diff --git a/BioModels/BIOMD0000000001/BIOMD0000000001_url.sedml b/BioModels/BIOMD0000000001/BIOMD0000000001_url.sedml new file mode 100644 index 00000000..bb4d00ef --- /dev/null +++ b/BioModels/BIOMD0000000001/BIOMD0000000001_url.sedml @@ -0,0 +1,634 @@ + + + + + + + + + + + + + + + + + auto_time_for_task1_var + + + + + + + + auto_dg_for_task1_BLL__x + + + + + + + + auto_dg_for_task1_IL__x + + + + + + + + auto_dg_for_task1_AL__x + + + + + + + + auto_dg_for_task1_A__x + + + + + + + + auto_dg_for_task1_BL__x + + + + + + + + auto_dg_for_task1_B__x + + + + + + + + auto_dg_for_task1_DLL__x + + + + + + + + auto_dg_for_task1_D__x + + + + + + + + auto_dg_for_task1_ILL__x + + + + + + + + auto_dg_for_task1_DL__x + + + + + + + + auto_dg_for_task1_I__x + + + + + + + + auto_dg_for_task1_ALL__x + + + + + + + + auto_dg_for_task1_kf_0__x + + + + + + + + auto_dg_for_task1_kr_0__x + + + + + + + + auto_dg_for_task1_kf_1__x + + + + + + + + auto_dg_for_task1_kr_1__x + + + + + + + + auto_dg_for_task1_kf_2__x + + + + + + + + auto_dg_for_task1_kr_2__x + + + + + + + + auto_dg_for_task1_kf_3__x + + + + + + + + auto_dg_for_task1_kr_3__x + + + + + + + + auto_dg_for_task1_kf_4__x + + + + + + + + auto_dg_for_task1_kr_4__x + + + + + + + + auto_dg_for_task1_kf_5__x + + + + + + + + auto_dg_for_task1_kr_5__x + + + + + + + + auto_dg_for_task1_kf_6__x + + + + + + + + auto_dg_for_task1_kr_6__x + + + + + + + + auto_dg_for_task1_kf_7__x + + + + + + + + auto_dg_for_task1_kr_7__x + + + + + + + + auto_dg_for_task1_kf_8__x + + + + + + + + auto_dg_for_task1_kr_8__x + + + + + + + + auto_dg_for_task1_kf_9__x + + + + + + + + auto_dg_for_task1_kr_9__x + + + + + + + + auto_dg_for_task1_kf_10__x + + + + + + + + auto_dg_for_task1_kr_10__x + + + + + + + + auto_dg_for_task1_kf_11__x + + + + + + + + auto_dg_for_task1_kr_11__x + + + + + + + + auto_dg_for_task1_kf_12__x + + + + + + + + auto_dg_for_task1_kr_12__x + + + + + + + + auto_dg_for_task1_kf_13__x + + + + + + + + auto_dg_for_task1_kr_13__x + + + + + + + + auto_dg_for_task1_kf_14__x + + + + + + + + auto_dg_for_task1_kr_14__x + + + + + + + + auto_dg_for_task1_kf_15__x + + + + + + + + auto_dg_for_task1_kr_15__x + + + + + + + + auto_dg_for_task1_kf_16__x + + + + + + + + auto_dg_for_task1_kr_16__x + + + + + + + + auto_dg_for_task1_t2__x + + + + + + + + auto_dg_for_task1_comp1__x + + + + + + + + auto_dg_for_task1_React0__x + + + + + + + + auto_dg_for_task1_React1__x + + + + + + + + auto_dg_for_task1_React2__x + + + + + + + + auto_dg_for_task1_React3__x + + + + + + + + auto_dg_for_task1_React4__x + + + + + + + + auto_dg_for_task1_React5__x + + + + + + + + auto_dg_for_task1_React6__x + + + + + + + + auto_dg_for_task1_React7__x + + + + + + + + auto_dg_for_task1_React8__x + + + + + + + + auto_dg_for_task1_React9__x + + + + + + + + auto_dg_for_task1_React10__x + + + + + + + + auto_dg_for_task1_React11__x + + + + + + + + auto_dg_for_task1_React12__x + + + + + + + + auto_dg_for_task1_React13__x + + + + + + + + auto_dg_for_task1_React14__x + + + + + + + + auto_dg_for_task1_React15__x + + + + + + + + auto_dg_for_task1_React16__x + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/BioModels/BIOMD0000000001/BIOMD0000000001_url.xml b/BioModels/BIOMD0000000001/BIOMD0000000001_url.xml new file mode 100644 index 00000000..411e0c65 --- /dev/null +++ b/BioModels/BIOMD0000000001/BIOMD0000000001_url.xml @@ -0,0 +1,1343 @@ + + + + + +
Edelstein1996 - EPSP ACh event
+
+

Model of a nicotinic Excitatory Post-Synaptic Potential in a + Torpedo electric organ. Acetylcholine is not represented + explicitely, but by an event that changes the constants of + transition from unliganded to liganded.  +

+
+
+

This model has initially been encoded using StochSim.

+
+
+

This model is described in the article:

+
+ A kinetic mechanism for + nicotinic acetylcholine receptors based on multiple allosteric + transitions. +
+
Edelstein SJ, Schaad O, Henry E, + Bertrand D, Changeux JP.
+
Biol Cybern 1996 Nov; 75(5): + 361-379
+

Abstract:

+
+

Nicotinic acetylcholine receptors are transmembrane + oligomeric proteins that mediate interconversions between open + and closed channel states under the control of + neurotransmitters. Fast in vitro chemical kinetics and in vivo + electrophysiological recordings are consistent with the + following multi-step scheme. Upon binding of agonists, receptor + molecules in the closed but activatable resting state (the + Basal state, B) undergo rapid transitions to states of higher + affinities with either open channels (the Active state, A) or + closed channels (the initial Inactivatable and fully + Desensitized states, I and D). In order to represent the + functional properties of such receptors, we have developed a + kinetic model that links conformational interconversion rates + to agonist binding and extends the general principles of the + Monod-Wyman-Changeux model of allosteric transitions. The + crucial assumption is that the linkage is controlled by the + position of the interconversion transition states on a + hypothetical linear reaction coordinate. Application of the + model to the peripheral nicotine acetylcholine receptor (nAChR) + accounts for the main properties of ligand-gating, including + single-channel events, and several new relationships are + predicted. Kinetic simulations reveal errors inherent in using + the dose-response analysis, but justify its application under + defined conditions. The model predicts that (in order to + overcome the intrinsic stability of the B state and to produce + the appropriate cooperativity) channel activation is driven by + an A state with a Kd in the 50 nM range, hence some 140-fold + stronger than the apparent affinity of the open state deduced + previously. According to the model, recovery from the + desensitized states may occur via rapid transit through the A + state with minimal channel opening, thus without necessarily + undergoing a distinct recovery pathway, as assumed in the + standard 'cycle' model. Transitions to the desensitized states + by low concentration 'pre-pulses' are predicted to occur + without significant channel opening, but equilibrium values of + IC50 can be obtained only with long pre-pulse times. + Predictions are also made concerning allosteric effectors and + their possible role in coincidence detection. In terms of + future developments, the analysis presented here provides a + physical basis for constructing more biologically realistic + models of synaptic modulation that may be applied to artificial + neural networks.

+
+
+
+

This model is hosted on + BioModels Database + and identified by: + BIOMD0000000001.

+

To cite BioModels Database, please use: + BioModels Database: + An enhanced, curated and annotated resource for published + quantitative kinetic models.

+
+
+

To the extent possible under law, all copyright and related or + neighbouring rights to this encoded model have been dedicated to + the public domain worldwide. Please refer to + CC0 + Public Domain Dedication for more information.

