From 682a9ff5405d49a33c61ab787d44ff8c517acedb Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Wed, 20 Nov 2024 11:36:30 +0000 Subject: [PATCH 1/5] add fbc attribute if missing (draft, temp files not deleted but added attributes in valid positions) --- .../results_compatibility_biosimulators.md | 46 ++++++------- ..._test_suite_compatibility_biosimulators.py | 10 +-- utils/__init__.py | 66 +++++++++++++++++-- 3 files changed, 89 insertions(+), 33 deletions(-) diff --git a/test_suite/test_01186/tests/results_compatibility_biosimulators.md b/test_suite/test_01186/tests/results_compatibility_biosimulators.md index 75531136..ca8741e2 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) | -|:-------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------|:---------| -|
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
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logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp525281` 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 `./tmp737376` 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
| | | -|
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

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logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp791132` 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 `./tmp713737` 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
| | | -|
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
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logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp820974` 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 `./tmp938788` 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
| | | -|
Brian 2https://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

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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/
|
✅ 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
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logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp243212` 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 `./tmp693225` 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
| | | -|
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 `./tmp918177` 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 `./tmp324352` 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
| | | -|
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 `./tmp16472` 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 `./tmp666700` 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
| | | -|
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 `./tmp707249` 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 `./tmp75439` 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
| | | -|
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
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logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp453181` 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 `./tmp40539` 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
| | | -|
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 `./tmp250973` 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 `./tmp267947` 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
| | | -|
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 `./tmp576715` 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 `./tmp701617` 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
| | | -|
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

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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
| | | -|
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
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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
| | | -|
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
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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
| | | -|
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
| | | -|
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
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logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp20997` 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 `./tmp824724` 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
| | | -|
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 `./tmp514290` 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 `./tmp737329` 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
| | | -|
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.

| | | -|
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
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logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp14673` 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 `./tmp748833` 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
| | | -|
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.
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❌ FAILview
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logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | -|
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 +| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------|:---------| +|
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:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

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

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
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:
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
| | | +|
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:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
Brian 2https://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
| | | +|
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:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

'MLStripper' object has no attribute 'unescape'

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

The SED document did not execute successfully:

'MLStripper' object has no attribute 'unescape'

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
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:
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 `cobra.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/opencobra/cobrapy/issues .

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 `cobra.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/opencobra/cobrapy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
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:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'ValueError':No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy

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

The SED document did not execute successfully:

class 'ValueError':No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
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:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

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

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
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:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Namespaces must include 1 SBML qual namespace.

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

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

The SED document did not execute successfully:

Namespaces must include 1 SBML qual namespace.

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
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:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

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

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
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:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

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

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
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
| | | +|
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
| | | +|
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
| | | +|
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
| | | +|
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:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

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

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
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:
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
| | | +|
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.

| | | +|
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:
flux balance analysis

