small sample of models if max_count > 0 and count >= max_count: break @@ -234,7 +237,7 @@ def main(): test_folder = 'tests' engine_list = list(utils.ENGINES.keys()) - engine_list = ['copasi'] + utils.run_biosimulators_remotely_and_locally(engine_list, os.path.basename(sedml_file), os.path.basename(sbml_file), @@ -243,4 +246,5 @@ def main(): test_folder=test_folder) if __name__ == "__main__": + cases = ["BIOMD0000000001","BIOMD0000000138"] main() \ No newline at end of file From a8bf0290154044f738d566d0baf065ec8e5e8155 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 12 Nov 2024 16:40:44 +0000 Subject: [PATCH 22/22] Add remove_output option to and modify biomodels script --- ...t_biomodels_compatibility_biosimulators.py | 7 +++-- utils/__init__.py | 30 +++++++++++-------- 2 files changed, 23 insertions(+), 14 deletions(-) diff --git a/BioModels/test_biomodels_compatibility_biosimulators.py b/BioModels/test_biomodels_compatibility_biosimulators.py index 89bb5ecb..2acbe56d 100644 --- a/BioModels/test_biomodels_compatibility_biosimulators.py +++ b/BioModels/test_biomodels_compatibility_biosimulators.py @@ -236,15 +236,18 @@ def main(): if not sedml_file: continue # no further tests possible test_folder = 'tests' - engine_list = list(utils.ENGINES.keys()) + # engine_list = list(utils.ENGINES.keys()) utils.run_biosimulators_remotely_and_locally(engine_list, os.path.basename(sedml_file), os.path.basename(sbml_file), os.path.join(test_folder,'d1_plots_remote'), os.path.join(test_folder,'d1_plots_local'), - test_folder=test_folder) + test_folder=test_folder, + remove_output=remove_output) if __name__ == "__main__": cases = ["BIOMD0000000001","BIOMD0000000138"] + remove_output = False + engine_list = ['copasi'] main() \ No newline at end of file diff --git a/utils/__init__.py b/utils/__init__.py index 5d36c788..3053d4ca 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -1188,7 +1188,8 @@ def run_biosimulators_remotely(engine_keys, sedml_file_name, sbml_file_name, d1_plots_remote_dir, - test_folder='tests'): + test_folder='tests', + remove_output_remote=True): """ run with directory pointing towards the location of the sedml and sbml files""" @@ -1220,10 +1221,10 @@ def run_biosimulators_remotely(engine_keys, file_paths = find_files(remote_output_dir, '.pdf') move_d1_files(file_paths, d1_plots_remote_dir) - # remove the remote results directory - if os.path.exists(remote_output_dir): - shutil.rmtree(remote_output_dir) - print('Removed ' + remote_output_dir + ' folder') + if remove_output_remote == True:# remove the remote results directory + if os.path.exists(remote_output_dir): + shutil.rmtree(remote_output_dir) + print('Removed ' + remote_output_dir + ' folder') return results_remote @@ -1231,7 +1232,8 @@ def run_biosimulators_locally(engine_keys, sedml_file_name, sbml_file_name, d1_plots_local_dir, - test_folder='tests'): + test_folder='tests', + remove_output_local=True): engines = {k: v for k, v in ENGINES.items() if k in engine_keys} results_local = {} @@ -1250,9 +1252,10 @@ def run_biosimulators_locally(engine_keys, move_d1_files(file_paths, d1_plots_local_dir) # if it exists remove the output folder - if os.path.exists(local_output_dir): - shutil.rmtree(local_output_dir) - print('Removed ' + local_output_dir + ' folder') + if remove_output_local == True: + if os.path.exists(local_output_dir): + shutil.rmtree(local_output_dir) + print('Removed ' + local_output_dir + ' folder') return results_local @@ -1316,19 +1319,22 @@ def run_biosimulators_remotely_and_locally(engine_keys, sbml_file_name, d1_plots_remote_dir, d1_plots_local_dir, - test_folder='tests'): + test_folder='tests', + remove_output=True): results_remote = run_biosimulators_remotely(engine_keys, sedml_file_name=sedml_file_name, sbml_file_name=sbml_file_name, d1_plots_remote_dir=d1_plots_remote_dir, - test_folder=test_folder) + test_folder=test_folder, + remove_output_remote = remove_output) results_local = run_biosimulators_locally(engine_keys, sedml_file_name=sedml_file_name, sbml_file_name=sbml_file_name, d1_plots_local_dir=d1_plots_local_dir, - test_folder=test_folder) + test_folder=test_folder, + remove_output_local = remove_output) results_table = create_combined_results_table(results_remote, results_local,