+
+ + + + + + + + + + Le Novère + Nicolas + + lenov@ebi.ac.uk + + EMBL-EBI + + + + + + 2005-02-02T14:56:11Z + + + 2017-05-19T14:33:51Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

biliganded basal state

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

monoliganded intermediate

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

monoliganded active state

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

unkiganded active state

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

monoliganded basal state

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

unliganded basal state

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

biliganded desensitised state

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

fully desensitised state

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

biliganded intermediate

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

monoliganded desensitised state

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

unliganted intermediate

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

biliganted active state

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

first ligand on basal

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

kf_0 * B - kr_0 * BL

+ + + + + + comp1 + + + + + kf_0 + B + + + + kr_0 + BL + + + + + + + + + +

second ligand on basal

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

kf_1 * BL - kr_1 * BLL

+ + + + + + comp1 + + + + + kf_1 + BL + + + + kr_1 + BLL + + + + + + + + + +

opening of biliganded

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

kf_2 * BLL - kr_2 * ALL

+ + + + + + comp1 + + + + + kf_2 + BLL + + + + kr_2 + ALL + + + + + + + + + +

first ligand on active

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

kf_3 * A - kr_3 * AL

+ + + + + + comp1 + + + + + kf_3 + A + + + + kr_3 + AL + + + + + + + + + +

second ligand on active

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

kf_4 * AL - kr_4 * ALL

+ + + + + + comp1 + + + + + kf_4 + AL + + + + kr_4 + ALL + + + + + + + + + +

opening of unliganded

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

kf_5 * B - kr_5 * A

+ + + + + + comp1 + + + + + kf_5 + B + + + + kr_5 + A + + + + + + + + + +

opening of monoliganded

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

kf_6 * BL - kr_6 * AL

+ + + + + + comp1 + + + + + kf_6 + BL + + + + kr_6 + AL + + + + + + + + + +

first ligand on intermediate

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

kf_7 * I - kr_7 * IL

+ + + + + + comp1 + + + + + kf_7 + I + + + + kr_7 + IL + + + + + + + + + +

second ligand on intermediate

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

kf_8 * IL - kr_8 * ILL

+ + + + + + comp1 + + + + + kf_8 + IL + + + + kr_8 + ILL + + + + + + + + + +

unliganded active <=> unliganded intermediate

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

kf_9 * A - kr_9 * I

+ + + + + + comp1 + + + + + kf_9 + A + + + + kr_9 + I + + + + + + + + + +

monoliganded active <=> monoliganded intermediate

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

kf_10 * AL - kr_10 * IL

+ + + + + + comp1 + + + + + kf_10 + AL + + + + kr_10 + IL + + + + + + + + + +

biliganded active <=> biliganded intermediate

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

kf_11 * ALL - kr_11 * ILL

+ + + + + + comp1 + + + + + kf_11 + ALL + + + + kr_11 + ILL + + + + + + + + + +

first ligand on desensitised

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

kf_12 * D - kr_12 * DL

+ + + + + + comp1 + + + + + kf_12 + D + + + + kr_12 + DL + + + + + + + + + +

second ligand on desensitised

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

kf_13 * DL - kr_13 * DLL

+ + + + + + comp1 + + + + + kf_13 + DL + + + + kr_13 + DLL + + + + + + + + + +

unliganded intermediate <=> unliganded desensitised

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

kf_14 * I - kr_14 * D

+ + + + + + comp1 + + + + + kf_14 + I + + + + kr_14 + D + + + + + + + + + +

monoliganded intermediate <=> monoliganded desensitised

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

kf_15 * IL - kr_15 * DL

+ + + + + + comp1 + + + + + kf_15 + IL + + + + kr_15 + DL + + + + + + + + + +

biliganded intermediate <=> biliganded desensitised

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

kf_16 * ILL - kr_16 * DLL

+ + + + + + comp1 + + + + + kf_16 + ILL + + + + kr_16 + DLL + + + + + + + + + + + + + + + + + + + + + + + + + + time + t2 + + + + + + + 0 + + + + + 0 + + + + + 0 + + + + + 0 + + + + + 0 + + + + + 0 + + + + + 0 + + + + + 0 + + + + + + + \ No newline at end of file diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_local/amici_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_local/amici_autogen_plot_for_task1.pdf new file mode 100644 index 00000000..7b5369d8 Binary files /dev/null and b/BioModels/BIOMD0000000001/tests/d1_plots_local/amici_autogen_plot_for_task1.pdf differ diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_local/copasi_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_local/copasi_autogen_plot_for_task1.pdf new file mode 100644 index 00000000..aaaf90e0 Binary files /dev/null and b/BioModels/BIOMD0000000001/tests/d1_plots_local/copasi_autogen_plot_for_task1.pdf differ diff --git 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mode 100644 index 00000000..2a526468 Binary files /dev/null and b/BioModels/BIOMD0000000001/tests/d1_plots_remote/vcell_autogen_plot_for_task1.pdf differ diff --git a/BioModels/BIOMD0000000001/tests/results_compatibility_biosimulators.md b/BioModels/BIOMD0000000001/tests/results_compatibility_biosimulators.md new file mode 100644 index 00000000..9b9f7574 --- /dev/null +++ b/BioModels/BIOMD0000000001/tests/results_compatibility_biosimulators.md @@ -0,0 +1,23 @@ +| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------|:-----------------------------------------------------------------------| +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be 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 file extensions ('xml', 'sedml') suggest the input file types may be compatible with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

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

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be 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/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with cbmpy.

['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be 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 `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with copasi.

['SBML', 'SED-ML'] are compatible with copasi.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be 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 `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

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

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be 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 `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be 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:

Could not load MassModel 'BIOMD0000000001'

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| plot | | +|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be 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 file extensions ('xml', 'sedml') suggest the input file types may be compatible with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

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

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

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

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be 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 file extensions ('xml', 'sedml') suggest the input file types may be compatible with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

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

The file extensions ('xml', 'sedml') suggest the input file types may be 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/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with tellurium.

['SBML', 'SED-ML'] are compatible with tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
VCellhttps://github.com/virtualcell/vcell
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with vcell.