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
flux balance analysis

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
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.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +|
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/test_suite/test_test_suite_compatibility_biosimulators.py b/test_suite/test_test_suite_compatibility_biosimulators.py index 6bbfd5da..506a2461 100644 --- a/test_suite/test_test_suite_compatibility_biosimulators.py +++ b/test_suite/test_test_suite_compatibility_biosimulators.py @@ -54,7 +54,7 @@ def parse_arguments(): ) parser.add_argument( - "--suite-path", + "--suite_path", action="store", type=str, default=".", @@ -158,7 +158,9 @@ def process_cases(args): if __name__ == "__main__": - args = parse_arguments() - + args = parse_arguments() + args.cases = ['01186'] + args.sbml_level_version = 'l3v2' + user_folder = os.path.expanduser("~") + args.suite_path = os.path.join(user_folder, "Documents", "compbiolibs", "SBML_test_suite", "semantic") process_cases(args) - diff --git a/utils/__init__.py b/utils/__init__.py index 1b7e4eaf..89f06b00 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -264,10 +264,44 @@ def add_xmlns_sbml_attribute(sedml_filepath, sbml_filepath, output_filepath=None with open(output_filepath,"w") as fout: fout.write(sedstr) +def add_xmlns_fbc_attribute(sedml_filepath, sbml_filepath, output_filepath=None): + ''' + add an xmlns:sbml attribute to the sedml file that matches the sbml file + raise an error if the attribute is already present + output fixed file to output_filepath which defaults to sedml_filepath + ''' + sedstr = "" + if output_filepath: + if os.path.exists(output_filepath): + with open(output_filepath, 'r') as file: + sedstr = file.read() + if sedstr == "": + with open(sedml_filepath, 'r') as file: + sedstr = file.read() + + m = re.search(r']*>', sedstr) + location = m.span()[1]-1 + + if m == None: + raise ValueError(f'Invalid SedML file: main tag not found in {sedml_filepath}') + + with open(sbml_filepath, 'r') as file: + sbml_str = file.read() + + fbc_xmlns = re.search(r'xmlns:fbc="([^"]*)"', sbml_str).group(1) + missing_fbc_attribute = 'xmlns:fbc="' + fbc_xmlns + '"' + sedstr = sedstr[:location] + ' ' + missing_fbc_attribute + sedstr[location:] + + if output_filepath == None: + output_filepath = sedml_filepath + + with open(output_filepath,"w") as fout: + fout.write(sedstr) + def xmlns_sbml_attribute_missing(sedml_filepath): ''' - report True if the xmlns:sbml attribute is missing from the main sedml tag + True if the xmlns:sbml attribute is missing from the main sedml tag ''' with open(sedml_filepath, 'r') as file: @@ -282,6 +316,26 @@ def xmlns_sbml_attribute_missing(sedml_filepath): return True else: return False + + +def xmlns_fbc_attribute_missing(sbml_filepath,sedml_filepath): + ''' + True if the xmlns:fbc attribute is missing from the main sedml tag of the SED-ML file but present in the SBML file + ''' + with open(sbml_filepath, 'r') as file: + sbmlstr = file.read() + + with open(sedml_filepath, 'r') as file: + sedstr = file.read() + + sbmlstr_fbc = re.search(r'xmlns:fbc="([^"]*)"', sbmlstr) + sedstr_fbc = re.search(r'xmlns:fbc="([^"]*)"', sedstr) + + if sbmlstr_fbc and not sedstr_fbc: + return True + else: + return False + def get_temp_file(): ''' @@ -308,14 +362,14 @@ def create_omex(sedml_filepath, sbml_filepath, omex_filepath=None, silent_overwr if os.path.exists(omex_filepath) and silent_overwrite: os.remove(omex_filepath) - tmp_sedml_filepath = None + tmp_sedml_filepath = get_temp_file() if add_missing_xmlns: if xmlns_sbml_attribute_missing(sedml_filepath): - #create a temporary sedml file with the missing attribute added - tmp_sedml_filepath = get_temp_file() add_xmlns_sbml_attribute(sedml_filepath, sbml_filepath, tmp_sedml_filepath) - sedml_filepath = tmp_sedml_filepath - + if xmlns_fbc_attribute_missing(sbml_filepath,sedml_filepath): + add_xmlns_fbc_attribute(sedml_filepath, sbml_filepath, tmp_sedml_filepath) + + sedml_filepath = tmp_sedml_filepath sbml_file_entry_format = get_entry_format(sbml_filepath, 'SBML') sedml_file_entry_format = get_entry_format(sedml_filepath, 'SEDML') From 10bbcbb58899b5fc1f3d37d1b70ee18f81b34b35 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Wed, 20 Nov 2024 11:43:16 +0000 Subject: [PATCH 2/5] add results json files --- .../test_01186/tests/results_local.json | 947 +++++++++++++++++- .../test_01186/tests/results_remote.json | 913 ++++++++++++++--- 2 files changed, 1693 insertions(+), 167 deletions(-) diff --git a/test_suite/test_01186/tests/results_local.json b/test_suite/test_01186/tests/results_local.json index 03738436..a898fe5b 100644 --- a/test_suite/test_01186/tests/results_local.json +++ b/test_suite/test_01186/tests/results_local.json @@ -1,107 +1,970 @@ { "amici": { - "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, + "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": 0.659804, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.192798, + "exception": { + "message": "The SED document did not execute successfully:\n\n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "SedmlExecutionError" + }, + "location": "tmp631899", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp631899:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp631899 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.055983, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.03982, + "exception": { + "message": "SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, "detailed_error_log": {} }, "brian2": { - "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, + "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": 0.054658, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, "detailed_error_log": {} }, "bionetgen": { - "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, + "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": 0.574268, + "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 `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 `./tmp262577` 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": [ + { + "duration": 0.205364, + "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": "tmp262577", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp262577:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp262577 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.065725, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.026619, + "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": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, + "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": 0.559574, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "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 `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 `./tmp405090` 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": [ + { + "duration": 0.224628, + "exception": { + "message": "The SED document did not execute successfully:\n\n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "SedmlExecutionError" + }, + "location": "tmp405090", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp405090:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp405090 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.069903, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.038456, + "exception": { + "message": "SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, "detailed_error_log": {} }, "cbmpy": { - "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, + "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": 0.965321, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n 'MLStripper' object has no attribute 'unescape'", + "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 `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 `./tmp264896` 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": [ + { + "duration": 0.246046, + "exception": { + "message": "The SED document did not execute successfully:\n\n 'MLStripper' object has no attribute 'unescape'", + "type": "SedmlExecutionError" + }, + "location": "tmp264896", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp264896:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp264896 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ...FBC version: 1\r\nM.getNumReactions: 26\r\nM.getNumSpecies: 23\r\nFBC.getNumObjectives: 1\r\nFBC.getNumGeneAssociations: 0\r\nFBC.getNumFluxBounds: 52\r\n \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.084688, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.055077, + "exception": { + "message": "'MLStripper' object has no attribute 'unescape'", + "type": "AttributeError" + }, + "id": "task_1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `R26` has warnings.\r\n - XPath could not be validated.\r\n- Variable `OBJF` has warnings.\r\n - XPath could not be validated.\r\n- Variable `R01` 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": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, "detailed_error_log": {} }, "cobrapy": { - "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, + "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": 0.52649, + "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 `cobra.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/opencobra/cobrapy/issues .", + "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 `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 `./tmp465918` 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": [ + { + "duration": 0.225745, + "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 `cobra.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/opencobra/cobrapy/issues .", + "type": "SedmlExecutionError" + }, + "location": "tmp465918", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp465918:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp465918 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.05256, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.080766, + "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 `cobra.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/opencobra/cobrapy/issues .", + "type": "CobraSBMLError" + }, + "id": "task_1", + "output": "Loading SBML model without fbc:strict=\"true\"\r\nLoading SBML with fbc-v1 (models should be encoded using fbc-v2)\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, "detailed_error_log": {} }, "copasi": { - "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, + "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": 0.58955, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n :No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy", + "type": "CombineArchiveExecutionError" + }, + "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 `./tmp87281` 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": [ + { + "duration": 0.35763, + "exception": { + "message": "The SED document did not execute successfully:\n\n :No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy", + "type": "SedmlExecutionError" + }, + "location": "tmp87281", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp87281:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp87281 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed - No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.070381, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.19495, + "exception": { + "message": "No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy", + "type": "ValueError" + }, + "id": "task_1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `R26` has warnings.\r\n - XPath could not be validated.\r\n- Variable `R01` has warnings.\r\n - XPath could not be validated.\r\n- Variable `OBJF` 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/tmp0u0m0y4_/./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", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, "detailed_error_log": {} }, "gillespy2": { - "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, + "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": 0.548584, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "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 `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 `./tmp88676` 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": [ + { + "duration": 0.187783, + "exception": { + "message": "The SED document did not execute successfully:\n\n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "SedmlExecutionError" + }, + "location": "tmp88676", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp88676:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp88676 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.059132, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.032324, + "exception": { + "message": "SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, "detailed_error_log": {} }, "ginsim": { - "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, + "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": 0.556551, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Namespaces must include 1 SBML qual namespace.", + "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 `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 `./tmp583816` 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": [ + { + "duration": 0.172701, + "exception": { + "message": "The SED document did not execute successfully:\n\n Namespaces must include 1 SBML qual namespace.", + "type": "SedmlExecutionError" + }, + "location": "tmp583816", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp583816:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp583816 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.054527, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.032438, + "exception": { + "message": "Namespaces must include 1 SBML qual namespace.", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, "detailed_error_log": {} }, "libsbmlsim": { - "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, + "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": 0.501222, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "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 `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 `./tmp81617` 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": [ + { + "duration": 0.200552, + "exception": { + "message": "The SED document did not execute successfully:\n\n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "SedmlExecutionError" + }, + "location": "tmp81617", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp81617:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp81617 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.061438, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.030288, + "exception": { + "message": "SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, "detailed_error_log": {} }, "masspy": { - "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, + "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": 0.414209, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "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 `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 `./tmp798152` 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": [ + { + "duration": 0.195616, + "exception": { + "message": "The SED document did not execute successfully:\n\n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "SedmlExecutionError" + }, + "location": "tmp798152", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp798152:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp798152 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.068827, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.030965, + "exception": { + "message": "SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, "detailed_error_log": {} }, "netpyne": { - "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, + "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": 0.048166, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, "detailed_error_log": {} }, "neuron": { - "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, + "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": 0.038829, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, "detailed_error_log": {} }, "opencor": { - "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, + "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": 0.029302, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, "detailed_error_log": {} }, "pyneuroml": { - "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, + "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": 0.049181, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, "detailed_error_log": {} }, "pysces": { - "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, + "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": 0.689016, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n :SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "CombineArchiveExecutionError" + }, + "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 `./tmp562922` 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": [ + { + "duration": 0.238056, + "exception": { + "message": "The SED document did not execute successfully:\n\n :SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "SedmlExecutionError" + }, + "location": "tmp562922", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp562922:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp562922 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed - SteadyStateSimulation `simulation_1` is not supported.\r\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\r\n - UniformTimeCourseSimulation\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.077572, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.038227, + "exception": { + "message": "SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, "detailed_error_log": {} }, "rbapy": { - "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, + "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": 0.478318, + "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 `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 `./tmp45257` 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": [ + { + "duration": 0.186136, + "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(\\.|$)` such as `urn:sedml:language:rba`).", + "type": "SedmlExecutionError" + }, + "location": "tmp45257", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp45257:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp45257 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.063429, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.028138, + "exception": { + "message": "Language for model `model_1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.|$)` 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": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", + "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": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, + "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": 0.754038, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n :Algorithm substitution for \"flux balance analysis\" (http://www.biomodels.net/kisao/KISAO#KISAO_0000437) for policy SIMILAR_VARIABLES is not supported.", + "type": "CombineArchiveExecutionError" + }, + "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 `./tmp688493` 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": [ + { + "duration": 0.370785, + "exception": { + "message": "The SED document did not execute successfully:\n\n :Algorithm substitution for \"flux balance analysis\" (http://www.biomodels.net/kisao/KISAO#KISAO_0000437) for policy SIMILAR_VARIABLES is not supported.", + "type": "SedmlExecutionError" + }, + "location": "tmp688493", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp688493:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp688493 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed - Algorithm substitution for \"flux balance analysis\" (http://www.biomodels.net/kisao/KISAO#KISAO_0000437) for policy SIMILAR_VARIABLES is not supported.\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.066773, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.191627, + "exception": { + "message": "Algorithm substitution for \"flux balance analysis\" (http://www.biomodels.net/kisao/KISAO#KISAO_0000437) for policy SIMILAR_VARIABLES is not supported.", + "type": "NotImplementedError" + }, + "id": "task_1", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33m- Variable `R26` has warnings.\r\n - XPath could not be validated.\r\n- Variable `OBJF` has warnings.\r\n - XPath could not be validated.