['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
✅ PASSview
download
logs

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

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/BioModels/BIOMD0000000001/tests/results_local.json b/BioModels/BIOMD0000000001/tests/results_local.json new file mode 100644 index 00000000..607166d7 --- /dev/null +++ b/BioModels/BIOMD0000000001/tests/results_local.json @@ -0,0 +1,2167 @@ +{ + "amici": { + "exception_message": "", + "log_yml": { + "duration": 345.061273, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 344.712319, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ALL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_t2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_comp1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React16", + "status": "SUCCEEDED" + } + ], + "duration": 25.52741, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ALL", + "status": "SUCCEEDED" + } + ], + "duration": 10.885187, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000496", + "duration": 308.129996, + "exception": null, + "id": "task1", + "output": "2024-11-19 09:58:49.944 - amici.swig_wrappers - DEBUG - [CVODES:CVode:TOO_MUCH_WORK] AMICI ERROR: in module CVODES in function CVode : At t = 455.172, mxstep steps taken before reaching tout. \r\n2024-11-19 09:58:49.944 - amici.swig_wrappers - ERROR - [FORWARD_FAILURE] AMICI forward simulation failed at t = 455.172: AMICI failed to integrate the forward problem\r\n", + "simulatorDetails": [ + { + "key": "solver", + "value": "amici.amici.CVodeSolver" + }, + { + "key": "method", + "value": "amici.swig_wrappers.runAmiciSimulation" + }, + { + "key": "arguments", + "value": {} + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "brian2": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.070201, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpjiz9loaw/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n [py.warnings]\r\npyNeuroML >>> WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpjiz9loaw/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "bionetgen": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1", + "log_yml": { + "duration": 0.299193, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpk1vrgtil/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "boolnet": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1", + "log_yml": { + "duration": 0.244705, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpgwq63r9x/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cbmpy": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.295067, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpea9v4i1l/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cobrapy": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.188426, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp4ikj0x1c/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "copasi": { + "exception_message": "", + "log_yml": { + "duration": 44.757602, + "exception": null, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpdbztmaty/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpdbztmaty/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 44.321433, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ALL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_t2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_comp1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React16", + "status": "SUCCEEDED" + } + ], + "duration": 26.531954, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ALL", + "status": "SUCCEEDED" + } + ], + "duration": 13.399035, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000560", + "duration": 4.085217, + "exception": null, + "id": "task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task1_kf_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_B__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_I__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_IL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_A__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ILL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_AL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_comp1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_t2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_D__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ALL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_16__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `BIOMD0000000001_url` may be invalid.\r\n - The model file `/tmp/tmpdbztmaty/./BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'LSODA/LSODAR hybrid method' (KISAO_0000560) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "simulatorDetails": [ + { + "key": "methodName", + "value": "lsoda" + }, + { + "key": "parameters", + "value": null + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "gillespy2": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/gillespy2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.269059, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpk996qbgr/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "ginsim": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.215349, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp7ujh4tae/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "libsbmlsim": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/libsbmlsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.181664, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpvf8mjq9l/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "masspy": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.194957, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mSedmlFeatureNotSupportedWarning\u001b[0m: \u001b[33m`/tmp/tmplpf58_yz/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "netpyne": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1", + "log_yml": { + "duration": 0.045945, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "neuron": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1", + "log_yml": { + "duration": 0.075117, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpr20_52il/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "opencor": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1", + "log_yml": { + "duration": 0.079007, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpo64fo3wz/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pyneuroml": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1", + "log_yml": { + "duration": 0.051567, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpht6_guy4/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pysces": { + "exception_message": "", + "log_yml": { + "duration": 50.11715, + "exception": null, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpn0re_la7/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpn0re_la7/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 49.733133, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V4\r\nINFO: Rescaling compartment with size 1e-16 to 1.0\r\ncsymbol time defined as \"time\" in event \r\nInfo: single compartment model: locating \"React0\" in default compartment\r\nInfo: single compartment model: locating \"React1\" in default compartment\r\nInfo: single compartment model: locating \"React2\" in default compartment\r\nInfo: single compartment model: locating \"React3\" in default compartment\r\nInfo: single compartment model: locating \"React4\" in default compartment\r\nInfo: single compartment model: locating \"React5\" in default compartment\r\nInfo: single compartment model: locating \"React6\" in default compartment\r\nInfo: single compartment model: locating \"React7\" in default compartment\r\nInfo: single compartment model: locating \"React8\" in default compartment\r\nInfo: single compartment model: locating \"React9\" in default compartment\r\nInfo: single compartment model: locating \"React10\" in default compartment\r\nInfo: single compartment model: locating \"React11\" in default compartment\r\nInfo: single compartment model: locating \"React12\" in default compartment\r\nInfo: single compartment model: locating \"React13\" in default compartment\r\nInfo: single compartment model: locating \"React14\" in default compartment\r\nInfo: single compartment model: locating \"React15\" in default compartment\r\nInfo: single compartment model: locating \"React16\" in default compartment\r\nWriting file: /tmp/tmpq6ma9hof.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpj_50x55w.xml\r\nout: /tmp/tmpq6ma9hof.psc\r\nUsing model directory: /Pysces/psc\r\n/tmp/tmpq6ma9hof.psc loading ..... \r\nParsing file: /tmp/tmpq6ma9hof.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"t2\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . done.\r\n \r\nEvent(s) detected.\r\n\r\nINFO: events detected and we have Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nevent RemovalACh is evaluating at 20.000998\r\nevent RemovalACh is assigning at 20.000998 (delay=0.0)\r\nexecuting RemovalACh\r\nCVODE time for 100001 points: 7.120683193206787\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ALL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_t2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_comp1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React16", + "status": "SUCCEEDED" + } + ], + "duration": 28.192101, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ALL", + "status": "SUCCEEDED" + } + ], + "duration": 13.982287, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 7.299818, + "exception": null, + "id": "task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task1_DL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_A__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_I__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_AL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_comp1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ALL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_t2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_B__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_IL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_D__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ILL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_6__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "simulatorDetails": [ + { + "key": "method", + "value": "pysces.PyscesModel.Simulate" + }, + { + "key": "arguments", + "value": { + "cvode_abstol": 1e-09, + "cvode_access_solver": true, + "cvode_h0": 0.0, + "cvode_hmax": 0.0, + "cvode_hmin": 0.0, + "cvode_mxord": 5, + "cvode_mxstep": 5000, + "cvode_reltol": 1e-09, + "cvode_return_event_timepoints": false, + "cvode_stats": false, + "cvode_track_assignment_rules": true + } + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "rbapy": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.211235, + "exception": { + "message": "`/root/in/BIOMD0000000001_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpye2xsxa5/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` may be invalid.\r\n - Model `BIOMD0000000001_url` may be invalid.\r\n - The model file `BIOMD0000000001_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_1 * BL - kr_1 * BLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_2 * BLL - kr_2 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_3 * A - kr_3 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_4 * AL - kr_4 * ALL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_5 * B - kr_5 * A)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_6 * BL - kr_6 * AL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_7 * I - kr_7 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_8 * IL - kr_8 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_9 * A - kr_9 * I)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_10 * AL - kr_10 * IL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_11 * ALL - kr_11 * ILL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_12 * D - kr_12 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_13 * DL - kr_13 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_14 * I - kr_14 * D)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_15 * IL - kr_15 * DL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_16 * ILL - kr_16 * DLL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gt(time, t2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_0' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_1' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_2' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_3' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_4' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_5' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_6' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_7' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_8' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_9' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_10' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_11' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_12' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_13' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_14' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_15' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kr_16' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 't2' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "smoldyn": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1", + "log_yml": {}, + "detailed_error_log": {} + }, + "tellurium": { + "exception_message": "", + "log_yml": { + "duration": 40.289412, + "exception": null, + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmpx3ltypf9/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` has warnings.\r\n - Model `BIOMD0000000001_url` has warnings.\r\n - The model file `BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmpx3ltypf9/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n", + "sedDocuments": [ + { + "duration": 39.849291, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ALL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_t2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_comp1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React16", + "status": "SUCCEEDED" + } + ], + "duration": 25.996882, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ALL", + "status": "SUCCEEDED" + } + ], + "duration": 12.508398, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning:\r\n\r\n\u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n\r\n", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 1.183695, + "exception": null, + "id": "task1", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33m- Variable `auto_dg_for_task1_React4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_4__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_8__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ILL__x` has warnings.\r\n - XPath could not be 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XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_IL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_AL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_I__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_12__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_BL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_14__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_7__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_5__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_1__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_B__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_11__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_D__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_A__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_13__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_0__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React15__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_t2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React2__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_DLL__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_16__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kr_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React9__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_10__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React6__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kf_3__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_React11__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mModel `BIOMD0000000001_url` may be invalid.\r\n - The model file `/tmp/tmpx3ltypf9/./BIOMD0000000001_url.xml` has warnings.\r\n - 26 warnings of type SBML unit consistency (99505). The following is the first warning at line 467, column 8:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'comp1 * (kf_0 * B - kr_0 * BL)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 35 warnings of type Modeling practice (80701). The following is the first warning at line 406, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kf_0' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning:\r\n\r\n\u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n\r\n", + "simulatorDetails": [ + { + "key": "method", + "value": "simulate" + }, + { + "key": "solver", + "value": "cvode" + }, + { + "key": "relative_tolerance", + "value": 1e-06 + }, + { + "key": "absolute_tolerance", + "value": 1e-12 + }, + { + "key": "stiff", + "value": true + }, + { + "key": "maximum_bdf_order", + "value": 5 + }, + { + "key": "maximum_adams_order", + "value": 12 + }, + { + "key": "maximum_num_steps", + "value": 20000 + }, + { + "key": "maximum_time_step", + "value": 0.0 + }, + { + "key": "minimum_time_step", + "value": 0.0 + }, + { + "key": "initial_time_step", + "value": 0.0 + }, + { + "key": "multiple_steps", + "value": false + }, + { + "key": "variable_step_size", + "value": false + }, + { + "key": "max_output_rows", + "value": 100000 + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "vcell": { + "exception_message": "", + "log_yml": { + "duration": 103, + "exception": null, + "output": "Processing BIOMD0000000001_url.sedml. Done", + "sedDocuments": [ + { + "duration": null, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Initializing SED-ML document... done. Successful translation of SED-ML file. Building solvers and starting simulation of all tasks... Generating outputs... Generating CSV file... Done. Generating HDF5 file...", + "outputs": [ + { + "curves": [ + { + "id": "autogen_curve_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_curve_task1_ALL", + "status": "SUCCEEDED" + } + ], + "duration": null, + "exception": null, + "id": "autogen_plot_for_task1", + "output": null, + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ALL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_t2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_comp1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React16", + "status": "SUCCEEDED" + } + ], + "duration": null, + "exception": null, + "id": "autogen_report_for_task1", + "output": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 33, + "exception": null, + "id": "task1", + "output": "Initializing simulation job 0 ... done. Starting simulation... done.", + "simulatorDetails": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "xpp": { + "exception_message": "Command '-i /root/in/BIOMD0000000001_url.