\r\n- Variable `R01` 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/tmpqnraj412/./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", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, "detailed_error_log": {} }, "vcell": { - "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, - "detailed_error_log": {} + "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 tmp849351. Done", + "sedDocuments": [], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": { + "status": "FAIL", + "error_message": "Runtime Exception" + } }, "xpp": { - "exception_message": "Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')", - "log_yml": {}, + "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": 0.041713, + "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 index d4dd2246..cfabd145 100644 --- a/test_suite/test_01186/tests/results_remote.json +++ b/test_suite/test_01186/tests/results_remote.json @@ -1,28 +1,79 @@ { "amici": { "response": 201, - "view": "https://api.biosimulations.org/runs/6731e621b678b3883bb6a222", - "download": "https://api.biosimulations.org/results/6731e621b678b3883bb6a222/download", - "logs": "https://api.biosimulations.org/logs/6731e621b678b3883bb6a222?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc8350d09353e8f126c44", + "download": "https://api.biosimulations.org/results/673dc8350d09353e8f126c44/download", + "logs": "https://api.biosimulations.org/logs/673dc8350d09353e8f126c44?includeOutput=true", "log_yml": { - "duration": 0.333322, + "duration": 0.543222, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp962614` 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" + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "CombineArchiveExecutionError" }, "output": "", - "sedDocuments": [], + "sedDocuments": [ + { + "duration": 0.199583, + "exception": { + "message": "The SED document did not execute successfully:\n\n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "SedmlExecutionError" + }, + "location": "tmp17830", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp17830:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp17830 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.066567, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.032465, + "exception": { + "message": "SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], "skipReason": null, "status": "FAILED" } }, "brian2": { "response": 201, - "view": "https://api.biosimulations.org/runs/6731e6220d09353e8f104bcc", - "download": "https://api.biosimulations.org/results/6731e6220d09353e8f104bcc/download", - "logs": "https://api.biosimulations.org/logs/6731e6220d09353e8f104bcc?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc8365a60072d20f7672f", + "download": "https://api.biosimulations.org/results/673dc8365a60072d20f7672f/download", + "logs": "https://api.biosimulations.org/logs/673dc8365a60072d20f7672f?includeOutput=true", "log_yml": { - "duration": 0.062603, + "duration": 0.06842, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" @@ -35,164 +86,623 @@ }, "bionetgen": { "response": 201, - "view": "https://api.biosimulations.org/runs/6731e624b678b3883bb6a226", - "download": "https://api.biosimulations.org/results/6731e624b678b3883bb6a226/download", - "logs": "https://api.biosimulations.org/logs/6731e624b678b3883bb6a226?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc839b678b3883bb8c67a", + "download": "https://api.biosimulations.org/results/673dc839b678b3883bb8c67a/download", + "logs": "https://api.biosimulations.org/logs/673dc839b678b3883bb8c67a?includeOutput=true", "log_yml": { - "duration": 0.206333, + "duration": 0.402851, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp55567` 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" + "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(\\.|$)` such as `urn:sedml:language:bngl`).", + "type": "CombineArchiveExecutionError" }, "output": "", - "sedDocuments": [], + "sedDocuments": [ + { + "duration": 0.167628, + "exception": { + "message": "The SED document did not execute successfully:\n\n Language for model `model_1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.|$)` such as `urn:sedml:language:bngl`).", + "type": "SedmlExecutionError" + }, + "location": "tmp696792", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp696792:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp696792 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.059996, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.025898, + "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" } }, "boolnet": { "response": 201, - "view": "https://api.biosimulations.org/runs/6731e6260d09353e8f104bd1", - "download": "https://api.biosimulations.org/results/6731e6260d09353e8f104bd1/download", - "logs": "https://api.biosimulations.org/logs/6731e6260d09353e8f104bd1?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc83b5a60072d20f76733", + "download": "https://api.biosimulations.org/results/673dc83b5a60072d20f76733/download", + "logs": "https://api.biosimulations.org/logs/673dc83b5a60072d20f76733?includeOutput=true", "log_yml": { - "duration": 0.201617, + "duration": 0.436977, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp446179` 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" + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "CombineArchiveExecutionError" }, "output": "", - "sedDocuments": [], + "sedDocuments": [ + { + "duration": 0.188662, + "exception": { + "message": "The SED document did not execute successfully:\n\n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "SedmlExecutionError" + }, + "location": "tmp920900", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp920900:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp920900 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.06465, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.033207, + "exception": { + "message": "SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], "skipReason": null, "status": "FAILED" } }, "cbmpy": { "response": 201, - "view": "https://api.biosimulations.org/runs/6731e6280d09353e8f104bd4", - "download": "https://api.biosimulations.org/results/6731e6280d09353e8f104bd4/download", - "logs": "https://api.biosimulations.org/logs/6731e6280d09353e8f104bd4?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc83c0d09353e8f126c49", + "download": "https://api.biosimulations.org/results/673dc83c0d09353e8f126c49/download", + "logs": "https://api.biosimulations.org/logs/673dc83c0d09353e8f126c49?includeOutput=true", "log_yml": { - "duration": 0.336249, + "duration": 0.488282, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp721457` 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" + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n 'MLStripper' object has no attribute 'unescape'", + "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", - "sedDocuments": [], + "sedDocuments": [ + { + "duration": 0.185775, + "exception": { + "message": "The SED document did not execute successfully:\n\n 'MLStripper' object has no attribute 'unescape'", + "type": "SedmlExecutionError" + }, + "location": "tmp574833", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp574833:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp574833 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ...FBC version: 1\r\nM.getNumReactions: 26\r\nM.getNumSpecies: 23\r\nFBC.getNumObjectives: 1\r\nFBC.getNumGeneAssociations: 0\r\nFBC.getNumFluxBounds: 52\r\n \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.058784, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.049141, + "exception": { + "message": "'MLStripper' object has no attribute 'unescape'", + "type": "AttributeError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], "skipReason": null, "status": "FAILED" } }, "cobrapy": { "response": 201, - "view": "https://api.biosimulations.org/runs/6731e629b678b3883bb6a229", - "download": "https://api.biosimulations.org/results/6731e629b678b3883bb6a229/download", - "logs": "https://api.biosimulations.org/logs/6731e629b678b3883bb6a229?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc83eb678b3883bb8c67f", + "download": "https://api.biosimulations.org/results/673dc83eb678b3883bb8c67f/download", + "logs": "https://api.biosimulations.org/logs/673dc83eb678b3883bb8c67f?includeOutput=true", "log_yml": { - "duration": 0.200704, + "duration": 0.951314, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp482300` 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" + "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 `cobra.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/opencobra/cobrapy/issues .", + "type": "CombineArchiveExecutionError" }, "output": "", - "sedDocuments": [], + "sedDocuments": [ + { + "duration": 0.728184, + "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 `cobra.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/opencobra/cobrapy/issues .", + "type": "SedmlExecutionError" + }, + "location": "tmp263562", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp263562:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp263562 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.060467, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.578372, + "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 `cobra.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/opencobra/cobrapy/issues .", + "type": "CobraSBMLError" + }, + "id": "task_1", + "output": "Loading SBML model without fbc:strict=\"true\"\r\nLoading SBML with fbc-v1 (models should be encoded using fbc-v2)\r\nSet parameter GURO_PAR_SPECIAL\r\nSet parameter TokenServer to value \"gurobi.cam.uchc.edu\"\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], "skipReason": null, "status": "FAILED" } }, "copasi": { "response": 201, - "view": "https://api.biosimulations.org/runs/6731e62cb678b3883bb6a22c", - "download": "https://api.biosimulations.org/results/6731e62cb678b3883bb6a22c/download", - "logs": "https://api.biosimulations.org/logs/6731e62cb678b3883bb6a22c?