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1", + "log_yml": { + "duration": 0.09879, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpjba2rckk/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + } +} \ No newline at end of file diff --git a/BioModels/BIOMD0000000001/tests/results_remote.json b/BioModels/BIOMD0000000001/tests/results_remote.json new file mode 100644 index 00000000..63eca8a7 --- /dev/null +++ b/BioModels/BIOMD0000000001/tests/results_remote.json @@ -0,0 +1,2580 @@ +{ + "amici": { + "response": 201, + "view": "https://api.biosimulations.org/runs/673c5d8c0d09353e8f124846", + "download": "https://api.biosimulations.org/results/673c5d8c0d09353e8f124846/download", + "logs": "https://api.biosimulations.org/logs/673c5d8c0d09353e8f124846?includeOutput=true", + "log_yml": { + "duration": 399.401152, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 398.906364, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ALL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_3", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_4", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_5", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_6", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_7", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_8", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_9", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_10", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_11", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_12", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_13", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_14", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_15", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kf_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kr_16", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_t2", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_comp1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_React0", + "status": 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a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "boolnet": { + "response": 201, + "view": "https://api.biosimulations.org/runs/673c5d920d09353e8f124850", + "download": "https://api.biosimulations.org/results/673c5d920d09353e8f124850/download", + "logs": "https://api.biosimulations.org/logs/673c5d920d09353e8f124850?includeOutput=true", + "log_yml": { + "duration": 0.24272, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "cbmpy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/673c5d950d09353e8f124853", + "download": "https://api.biosimulations.org/results/673c5d950d09353e8f124853/download", + "logs": "https://api.biosimulations.org/logs/673c5d950d09353e8f124853?includeOutput=true", + "log_yml": { + "duration": 0.307212, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "cobrapy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/673c5d970d09353e8f124858", + "download": "https://api.biosimulations.org/results/673c5d970d09353e8f124858/download", + "logs": "https://api.biosimulations.org/logs/673c5d970d09353e8f124858?includeOutput=true", + "log_yml": { + "duration": 0.220452, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "copasi": { + "response": 201, + "view": "https://api.biosimulations.org/runs/673c5d9ab678b3883bb8a00e", + "download": "https://api.biosimulations.org/results/673c5d9ab678b3883bb8a00e/download", + "logs": "https://api.biosimulations.org/logs/673c5d9ab678b3883bb8a00e?includeOutput=true", + "log_yml": { + "duration": 54.716714, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 54.325968, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...woohoo!\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": 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"simulatorDetails": [ + { + "key": "methodName", + "value": "lsoda" + }, + { + "key": "parameters", + "value": null + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + }, + "gillespy2": { + "response": 201, + "view": "https://api.biosimulations.org/runs/673c5d9cb678b3883bb8a015", + "download": "https://api.biosimulations.org/results/673c5d9cb678b3883bb8a015/download", + "logs": "https://api.biosimulations.org/logs/673c5d9cb678b3883bb8a015?includeOutput=true", + "log_yml": { + "duration": 0.228324, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "ginsim": { + "response": 201, + "view": "https://api.biosimulations.org/runs/673c5d9eb678b3883bb8a019", + "download": "https://api.biosimulations.org/results/673c5d9eb678b3883bb8a019/download", + "logs": "https://api.biosimulations.org/logs/673c5d9eb678b3883bb8a019?includeOutput=true", + "log_yml": { + "duration": 0.216675, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "libsbmlsim": { + "response": 201, + "view": "https://api.biosimulations.org/runs/673c5da00d09353e8f124870", + "download": "https://api.biosimulations.org/results/673c5da00d09353e8f124870/download", + "logs": "https://api.biosimulations.org/logs/673c5da00d09353e8f124870?includeOutput=true", + "log_yml": { + "duration": 0.225096, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000001_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "masspy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/673c5da35a60072d20f74291", + "download": "https://api.biosimulations.org/results/673c5da35a60072d20f74291/download", + "logs": "https://api.biosimulations.org/logs/673c5da35a60072d20f74291?includeOutput=true", + "log_yml": { + "duration": 1.503824, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Could not load MassModel 'BIOMD0000000001'", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.956937, + "exception": { + "message": "The SED document did not execute successfully:\n\n Could not load MassModel 'BIOMD0000000001'", + "type": "SedmlExecutionError" + }, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_BLL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_IL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_AL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_A", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_BL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_B", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_DLL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_D", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ILL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_DL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_I", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ALL", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_0", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_0", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_2", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_2", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_3", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_3", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_4", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_4", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_5", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_5", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_6", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_6", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_7", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_7", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_8", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_8", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_9", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_9", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_10", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_10", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_11", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_11", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_12", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_12", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_13", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_13", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_14", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_14", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_15", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_15", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kf_16", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kr_16", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_t2", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_comp1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React0", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React2", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React3", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React4", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React5", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React6", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React7", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React8", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React9", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React10", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React11", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React12", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React13", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React14", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React15", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_React16", + "status": "SKIPPED" + } + ], + "duration": 0.061037, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_BLL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_IL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_AL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_A", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_BL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_B", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_DLL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_D", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_ILL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_DL", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_I", + "status": "SKIPPED" + }, + { + "id": "autogen_curve_task1_ALL", + "status": "SKIPPED" + } + ], + "duration": 0.344134, + "exception": null, + "id": "autogen_plot_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.341199, + "exception": { + "message": "Could not load MassModel 'BIOMD0000000001'", + "type": "MassSimulationError" + }, + "id": "task1", + "output": "\u001b[93mWARNING:\u001b[0m \u001b[93mModel does not contain SBML fbc package\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mModel does not contain SBML groups package\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'BIOMD0000000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'BIOMD0000000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'BIOMD0000000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'BIOMD0000000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'BIOMD0000000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'BLL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'BLL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'IL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'IL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'AL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'AL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'A' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'A'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'BL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'BL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'B' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'B'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'DLL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'DLL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'D' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'D'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'ILL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'ILL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'DL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'DL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'I' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'I'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mRate expressions are set to exclude compartments, but the initial condition is an InitialAmount for 'ALL' in the SBML model specie. \u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Species 'ALL'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React0'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React1'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React2'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React3'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React4'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React5'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React6'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React7'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React8'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React9'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React10'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React11'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React12'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React13'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React14'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React15'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React16'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React0'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React1'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React2'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React3'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React4'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React5'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React6'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React7'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React8'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React9'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React10'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React11'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React12'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React13'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React14'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React15'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Reaction 'React16'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + } + }, + "netpyne": { + "response": 201, + "view": "https://api.biosimulations.org/runs/673c5da40d09353e8f12487b", + "download": "https://api.biosimulations.org/results/673c5da40d09353e8f12487b/download", + "logs": "https://api.biosimulations.org/logs/673c5da40d09353e8f12487b?includeOutput=true", + "log_yml": { + "duration": 0.057357, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "neuron": { + "response": 201, + "view": "https://api.biosimulations.org/runs/673c5da65a60072d20f7429d", + "download": "https://api.biosimulations.org/results/673c5da65a60072d20f7429d/download", + "logs": "https://api.biosimulations.org/logs/673c5da65a60072d20f7429d?includeOutput=true", + "log_yml": { + "duration": 0.053578, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "opencor": { + "response": 201, + "view": "https://api.biosimulations.org/runs/673c5da80d09353e8f124892", + "download": "https://api.biosimulations.org/results/673c5da80d09353e8f124892/download", + "logs": "https://api.biosimulations.org/logs/673c5da80d09353e8f124892?includeOutput=true", + "log_yml": { + "duration": 0.041006, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpuzt6zjfi/./BIOMD0000000001_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "pyneuroml": { + "response": 201, + "view": "https://api.biosimulations.org/runs/673c5daa5a60072d20f742af", + "download": "https://api.biosimulations.org/results/673c5daa5a60072d20f742af/download", + "logs": "https://api.biosimulations.org/logs/673c5daa5a60072d20f742af?includeOutput=true", + "log_yml": { + "duration": 0.053685, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "pysces": { + "response": 201, + "view": "https://api.biosimulations.org/runs/673c5dac0d09353e8f124896", + "download": "https://api.biosimulations.org/results/673c5dac0d09353e8f124896/download", + "logs": "https://api.biosimulations.org/logs/673c5dac0d09353e8f124896?includeOutput=true", + "log_yml": { + "duration": 51.927413, + "exception": null, + "output": "libtk8.6.so: cannot open shared object file: No such file or directory\r\n\r\nPySCeS defaults to matplotlib's TKagg backend if not specified in the user configuration file, set \"matplotlib_backend = \" \r\nMatplotlib interface loaded (pysces.plt.m)\r\nPitcon routines available\r\nNLEQ2 routines available\r\nSBML support available\r\nYou are using NumPy (2.1.2) with SciPy (1.14.1)\r\nAssimulo CVode available\r\nRateChar is available\r\nParallel scanner is available\r\n\r\nPySCeS environment\r\n******************\r\npysces.model_dir = /home/FCAM/crbmapi/Pysces/psc\r\npysces.output_dir = /home/FCAM/crbmapi/Pysces\r\n\r\n\r\n***********************************************************************\r\n* Welcome to PySCeS (1.2.2) - Python Simulator for Cellular Systems *\r\n* http://pysces.sourceforge.net *\r\n* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2024 *\r\n* Triple-J Group for Molecular Cell Physiology *\r\n* Stellenbosch University, ZA and VU University Amsterdam, NL *\r\n* PySCeS is distributed under the PySCeS (BSD style) licence, see *\r\n* LICENCE.txt (supplied with this release) for details *\r\n* Please cite PySCeS with: doi:10.1093/bioinformatics/bti046 *\r\n***********************************************************************\r\n", + "sedDocuments": [ + { + "duration": 51.566999, + "exception": null, + "location": "BIOMD0000000001_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n BIOMD0000000001_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 66 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_url.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot_for_task1`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V4\r\nINFO: Rescaling compartment with size 1e-16 to 1.0\r\ncsymbol time defined as \"time\" in event \r\nInfo: single compartment model: locating \"React0\" in default compartment\r\nInfo: single compartment model: locating \"React1\" in default compartment\r\nInfo: single compartment model: locating \"React2\" in default compartment\r\nInfo: single compartment model: locating \"React3\" in default compartment\r\nInfo: single compartment model: locating \"React4\" in default compartment\r\nInfo: single compartment model: locating \"React5\" in default compartment\r\nInfo: single compartment model: locating \"React6\" in default compartment\r\nInfo: single compartment model: locating \"React7\" in default compartment\r\nInfo: single compartment model: locating \"React8\" in default compartment\r\nInfo: single compartment model: locating \"React9\" in default compartment\r\nInfo: single compartment model: locating \"React10\" in default compartment\r\nInfo: single compartment model: locating \"React11\" in default compartment\r\nInfo: single compartment model: locating \"React12\" in default compartment\r\nInfo: single compartment model: locating \"React13\" in default compartment\r\nInfo: single compartment model: locating \"React14\" in default compartment\r\nInfo: single compartment model: locating \"React15\" in default compartment\r\nInfo: single compartment model: locating \"React16\" in default compartment\r\nWriting file: /tmp/tmpkv0bdkg1.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpa8hro1wx.xml\r\nout: /tmp/tmpkv0bdkg1.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmpkv0bdkg1.psc loading ..... \r\nParsing file: /tmp/tmpkv0bdkg1.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"t2\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . done.\r\n \r\nEvent(s) detected.\r\n\r\nINFO: events detected and we have Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nevent RemovalACh is evaluating at 20.000998\r\nevent RemovalACh is assigning at 20.000998 (delay=0.0)\r\nexecuting RemovalACh\r\nCVODE time for 100001 points: 7.514819145202637\r\n \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": 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Generating 2 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot_for_task1` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_IL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_AL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_A", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_BL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_B", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DLL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_D", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ILL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_DL", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_I", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ALL", + "status": "SUCCEEDED" + }, 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The model is encoded according to the paper Low dose of dopamine may stimulate prolactin secretion by increasing fast potassium currents + Figure5 has been reproduced by MathSBML. One need to change the value of ga in order to get the three correct results.