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc8410d09353e8f126c4d", + "download": "https://api.biosimulations.org/results/673dc8410d09353e8f126c4d/download", + "logs": "https://api.biosimulations.org/logs/673dc8410d09353e8f126c4d?includeOutput=true", "log_yml": { - "duration": 0.227353, + "duration": 0.567279, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp932942` 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" + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n :No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy", + "type": "CombineArchiveExecutionError" }, "output": "", - "sedDocuments": [], + "sedDocuments": [ + { + "duration": 0.324772, + "exception": { + "message": "The SED document did not execute successfully:\n\n :No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy", + "type": "SedmlExecutionError" + }, + "location": "tmp486117", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp486117:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp486117 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed - No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.061501, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.166781, + "exception": { + "message": "No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], "skipReason": null, "status": "FAILED" } }, "gillespy2": { "response": 201, - "view": "https://api.biosimulations.org/runs/6731e62db678b3883bb6a230", - "download": "https://api.biosimulations.org/results/6731e62db678b3883bb6a230/download", - "logs": "https://api.biosimulations.org/logs/6731e62db678b3883bb6a230?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc8435a60072d20f7673e", + "download": "https://api.biosimulations.org/results/673dc8435a60072d20f7673e/download", + "logs": "https://api.biosimulations.org/logs/673dc8435a60072d20f7673e?includeOutput=true", "log_yml": { - "duration": 0.208064, + "duration": 0.415317, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp452671` 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" + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "CombineArchiveExecutionError" }, "output": "", - "sedDocuments": [], + "sedDocuments": [ + { + "duration": 0.179577, + "exception": { + "message": "The SED document did not execute successfully:\n\n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "SedmlExecutionError" + }, + "location": "tmp795377", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp795377:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp795377 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.071484, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.029101, + "exception": { + "message": "SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], "skipReason": null, "status": "FAILED" } }, "ginsim": { "response": 201, - "view": "https://api.biosimulations.org/runs/6731e62f0d09353e8f104bd8", - "download": "https://api.biosimulations.org/results/6731e62f0d09353e8f104bd8/download", - "logs": "https://api.biosimulations.org/logs/6731e62f0d09353e8f104bd8?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc845b678b3883bb8c689", + "download": "https://api.biosimulations.org/results/673dc845b678b3883bb8c689/download", + "logs": "https://api.biosimulations.org/logs/673dc845b678b3883bb8c689?includeOutput=true", "log_yml": { - "duration": 0.192267, + "duration": 0.390368, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp292854` 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" + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Namespaces must include 1 SBML qual namespace.", + "type": "CombineArchiveExecutionError" }, "output": "", - "sedDocuments": [], + "sedDocuments": [ + { + "duration": 0.168172, + "exception": { + "message": "The SED document did not execute successfully:\n\n Namespaces must include 1 SBML qual namespace.", + "type": "SedmlExecutionError" + }, + "location": "tmp986701", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp986701:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp986701 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.057413, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.031401, + "exception": { + "message": "Namespaces must include 1 SBML qual namespace.", + "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/6731e6310d09353e8f104bdc", - "download": "https://api.biosimulations.org/results/6731e6310d09353e8f104bdc/download", - "logs": "https://api.biosimulations.org/logs/6731e6310d09353e8f104bdc?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc847b678b3883bb8c68f", + "download": "https://api.biosimulations.org/results/673dc847b678b3883bb8c68f/download", + "logs": "https://api.biosimulations.org/logs/673dc847b678b3883bb8c68f?includeOutput=true", "log_yml": { - "duration": 0.230186, + "duration": 0.380725, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp293403` 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" + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "CombineArchiveExecutionError" }, "output": "", - "sedDocuments": [], + "sedDocuments": [ + { + "duration": 0.161978, + "exception": { + "message": "The SED document did not execute successfully:\n\n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "SedmlExecutionError" + }, + "location": "tmp801520", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp801520:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp801520 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.059081, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.028432, + "exception": { + "message": "SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], "skipReason": null, "status": "FAILED" } }, "masspy": { "response": 201, - "view": "https://api.biosimulations.org/runs/6731e6335a60072d20f54d9b", - "download": "https://api.biosimulations.org/results/6731e6335a60072d20f54d9b/download", - "logs": "https://api.biosimulations.org/logs/6731e6335a60072d20f54d9b?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc8495a60072d20f76752", + "download": "https://api.biosimulations.org/results/673dc8495a60072d20f76752/download", + "logs": "https://api.biosimulations.org/logs/673dc8495a60072d20f76752?includeOutput=true", "log_yml": { - "duration": 0.419118, + "duration": 0.558002, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp256213` 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" + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "CombineArchiveExecutionError" }, "output": "", - "sedDocuments": [], + "sedDocuments": [ + { + "duration": 0.162937, + "exception": { + "message": "The SED document did not execute successfully:\n\n SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "SedmlExecutionError" + }, + "location": "tmp252491", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp252491:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp252491 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.055486, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.029615, + "exception": { + "message": "SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], "skipReason": null, "status": "FAILED" } }, "netpyne": { "response": 201, - "view": "https://api.biosimulations.org/runs/6731e6355a60072d20f54d9e", - "download": "https://api.biosimulations.org/results/6731e6355a60072d20f54d9e/download", - "logs": "https://api.biosimulations.org/logs/6731e6355a60072d20f54d9e?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc84b0d09353e8f126c81", + "download": "https://api.biosimulations.org/results/673dc84b0d09353e8f126c81/download", + "logs": "https://api.biosimulations.org/logs/673dc84b0d09353e8f126c81?includeOutput=true", "log_yml": { - "duration": 0.046382, + "duration": 0.043798, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" @@ -205,11 +715,11 @@ }, "neuron": { "response": 201, - "view": "https://api.biosimulations.org/runs/6731e6360d09353e8f104be0", - "download": "https://api.biosimulations.org/results/6731e6360d09353e8f104be0/download", - "logs": "https://api.biosimulations.org/logs/6731e6360d09353e8f104be0?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc84c0d09353e8f126c89", + "download": "https://api.biosimulations.org/results/673dc84c0d09353e8f126c89/download", + "logs": "https://api.biosimulations.org/logs/673dc84c0d09353e8f126c89?includeOutput=true", "log_yml": { - "duration": 0.042687, + "duration": 0.041593, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" @@ -222,11 +732,11 @@ }, "opencor": { "response": 201, - "view": "https://api.biosimulations.org/runs/6731e638b678b3883bb6a235", - "download": "https://api.biosimulations.org/results/6731e638b678b3883bb6a235/download", - "logs": "https://api.biosimulations.org/logs/6731e638b678b3883bb6a235?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc84f5a60072d20f76773", + "download": "https://api.biosimulations.org/results/673dc84f5a60072d20f76773/download", + "logs": "https://api.biosimulations.org/logs/673dc84f5a60072d20f76773?includeOutput=true", "log_yml": { - "duration": 0.023124, + "duration": 0.040749, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" @@ -239,11 +749,11 @@ }, "pyneuroml": { "response": 201, - "view": "https://api.biosimulations.org/runs/6731e63a5a60072d20f54dac", - "download": "https://api.biosimulations.org/results/6731e63a5a60072d20f54dac/download", - "logs": "https://api.biosimulations.org/logs/6731e63a5a60072d20f54dac?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc8525a60072d20f76783", + "download": "https://api.biosimulations.org/results/673dc8525a60072d20f76783/download", + "logs": "https://api.biosimulations.org/logs/673dc8525a60072d20f76783?includeOutput=true", "log_yml": { - "duration": 0.043338, + "duration": 0.043263, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" @@ -256,45 +766,147 @@ }, "pysces": { "response": 201, - "view": "https://api.biosimulations.org/runs/6731e63b0d09353e8f104bf1", - "download": "https://api.biosimulations.org/results/6731e63b0d09353e8f104bf1/download", - "logs": "https://api.biosimulations.org/logs/6731e63b0d09353e8f104bf1?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc8550d09353e8f126cb3", + "download": "https://api.biosimulations.org/results/673dc8550d09353e8f126cb3/download", + "logs": "https://api.biosimulations.org/logs/673dc8550d09353e8f126cb3?includeOutput=true", "log_yml": { - "duration": 0.228634, + "duration": 0.442877, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp921920` 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" + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n :SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "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": [], + "sedDocuments": [ + { + "duration": 0.188215, + "exception": { + "message": "The SED document did not execute successfully:\n\n :SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "SedmlExecutionError" + }, + "location": "tmp874863", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp874863:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp874863 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed - SteadyStateSimulation `simulation_1` is not supported.