+

the xppaut file of the model is avaiable on the following address offered by the author , http://www.math.fsu.edu/%7Ebertram/software/pituitary/JCNS_07.ode

+
+

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication + for more information.

+

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.

+
+

To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92. +

+ + + + + + + + + + + He + Enuo + + enuo@caltech.edu + + BNMC + + + + + + 2007-08-02T10:34:59Z + + + 2014-04-01T18:01:13Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ The concentration of Ca range can change from 0.1 to 0.3

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

+ For figure 5A, ga=0, figure5B, ga=8, figure5C, ga=25

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+ + + + + + + \ No newline at end of file diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_local/amici_autogen_plot1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_local/amici_autogen_plot1.pdf new file mode 100644 index 00000000..f6fce0ef Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_local/amici_autogen_plot1.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_local/amici_autogen_plot2.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_local/amici_autogen_plot2.pdf new file mode 100644 index 00000000..ad3e527f Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_local/amici_autogen_plot2.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_local/copasi_autogen_plot1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_local/copasi_autogen_plot1.pdf new file mode 100644 index 00000000..2d223251 Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_local/copasi_autogen_plot1.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_local/copasi_autogen_plot2.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_local/copasi_autogen_plot2.pdf new file mode 100644 index 00000000..f9520d51 Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_local/copasi_autogen_plot2.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_local/pysces_autogen_plot1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_local/pysces_autogen_plot1.pdf new file mode 100644 index 00000000..c3df80c2 Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_local/pysces_autogen_plot1.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_local/pysces_autogen_plot2.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_local/pysces_autogen_plot2.pdf new file mode 100644 index 00000000..c3df80c2 Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_local/pysces_autogen_plot2.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_local/tellurium_autogen_plot1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_local/tellurium_autogen_plot1.pdf new file mode 100644 index 00000000..95b9fd12 Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_local/tellurium_autogen_plot1.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_local/tellurium_autogen_plot2.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_local/tellurium_autogen_plot2.pdf new file mode 100644 index 00000000..d4cc3eac Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_local/tellurium_autogen_plot2.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_local/vcell_autogen_plot1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_local/vcell_autogen_plot1.pdf new file mode 100644 index 00000000..88a9b40c Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_local/vcell_autogen_plot1.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_local/vcell_autogen_plot2.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_local/vcell_autogen_plot2.pdf new file mode 100644 index 00000000..c1af1e4d Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_local/vcell_autogen_plot2.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_remote/amici_autogen_plot1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_remote/amici_autogen_plot1.pdf new file mode 100644 index 00000000..fd5d0caf Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_remote/amici_autogen_plot1.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_remote/amici_autogen_plot2.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_remote/amici_autogen_plot2.pdf new file mode 100644 index 00000000..fd5d0caf Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_remote/amici_autogen_plot2.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_remote/copasi_autogen_plot1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_remote/copasi_autogen_plot1.pdf new file mode 100644 index 00000000..4e979cda Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_remote/copasi_autogen_plot1.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_remote/copasi_autogen_plot2.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_remote/copasi_autogen_plot2.pdf new file mode 100644 index 00000000..948929f1 Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_remote/copasi_autogen_plot2.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_remote/masspy_autogen_plot1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_remote/masspy_autogen_plot1.pdf new file mode 100644 index 00000000..24f990ff Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_remote/masspy_autogen_plot1.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_remote/masspy_autogen_plot2.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_remote/masspy_autogen_plot2.pdf new file mode 100644 index 00000000..24f990ff Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_remote/masspy_autogen_plot2.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_remote/pysces_autogen_plot1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_remote/pysces_autogen_plot1.pdf new file mode 100644 index 00000000..35259daa Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_remote/pysces_autogen_plot1.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_remote/pysces_autogen_plot2.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_remote/pysces_autogen_plot2.pdf new file mode 100644 index 00000000..35259daa Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_remote/pysces_autogen_plot2.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_remote/tellurium_autogen_plot1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_remote/tellurium_autogen_plot1.pdf new file mode 100644 index 00000000..eee6a50d Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_remote/tellurium_autogen_plot1.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_remote/tellurium_autogen_plot2.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_remote/tellurium_autogen_plot2.pdf new file mode 100644 index 00000000..5dbd535e Binary files /dev/null and b/BioModels/BIOMD0000000138/tests/d1_plots_remote/tellurium_autogen_plot2.pdf differ diff --git a/BioModels/BIOMD0000000138/tests/results_compatibility_biosimulators.md b/BioModels/BIOMD0000000138/tests/results_compatibility_biosimulators.md new file mode 100644 index 00000000..7d6c70ea --- /dev/null +++ b/BioModels/BIOMD0000000138/tests/results_compatibility_biosimulators.md @@ -0,0 +1,23 @@ +| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------|:-----------------------------------------------------------------------| +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with amici.