\r\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\r\n - UniformTimeCourseSimulation\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.062675, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.030768, + "exception": { + "message": "SteadyStateSimulation `simulation_1` is not supported.\n - Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:\n - UniformTimeCourseSimulation", + "type": "ValueError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], "skipReason": null, "status": "FAILED" } }, "rbapy": { "response": 201, - "view": "https://api.biosimulations.org/runs/6731e63db678b3883bb6a255", - "download": "https://api.biosimulations.org/results/6731e63db678b3883bb6a255/download", - "logs": "https://api.biosimulations.org/logs/6731e63db678b3883bb6a255?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc857b678b3883bb8c6db", + "download": "https://api.biosimulations.org/results/673dc857b678b3883bb8c6db/download", + "logs": "https://api.biosimulations.org/logs/673dc857b678b3883bb8c6db?includeOutput=true", "log_yml": { - "duration": 0.194734, + "duration": 0.386135, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp24088` 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" + "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": [], + "sedDocuments": [ + { + "duration": 0.1606, + "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(\\.|$)` such as `urn:sedml:language:rba`).", + "type": "SedmlExecutionError" + }, + "location": "tmp320623", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp320623:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp320623 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.060538, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.025938, + "exception": { + "message": "Language for model `model_1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.|$)` 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/6731e63f5a60072d20f54dc2", - "download": "https://api.biosimulations.org/results/6731e63f5a60072d20f54dc2/download", - "logs": "https://api.biosimulations.org/logs/6731e63f5a60072d20f54dc2?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc8595a60072d20f767a5", + "download": "https://api.biosimulations.org/results/673dc8595a60072d20f767a5/download", + "logs": "https://api.biosimulations.org/logs/673dc8595a60072d20f767a5?includeOutput=true", "log_yml": { - "duration": 0.067342, + "duration": 0.040984, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" @@ -307,42 +919,93 @@ }, "tellurium": { "response": 201, - "view": "https://api.biosimulations.org/runs/6731e6415a60072d20f54dca", - "download": "https://api.biosimulations.org/results/6731e6415a60072d20f54dca/download", - "logs": "https://api.biosimulations.org/logs/6731e6415a60072d20f54dca?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc85ab678b3883bb8c6e9", + "download": "https://api.biosimulations.org/results/673dc85ab678b3883bb8c6e9/download", + "logs": "https://api.biosimulations.org/logs/673dc85ab678b3883bb8c6e9?includeOutput=true", "log_yml": { - "duration": 0.351666, + "duration": 0.892316, "exception": { - "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./tmp603270` 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" + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Algorithm substitution for \"flux balance analysis\" (http://www.biomodels.net/kisao/KISAO#KISAO_0000437) for policy SIMILAR_VARIABLES is not supported.", + "type": "CombineArchiveExecutionError" }, "output": "", - "sedDocuments": [], + "sedDocuments": [ + { + "duration": 0.45075, + "exception": { + "message": "The SED document did not execute successfully:\n\n Algorithm substitution for \"flux balance analysis\" (http://www.biomodels.net/kisao/KISAO#KISAO_0000437) for policy SIMILAR_VARIABLES is not supported.", + "type": "SedmlExecutionError" + }, + "location": "tmp114665", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n tmp114665:\r\n Tasks (1):\r\n task_1\r\n Reports (1):\r\n report_1: 3 data sets\r\n\r\nExecuting SED-ML file 1: tmp114665 ...\r\n Found 1 tasks and 1 outputs:\r\n Tasks:\r\n `task_1`\r\n Outputs:\r\n `report_1`\r\n Executing task 1: `task_1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 1 outputs ...\r\n Generating output 1: `report_1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "ds_R01_1", + "status": "SKIPPED" + }, + { + "id": "ds_R26_1", + "status": "SKIPPED" + }, + { + "id": "ds_OBJF_1", + "status": "SKIPPED" + } + ], + "duration": 0.068001, + "exception": null, + "id": "report_1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.301553, + "exception": { + "message": "Algorithm substitution for \"flux balance analysis\" (http://www.biomodels.net/kisao/KISAO#KISAO_0000437) for policy SIMILAR_VARIABLES is not supported.", + "type": "NotImplementedError" + }, + "id": "task_1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], "skipReason": null, "status": "FAILED" } }, "vcell": { "response": 201, - "view": "https://api.biosimulations.org/runs/6731e6455a60072d20f54dcf", - "download": "https://api.biosimulations.org/results/6731e6455a60072d20f54dcf/download", - "logs": "https://api.biosimulations.org/logs/6731e6455a60072d20f54dcf?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc85e5a60072d20f767b9", + "download": "https://api.biosimulations.org/results/673dc85e5a60072d20f767b9/download", + "logs": "https://api.biosimulations.org/logs/673dc85e5a60072d20f767b9?includeOutput=true", "log_yml": { - "duration": null, + "duration": 2, "exception": null, - "output": null, + "output": "Processing tmp815103. Done", "sedDocuments": [], "skipReason": null, - "status": "QUEUED" + "status": "SUCCEEDED" } }, "xpp": { "response": 201, - "view": "https://api.biosimulations.org/runs/6731e6460d09353e8f104c22", - "download": "https://api.biosimulations.org/results/6731e6460d09353e8f104c22/download", - "logs": "https://api.biosimulations.org/logs/6731e6460d09353e8f104c22?includeOutput=true", + "view": "https://api.biosimulations.org/runs/673dc8610d09353e8f126ceb", + "download": "https://api.biosimulations.org/results/673dc8610d09353e8f126ceb/download", + "logs": "https://api.biosimulations.org/logs/673dc8610d09353e8f126ceb?includeOutput=true", "log_yml": { - "duration": 0.063226, + "duration": 0.053811, "exception": { "message": "No module named 'libsbml'", "type": "ModuleNotFoundError" From e7263458fe75abd18f834e81c9526ca8d92894c5 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Wed, 20 Nov 2024 13:23:32 +0000 Subject: [PATCH 3/5] remove temp omex files and add 0001 to test suite cases --- test_suite/test_test_suite_compatibility_biosimulators.py | 2 +- utils/__init__.py | 6 +++++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/test_suite/test_test_suite_compatibility_biosimulators.py b/test_suite/test_test_suite_compatibility_biosimulators.py index 506a2461..d2a83f3b 100644 --- a/test_suite/test_test_suite_compatibility_biosimulators.py +++ b/test_suite/test_test_suite_compatibility_biosimulators.py @@ -159,7 +159,7 @@ def process_cases(args): if __name__ == "__main__": args = parse_arguments() - args.cases = ['01186'] + args.cases = ['00001','01186'] args.sbml_level_version = 'l3v2' user_folder = os.path.expanduser("~") args.suite_path = os.path.join(user_folder, "Documents", "compbiolibs", "SBML_test_suite", "semantic") diff --git a/utils/__init__.py b/utils/__init__.py index 89f06b00..2eb9fd43 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -608,7 +608,9 @@ def run_biosimulators_remote(engine,sedml_filepath,sbml_filepath): results_urls = biosimulations.submit_simulation_archive(\ archive_file=omex_file_name,\ sim_dict=sim_dict) - + + os.remove(omex_filepath) + return results_urls def get_remote_results(engine, download_link, output_dir='remote_results'): @@ -669,6 +671,8 @@ def run_biosimulators_docker(engine,sedml_filepath,sbml_filepath,output_dir='out if 'RuntimeException' in detailed_error_log: detailed_error_log_dict['status'] = 'FAIL' detailed_error_log_dict['error_message'] = "Runtime Exception" + + os.remove(omex_filepath) return {"exception_message":exception_message,"log_yml":log_yml_dict, "detailed_error_log":detailed_error_log_dict} From 27c085758677530b0d3c1e2ddef4e6be5f771e40 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Thu, 21 Nov 2024 15:49:32 +0000 Subject: [PATCH 4/5] improve compatibility messages and update tables --- .../results_compatibility_biosimulators.md | 46 +++++++++---------- .../results_compatibility_biosimulators.md | 46 +++++++++---------- .../results_compatibility_biosimulators.md | 46 +++++++++---------- ..._test_suite_compatibility_biosimulators.py | 1 + utils/__init__.py | 38 ++++++++++----- 5 files changed, 97 insertions(+), 80 deletions(-) diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md index e41ce7f0..96c6c81b 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) | -|:-------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------| -|
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 | -|
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 | -|
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 | -|
Brian 2https://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
| | | -|
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 | -|
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 | -|
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 | -|
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 | -|
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 | -|
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 | -|
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 | -|
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
| | | -|
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
| | | -|
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
| | | -|
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
| | | -|
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 | -|
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 | -|
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.