['SBML', 'SED-ML'] are compatible with amici.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2

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

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

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

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be 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/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with cbmpy.

['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be 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 `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be 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 `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2

ERROR TYPE:
ValueError
| plot | plot | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with gillespy2.

['SBML', 'SED-ML'] are compatible with gillespy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

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

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be 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 `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| | | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be 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 `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
| plot | | +|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be 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 file extensions ('xml', 'sedml') suggest the input file types may be compatible with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

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

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

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

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with pysces.

['SBML', 'SED-ML'] are compatible with pysces.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2

ERROR TYPE:
ValueError
| plot | plot | +|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

ERROR TYPE:
ValueError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2
- Simulation `auto_ten_seconds` is invalid.
- Algorithm has an invalid KiSAO id `KISAO_0000694`.

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

The file extensions ('xml', 'sedml') suggest the input file types may be 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/
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with tellurium.

['SBML', 'SED-ML'] are compatible with tellurium.
|
❌ FAILview
download
logs

ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2

ERROR TYPE:
ValueError
|
❌ FAILERROR MESSAGE:
`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.
- Outputs must have unique ids. The following ids are repeated:
- autogen_plot2
- Each identified SED object must have a unique id. Multiple objects have the following ids:
- autogen_plot2

ERROR TYPE:
ValueError
| plot | plot | +|
VCellhttps://github.com/virtualcell/vcell
|
❓ UNSUREThe file extensions ('xml', 'sedml') suggest the input file types may be compatible with vcell.