| | | -|
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 | -|
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

| | | -|
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 +| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------| +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML are compatible with AMICI.
|
❌ FAILview
download
logs

ERROR MESSAGE:
Reached maximum number of steps

|
❌ FAILERROR MESSAGE:
Reached maximum number of steps

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

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with BioNetGen.

BNGL and 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 | +|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with BoolNet.

SBML-qual and 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 | +|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with Brian 2.

NeuroML, LEMS and SED-ML are compatible with Brian 2.
|
⚠ 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/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML 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 | +|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML 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 | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML are compatible with COPASI.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML are compatible with GillesPy2.
|
✅ PASSview
download
logs

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

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with GINsim.

SBML-qual and 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 | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML are compatible with LibSBMLSim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML 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 | +|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with NetPyNE.

NeuroML, LEMS and 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 ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with NEURON.

NeuroML, LEMS and 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 ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with OpenCOR.

SED-ML and CellML 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 ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with pyNeuroML.

NeuroML, LEMS and 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/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML 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 | +|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with RBApy.

RBApy and 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 | +|
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 SBML and SED-ML which is not compatible with Smoldyn.

Smoldyn and 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/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML are compatible with Tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
VCellhttps://github.com/virtualcell/vcell
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

BNGL, SED-ML and SBML are compatible with VCell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

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

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with XPP.

SED-ML and XPP 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 755a3c90..9cab69c5 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) | -|:-------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------|:--------------------------------------------------------| -|
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 | -|
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 | -|
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 | -|
Brian 2https://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
| | | -|
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 | -|
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 | -|
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 | -|
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 | -|
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 | -|
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 | -|
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 | -|
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
| | | -|
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
| | | -|
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
| | | -|
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
| | | -|
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 | -|
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 | -|
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.

| | | -|
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 | -|
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

| | | -|
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) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------|:--------------------------------------------------------| +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with AMICI.

SED-ML and SBML are compatible with AMICI.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
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 and SED-ML which is not compatible with BioNetGen.

SED-ML and BNGL 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 | +|
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 and SED-ML which is not compatible with BoolNet.

SBML-qual and 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 | +|
Brian 2https://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 and SED-ML which is not compatible with Brian 2.

SED-ML, LEMS and NeuroML are compatible with Brian 2.
|
⚠ 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/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with CBMPy.

SED-ML and SBML 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 | +|
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 and SED-ML which is compatible with COBRApy.

SED-ML and SBML 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 | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with COPASI.

SED-ML and SBML are compatible with COPASI.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with GillesPy2.

SED-ML and SBML are compatible with GillesPy2.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
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 and SED-ML which is not compatible with GINsim.

SBML-qual and 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 | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with LibSBMLSim.

SED-ML and SBML are compatible with LibSBMLSim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with MASSpy.

SED-ML and SBML 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 | +|
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 and SED-ML which is not compatible with NetPyNE.

SED-ML, LEMS and NeuroML 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 filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with NEURON.

SED-ML, LEMS and NeuroML 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 filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with OpenCOR.

SED-ML and CellML 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 filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with pyNeuroML.

SED-ML, LEMS and NeuroML 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/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with PySCeS.

SED-ML and SBML are compatible with PySCeS.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
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 and SED-ML which is not compatible with RBApy.

SED-ML and RBApy 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 | +|
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 and SED-ML which is not compatible with Smoldyn.

SED-ML and Smoldyn 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/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with Tellurium.

SED-ML and SBML are compatible with Tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
VCellhttps://github.com/virtualcell/vcell
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with VCell.

SED-ML, BNGL and SBML are compatible with VCell.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +|
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 and SED-ML which is not compatible with XPP.

SED-ML and XPP 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 ca8741e2..6c2279b7 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) | -|:-------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------|:---------| -|
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:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

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

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
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:
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
| | | -|
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:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
Brian 2https://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
| | | -|
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:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

'MLStripper' object has no attribute 'unescape'

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

The SED document did not execute successfully:

'MLStripper' object has no attribute 'unescape'

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
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:
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 `cobra.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/opencobra/cobrapy/issues .

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 `cobra.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/opencobra/cobrapy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
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:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'ValueError':No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy

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

The SED document did not execute successfully:

class 'ValueError':No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
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:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

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

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
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:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Namespaces must include 1 SBML qual namespace.

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

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

The SED document did not execute successfully:

Namespaces must include 1 SBML qual namespace.

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
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:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

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

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
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:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

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

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
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
| | | -|
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
| | | -|
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
| | | -|
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
| | | -|
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:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

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

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
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:
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
| | | -|
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.

| | | -|
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:
flux balance analysis

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
flux balance analysis

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
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.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | -|
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 +| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------|:---------| +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with AMICI.

SED-ML and SBML are compatible with AMICI.
|
❌ FAILview
download
logs

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

The SED document did not execute successfully:

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

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
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 and SED-ML which is not compatible with BioNetGen.

SED-ML and BNGL 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
| | | +|
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 and SED-ML which is not compatible with BoolNet.

SBML-qual and 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:

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

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
Brian 2https://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 and SED-ML which is not compatible with Brian 2.

SED-ML, LEMS and NeuroML are compatible with Brian 2.
|
⚠ 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/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with CBMPy.

SED-ML and SBML are compatible with CBMPy.
|
❌ FAILview
download
logs

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

The SED document did not execute successfully:

'MLStripper' object has no attribute 'unescape'

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

The SED document did not execute successfully:

'MLStripper' object has no attribute 'unescape'

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
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 and SED-ML which is compatible with COBRApy.

SED-ML and SBML are compatible with COBRApy.
|
❌ 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 `cobra.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/opencobra/cobrapy/issues .

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 `cobra.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/opencobra/cobrapy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with COPASI.

SED-ML and SBML are compatible with COPASI.
|
❌ FAILview
download
logs

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

The SED document did not execute successfully:

class 'ValueError':No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy

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

The SED document did not execute successfully:

class 'ValueError':No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with GillesPy2.

SED-ML and SBML are compatible with GillesPy2.
|
❌ FAILview
download
logs

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

The SED document did not execute successfully:

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

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
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 and SED-ML which is not compatible with GINsim.

SBML-qual and 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:

Namespaces must include 1 SBML qual namespace.

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

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

The SED document did not execute successfully:

Namespaces must include 1 SBML qual namespace.

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with LibSBMLSim.

SED-ML and SBML are compatible with LibSBMLSim.
|
❌ FAILview
download
logs

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

The SED document did not execute successfully:

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

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with MASSpy.

SED-ML and SBML are compatible with MASSpy.
|
❌ FAILview
download
logs

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

The SED document did not execute successfully:

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

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
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 and SED-ML which is not compatible with NetPyNE.

SED-ML, LEMS and NeuroML 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 filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with NEURON.

SED-ML, LEMS and NeuroML 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 filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with OpenCOR.

SED-ML and CellML 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 filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with pyNeuroML.

SED-ML, LEMS and NeuroML 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/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with PySCeS.

SED-ML and SBML are compatible with PySCeS.
|
❌ FAILview
download
logs

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

The SED document did not execute successfully:

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

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
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 and SED-ML which is not compatible with RBApy.

SED-ML and RBApy 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
| | | +|
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 and SED-ML which is not compatible with Smoldyn.

SED-ML and Smoldyn 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/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with Tellurium.

SED-ML and SBML are compatible with Tellurium.
|
❌ FAILview
download
logs

ERROR MESSAGE:
flux balance analysis

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
flux balance analysis

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
VCellhttps://github.com/virtualcell/vcell
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with VCell.

SED-ML, BNGL and SBML are compatible with VCell.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +|
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 and SED-ML which is not compatible with XPP.

SED-ML and XPP 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_compatibility_biosimulators.py b/test_suite/test_test_suite_compatibility_biosimulators.py index d2a83f3b..189fe00c 100644 --- a/test_suite/test_test_suite_compatibility_biosimulators.py +++ b/test_suite/test_test_suite_compatibility_biosimulators.py @@ -148,6 +148,7 @@ def process_cases(args): print(f"Changed to {new_directory}") engine_list = list(engines.keys()) + # engine_list = engine_list[:5] utils.run_biosimulators_remotely_and_locally(engine_list, os.path.basename(sedml_file_path), diff --git a/utils/__init__.py b/utils/__init__.py index 2eb9fd43..d2c934e3 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -509,23 +509,39 @@ def check_file_compatibility_test(engine, model_filepath, experiment_filepath): ''' file_extensions = get_filetypes(model_filepath, experiment_filepath) engine_filetypes_tuple_list = ENGINES[engine]['formats'] + engine_name = ENGINES[engine]['name'] 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())] + unique_compatible_filetpyes = list(set(compatible_filetypes)) + + unique_compatible_filetpyes_strings = ', '.join(unique_compatible_filetpyes[:-1]) + ' and ' + unique_compatible_filetpyes[-1] if len(unique_compatible_filetpyes) > 1 else unique_compatible_filetpyes[0] + + file_types = [TYPES[i] for i in file_extensions] + filetypes_strings = ', '.join(file_types[:-1]) + ' and ' + file_types[-1] if len(file_types) > 1 else file_types[0] + + if file_extensions == ('sbml', 'sedml') and file_extensions not in engine_filetypes_tuple_list: + return 'FAIL', (f"The file extensions {file_extensions} suggest the input file types are {filetypes_strings} which is not compatible with {engine_name}.

{unique_compatible_filetpyes_strings} are compatible with {engine_name}.") 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}.") + return 'pass', (f"The file extensions {file_extensions} suggest the input file types are {filetypes_strings}.

{unique_compatible_filetpyes_strings} are compatible with {engine_name}.") + 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_tuple = ('sbml', 'sedml') + file_types = [TYPES[i] for i in file_types_tuple] + filetypes_strings = ', '.join(file_types[:-1]) + ' and ' + file_types[-1] if len(file_types) > 1 else file_types[0] + if file_types_tuple in engine_filetypes_tuple_list: + return 'pass', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {filetypes_strings} which is compatible with {engine_name}.

{unique_compatible_filetpyes_strings} are compatible with {engine_name}.") + else: + return 'FAIL', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {filetypes_strings} which is not compatible with {engine_name}.

{unique_compatible_filetpyes_strings} are compatible with {engine_name}.") 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}.") - + return 'unsure', (f"The file extensions {file_extensions} suggest the input file types may not be compatibe with {engine_name}.

{unique_compatible_filetpyes_strings} are compatible with {engine_name}.") + def collapsible_content(content, title='Details'): """ From 0e3e982f0780b4a3ac9031503950eb8438f11b70 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 26 Nov 2024 12:09:01 +0000 Subject: [PATCH 5/5] update results table SBML example --- .../results_compatibility_biosimulators.md | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md index 96c6c81b..22b1eb79 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) | |:-------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------| -|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML are compatible with AMICI.
|
❌ FAILview
download
logs

ERROR MESSAGE:
Reached maximum number of steps

|
❌ FAILERROR MESSAGE:
Reached maximum number of steps

| plot | plot | +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and 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 | |
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with BioNetGen.

BNGL and 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 | -|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with BoolNet.

SBML-qual and 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 | +|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with BoolNet.

SED-ML and SBML-qual 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 | |
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with Brian 2.

NeuroML, LEMS and SED-ML are compatible with Brian 2.
|
⚠ 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/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML 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 | -|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML 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 | -|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML are compatible with COPASI.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML are compatible with GillesPy2.
|
✅ PASSview
download
logs

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

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with GINsim.

SBML-qual and 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 | -|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML are compatible with LibSBMLSim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML 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 | +|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and 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 | +|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and 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 | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with COPASI.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with GillesPy2.
|
✅ PASSview
download
logs

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

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with GINsim.

SED-ML and SBML-qual 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 | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with LibSBMLSim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and 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 | |
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with NetPyNE.

NeuroML, LEMS and 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 ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with NEURON.

NeuroML, LEMS and 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 ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with OpenCOR.

SED-ML and CellML 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
| | | +|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with OpenCOR.

CellML and 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 ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with pyNeuroML.

NeuroML, LEMS and 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/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML 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 | +|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and 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 | |
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with RBApy.

RBApy and 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 | -|
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 SBML and SED-ML which is not compatible with Smoldyn.

Smoldyn and 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/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SED-ML and SBML are compatible with Tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
VCellhttps://github.com/virtualcell/vcell
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

BNGL, SED-ML and SBML are compatible with VCell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +|
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 SBML and SED-ML which is not compatible with Smoldyn.

SED-ML and Smoldyn 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/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with Tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
VCellhttps://github.com/virtualcell/vcell
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

BNGL, SBML and SED-ML are compatible with VCell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | |
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with XPP.

SED-ML and XPP 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