['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

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

The file extensions ('xml', 'sedml') suggest the input file types may be compatible with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/BioModels/BIOMD0000000138/tests/results_local.json b/BioModels/BIOMD0000000138/tests/results_local.json new file mode 100644 index 00000000..6d361657 --- /dev/null +++ b/BioModels/BIOMD0000000138/tests/results_local.json @@ -0,0 +1,1631 @@ +{ + "amici": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/amici' returned non-zero exit status 1", + "log_yml": { + "duration": 1.327694, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n rateRule \"lambda * (phik - n) / taun\" contains an unsupported expression: Sympify of expression 'could not parse 'lambda * (phik - n) / taun'' failed, because of exception being raised:\n TokenError: Starred arguments in lambda not supported.", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.919753, + "exception": { + "message": "The SED document did not execute successfully:\n\n rateRule \"lambda * (phik - n) / taun\" contains an unsupported expression: Sympify of expression 'could not parse 'lambda * (phik - n) / taun'' failed, because of exception being raised:\n TokenError: Starred arguments in lambda not supported.", + "type": "SedmlExecutionError" + }, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 3 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (3):\r\n autogen_plot1: 1 curves\r\n autogen_plot2: 1 curves\r\n autogen_plot3: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 4 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot1`\r\n `autogen_plot2`\r\n `autogen_plot3`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 4 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 3: `autogen_plot2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 4: `autogen_plot3` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_c", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vca", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_Cm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gcal", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gsk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ga", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_va", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sa", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_taun", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_tauh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_lambda", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kc", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ks", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ff", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_alpha", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phih", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phif", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phical", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cinf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ica", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_isk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ibk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_n", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_h", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_V", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cell", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SKIPPED" + } + ], + "duration": 0.050763, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SKIPPED" + } + ], + "duration": 0.264934, + "exception": null, + "id": "autogen_plot1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_for_task1_V", + "status": "SKIPPED" + } + ], + "duration": 0.182554, + "exception": null, + "id": "autogen_plot2", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_for_task1_vk", + "status": "SKIPPED" + } + ], + "duration": 0.170817, + "exception": null, + "id": "autogen_plot3", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.090092, + "exception": { + "message": "rateRule \"lambda * (phik - n) / taun\" contains an unsupported expression: Sympify of expression 'could not parse 'lambda * (phik - n) / taun'' failed, because of exception being raised:\nTokenError: Starred arguments in lambda not supported.", + "type": "SBMLException" + }, + "id": "task1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "brian2": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.078752, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "WARNING /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpnbtryz96/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n [py.warnings]\r\npyNeuroML >>> WARNING - /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpnbtryz96/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "bionetgen": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1", + "log_yml": { + "duration": 0.137257, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp1hfxb1k_/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "boolnet": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1", + "log_yml": { + "duration": 0.163477, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpx4ed22ha/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cbmpy": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.265387, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpn2t50ntg/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cobrapy": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.18121, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpggckd_22/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "copasi": { + "exception_message": "", + "log_yml": { + "duration": 21.274612, + "exception": null, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpyne0jvhm/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpyne0jvhm/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 20.833371, + "exception": null, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 3 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (3):\r\n autogen_plot1: 1 curves\r\n autogen_plot2: 1 curves\r\n autogen_plot3: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 4 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot1`\r\n `autogen_plot2`\r\n `autogen_plot3`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 4 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 3: `autogen_plot2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 4: `autogen_plot3` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_c", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vca", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_Cm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gcal", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gsk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ga", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_va", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_taun", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_tauh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_lambda", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ks", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ff", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_alpha", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phih", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phif", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phical", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cinf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ica", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_isk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ibk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_n", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_h", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_V", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cell", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SUCCEEDED" + } + ], + "duration": 13.560127, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SUCCEEDED" + } + ], + "duration": 1.601553, + "exception": null, + "id": "autogen_plot1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_for_task1_V", + "status": "SUCCEEDED" + } + ], + "duration": 1.51774, + "exception": null, + "id": "autogen_plot2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_for_task1_vk", + "status": "SUCCEEDED" + } + ], + "duration": 1.464575, + "exception": null, + "id": "autogen_plot3", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000560", + "duration": 2.479855, + "exception": null, + "id": "task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task1_ks__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_c__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phif__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_Cm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_h__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_tauh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ibk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ga__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_taun__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_n__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_isk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_reaction_0000004__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cell__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kc__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gsk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gcal__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ica__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sa__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ikdr__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_alpha__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_lambda__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_va__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_V__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ff__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cinf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phih__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vca__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phical__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `BIOMD0000000138_url` may be invalid.\r\n - The model file `/tmp/tmpyne0jvhm/./BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'LSODA/LSODAR hybrid method' (KISAO_0000560) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "simulatorDetails": [ + { + "key": "methodName", + "value": "lsoda" + }, + { + "key": "parameters", + "value": null + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "gillespy2": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/gillespy2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.14013, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpw3c__qs2/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "ginsim": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.239827, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpxz_0cvez/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "libsbmlsim": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/libsbmlsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.136508, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp_ti9exkh/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "masspy": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.195684, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mSedmlFeatureNotSupportedWarning\u001b[0m: \u001b[33m`/tmp/tmp0541o_1y/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "netpyne": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1", + "log_yml": { + "duration": 0.054786, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "neuron": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1", + "log_yml": { + "duration": 0.089654, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp6zvd7eaf/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "opencor": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1", + "log_yml": { + "duration": 0.082571, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp8lfs4oo0/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pyneuroml": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1", + "log_yml": { + "duration": 0.050177, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmphj27fwjc/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pysces": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1", + "log_yml": { + "duration": 6.349912, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n :'PysMod' object has no attribute 'lambda'", + "type": "CombineArchiveExecutionError" + }, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpue2cy78w/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpue2cy78w/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 6.037383, + "exception": { + "message": "The SED document did not execute successfully:\n\n :'PysMod' object has no attribute 'lambda'", + "type": "SedmlExecutionError" + }, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 3 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (3):\r\n autogen_plot1: 1 curves\r\n autogen_plot2: 1 curves\r\n autogen_plot3: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 4 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot1`\r\n `autogen_plot2`\r\n `autogen_plot3`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V1\r\nlambda is a reserved symbol, replacing with Lambda\r\n\r\n*******************************************************************\r\nIssues encountered in SBML translation (model processed anyway)\r\nSBML source: /tmp/tmpub1jsm9k.xml\r\n*******************************************************************\r\n\r\nReserved symbol lambda replaced with Lambda \r\n\r\n*******************************************************************\r\n\r\nInfo: single compartment model: locating \"reaction_0000004\" in default compartment\r\nWriting file: /tmp/tmpvmsv1kvp.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpub1jsm9k.xml\r\nout: /tmp/tmpvmsv1kvp.psc\r\nUsing model directory: /Pysces/psc\r\n/tmp/tmpvmsv1kvp.psc loading ..... \r\nParsing file: /tmp/tmpvmsv1kvp.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"vca\" has been initialised but does not occur in a rate equation\r\nInfo: \"vk\" has been initialised but does not occur in a rate equation\r\nInfo: \"Cm\" has been initialised but does not occur in a rate equation\r\nInfo: \"gk\" has been initialised but does not occur in a rate equation\r\nInfo: \"gcal\" has been initialised but does not occur in a rate equation\r\nInfo: \"gsk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ga\" has been initialised but does not occur in a rate equation\r\nInfo: \"gf\" has been initialised but does not occur in a rate equation\r\nInfo: \"vn\" has been initialised but does not occur in a rate equation\r\nInfo: \"va\" has been initialised but does not occur in a rate equation\r\nInfo: \"vm\" has been initialised but does not occur in a rate equation\r\nInfo: \"vh\" has been initialised but does not occur in a rate equation\r\nInfo: \"vf\" has been initialised but does not occur in a rate equation\r\nInfo: \"sn\" has been initialised but does not occur in a rate equation\r\nInfo: \"sa\" has been initialised but does not occur in a rate equation\r\nInfo: \"sm\" has been initialised but does not occur in a rate equation\r\nInfo: \"sh\" has been initialised but does not occur in a rate equation\r\nInfo: \"sf\" has been initialised but does not occur in a rate equation\r\nInfo: \"taun\" has been initialised but does not occur in a rate equation\r\nInfo: \"tauh\" has been initialised but does not occur in a rate equation\r\nInfo: \"Lambda\" has been initialised but does not occur in a rate equation\r\nInfo: \"ks\" has been initialised but does not occur in a rate equation\r\nInfo: \"phik\" has been initialised but does not occur in a rate equation\r\nInfo: \"phia\" has been initialised but does not occur in a rate equation\r\nInfo: \"phih\" has been initialised but does not occur in a rate equation\r\nInfo: \"phif\" has been initialised but does not occur in a rate equation\r\nInfo: \"phical\" has been initialised but does not occur in a rate equation\r\nInfo: \"cinf\" has been initialised but does not occur in a rate equation\r\nInfo: \"isk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ibk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ikdr\" has been initialised but does not occur in a rate equation\r\nInfo: \"ia\" has been initialised but does not occur in a rate equation\r\nInfo: \"ik\" has been initialised but does not occur in a rate equation\r\nInfo: \"n\" has been initialised but does not occur in a rate equation\r\nInfo: \"h\" has been initialised but does not occur in a rate equation\r\nInfo: \"V\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . no flux conservation\r\n done.\r\n \r\n\r\nAssignment rule(s) detected.\r\nRate rule(s) detected.\r\nINFO: RateRules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nINFO: Assignment Rules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nCVODE time for 100001 points: 3.946280002593994\r\nRateRules evaluated and added to mod.data_sim.\r\n \u001b[31mfailed - 'PysMod' object has no attribute 'lambda'\u001b[0m\r\n Generating 4 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 3: `autogen_plot2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 4: `autogen_plot3` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_c", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vca", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_Cm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gcal", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gsk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ga", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_va", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sa", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_taun", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_tauh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_lambda", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kc", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ks", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ff", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_alpha", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phih", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phif", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phical", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cinf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ica", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_isk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ibk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_n", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_h", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_V", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cell", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SKIPPED" + } + ], + "duration": 0.079275, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SKIPPED" + } + ], + "duration": 0.415905, + "exception": null, + "id": "autogen_plot1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_for_task1_V", + "status": "SKIPPED" + } + ], + "duration": 0.100176, + "exception": null, + "id": "autogen_plot2", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_for_task1_vk", + "status": "SKIPPED" + } + ], + "duration": 0.109016, + "exception": null, + "id": "autogen_plot3", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 5.14013, + "exception": { + "message": "'PysMod' object has no attribute 'lambda'", + "type": "AttributeError" + }, + "id": "task1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `auto_dg_for_task1_kc__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ks__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_va__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_lambda__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sa__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ga__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_taun__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gcal__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_h__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vca__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ica__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_alpha__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phical__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cell__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_V__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gsk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phif__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_Cm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_c__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_n__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_isk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ibk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_reaction_0000004__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_tauh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ff__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cinf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phih__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ikdr__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sm__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "rbapy": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.136502, + "exception": { + "message": "`/root/in/BIOMD0000000138_url.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmpcsezzj2y/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` may be invalid.\r\n - Model `BIOMD0000000138_url` may be invalid.\r\n - The model file `BIOMD0000000138_url.xml` may be invalid.\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((va - V) / sa))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((V - vh) / sh))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vf - V) / sf))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vm - V) / sm))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gcal * phical * (V - vca)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'pow(c, 2) / (pow(c, 2) + pow(ks, 2))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gsk * cinf * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gf * phif * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'gk * n * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'ga * phia * h * (V - vk)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'isk + ibk + ikdr + ia' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-(ica + ik) / Cm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression 'lambda * (phik - n) / taun' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(phih - h) / tauh' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '-ff * (alpha * ica + kc * c) * cell' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'Cm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gcal' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gsk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ga' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'gf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'va' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sn' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sa' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sm' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'sf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'taun' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'tauh' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'lambda' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'kc' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ks' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ff' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'alpha' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phih' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phif' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'phical' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'cinf' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ica' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'isk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ibk' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ikdr' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ia' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'ik' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'n' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'h' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'V' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "smoldyn": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1", + "log_yml": {}, + "detailed_error_log": {} + }, + "tellurium": { + "exception_message": "", + "log_yml": { + "duration": 19.62254, + "exception": null, + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmpxvgd3ay6/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe SED document is potentially incorrect.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe COMBINE/OMEX archive has warnings.\r\n - OMEX manifests should not contain content entries for themselves.\r\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` has warnings.\r\n - Model `BIOMD0000000138_url` has warnings.\r\n - The model file `BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning:\r\n\r\n\u001b[33m`/tmp/tmpxvgd3ay6/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n\r\n", + "sedDocuments": [ + { + "duration": 19.212037, + "exception": null, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 3 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (3):\r\n autogen_plot1: 1 curves\r\n autogen_plot2: 1 curves\r\n autogen_plot3: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 4 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot1`\r\n `autogen_plot2`\r\n `autogen_plot3`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 4 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 3: `autogen_plot2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 4: `autogen_plot3` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_c", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vca", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_Cm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gcal", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gsk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ga", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_va", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_taun", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_tauh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_lambda", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ks", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ff", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_alpha", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phih", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phif", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phical", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cinf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ica", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_isk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ibk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_n", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_h", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_V", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cell", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SUCCEEDED" + } + ], + "duration": 13.677893, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SUCCEEDED" + } + ], + "duration": 1.595941, + "exception": null, + "id": "autogen_plot1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_for_task1_V", + "status": "SUCCEEDED" + } + ], + "duration": 1.504026, + "exception": null, + "id": "autogen_plot2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_for_task1_vk", + "status": "SUCCEEDED" + } + ], + "duration": 1.504957, + "exception": null, + "id": "autogen_plot3", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 0.756946, + "exception": null, + "id": "task1", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33m- Variable `auto_dg_for_task1_va__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gsk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ff__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_taun__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ks__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_V__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ga__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phih__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_n__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cell__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_alpha__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_Cm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ibk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sn__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phia__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_tauh__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ikdr__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phical__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phif__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_cinf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_c__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vca__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vf__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_ica__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_kc__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_vm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_phik__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_isk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gk__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_lambda__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sm__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_h__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_reaction_0000004__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sa__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_gcal__x` has warnings.\r\n - XPath could not be validated.\r\n- Variable `auto_dg_for_task1_sf__x` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mModel `BIOMD0000000138_url` may be invalid.\r\n - The model file `/tmp/tmpxvgd3ay6/./BIOMD0000000138_url.xml` has warnings.\r\n - 16 warnings of type SBML unit consistency (99505). The following is the first warning at line 182, column 6:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '1 / (1 + exp((vn - V) / sn))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 40 warnings of type Modeling practice (80701). The following is the first warning at line 134, column 6:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'vca' does not have a 'units' attribute.\u001b[0m\r\n\r\n/usr/local/lib/python3.11/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning:\r\n\r\n\u001b[33m'CVODE' (KISAO_0000019) will be substituted for 'ODE solver' (KISAO_0000694) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n\r\n", + "simulatorDetails": [ + { + "key": "method", + "value": "simulate" + }, + { + "key": "solver", + "value": "cvode" + }, + { + "key": "relative_tolerance", + "value": 1e-06 + }, + { + "key": "absolute_tolerance", + "value": 1e-12 + }, + { + "key": "stiff", + "value": true + }, + { + "key": "maximum_bdf_order", + "value": 5 + }, + { + "key": "maximum_adams_order", + "value": 12 + }, + { + "key": "maximum_num_steps", + "value": 20000 + }, + { + "key": "maximum_time_step", + "value": 0.0 + }, + { + "key": "minimum_time_step", + "value": 0.0 + }, + { + "key": "initial_time_step", + "value": 0.0 + }, + { + "key": "multiple_steps", + "value": false + }, + { + "key": "variable_step_size", + "value": false + }, + { + "key": "max_output_rows", + "value": 100000 + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "vcell": { + "exception_message": "", + "log_yml": { + "duration": 51, + "exception": null, + "output": "Processing BIOMD0000000138_url.sedml. Done", + "sedDocuments": [ + { + "duration": null, + "exception": null, + "location": "BIOMD0000000138_url.sedml", + "output": "Initializing SED-ML document... done. Successful translation of SED-ML file. Building solvers and starting simulation of all tasks... Generating outputs... Generating CSV file... Done. Generating HDF5 file...", + "outputs": [ + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SUCCEEDED" + } + ], + "duration": null, + "exception": null, + "id": "autogen_plot1", + "output": null, + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_for_task1_V", + "status": "SUCCEEDED" + } + ], + "duration": null, + "exception": null, + "id": "autogen_plot2", + "output": null, + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_for_task1_vk", + "status": "SUCCEEDED" + } + ], + "duration": null, + "exception": null, + "id": "autogen_plot3", + "output": null, + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_c", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vca", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_Cm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gcal", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gsk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ga", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_gf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_va", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sn", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sa", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sm", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_sf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_taun", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_tauh", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_lambda", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_kc", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ks", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ff", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_alpha", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phih", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phif", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_phical", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cinf", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ica", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_isk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ibk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_n", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_h", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_V", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cell", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SUCCEEDED" + } + ], + "duration": null, + "exception": null, + "id": "autogen_report_for_task1", + "output": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 19, + "exception": null, + "id": "task1", + "output": "Initializing simulation job 0 ... done. Starting simulation... done.", + "simulatorDetails": null, + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "xpp": { + "exception_message": "Command '-i /root/in/BIOMD0000000138_url.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1", + "log_yml": { + "duration": 0.055421, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp_xh0paiw/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only a few features introduced after L1V3 are supported. Most newer features, such as finer stylistic control of plots and parameter estimation, are not yet supported.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + } +} \ No newline at end of file diff --git a/BioModels/BIOMD0000000138/tests/results_remote.json b/BioModels/BIOMD0000000138/tests/results_remote.json new file mode 100644 index 00000000..0a6b8b92 --- /dev/null +++ b/BioModels/BIOMD0000000138/tests/results_remote.json @@ -0,0 +1,1659 @@ +{ + "amici": [ + "FAIL", + "Failed to download amici results.", + "HTTPError" + ], + "brian2": [ + "FAIL", + "Failed to download brian2 results.", + "HTTPError" + ], + "bionetgen": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6735fca45a60072d20f5cf7e", + "download": "https://api.biosimulations.org/results/6735fca45a60072d20f5cf7e/download", + "logs": "https://api.biosimulations.org/logs/6735fca45a60072d20f5cf7e?includeOutput=true", + "log_yml": { + "duration": 12.710861, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "boolnet": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6735fca6b678b3883bb72747", + "download": "https://api.biosimulations.org/results/6735fca6b678b3883bb72747/download", + "logs": "https://api.biosimulations.org/logs/6735fca6b678b3883bb72747?includeOutput=true", + "log_yml": { + "duration": 0.183129, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "cbmpy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6735fca85a60072d20f5cf81", + "download": "https://api.biosimulations.org/results/6735fca85a60072d20f5cf81/download", + "logs": "https://api.biosimulations.org/logs/6735fca85a60072d20f5cf81?includeOutput=true", + "log_yml": { + "duration": 0.266413, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "cobrapy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6735fcaa0d09353e8f10cf46", + "download": "https://api.biosimulations.org/results/6735fcaa0d09353e8f10cf46/download", + "logs": "https://api.biosimulations.org/logs/6735fcaa0d09353e8f10cf46?includeOutput=true", + "log_yml": { + "duration": 0.173905, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "copasi": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6735fcad0d09353e8f10cf4c", + "download": "https://api.biosimulations.org/results/6735fcad0d09353e8f10cf4c/download", + "logs": "https://api.biosimulations.org/logs/6735fcad0d09353e8f10cf4c?includeOutput=true", + "log_yml": { + "duration": 31.82576, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 31.502274, + "exception": null, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 3 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (3):\r\n autogen_plot1: 1 curves\r\n autogen_plot2: 1 curves\r\n autogen_plot3: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 4 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot1`\r\n `autogen_plot2`\r\n `autogen_plot3`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 4 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `autogen_plot1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 3: `autogen_plot2` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 4: `autogen_plot3` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_c", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vca", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_vk", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_Cm", + "status": "SUCCEEDED" + }, + { + "id": 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"id": "autogen_task1_ia", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_ik", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_n", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_h", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_V", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_cell", + "status": "SUCCEEDED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SUCCEEDED" + } + ], + "duration": 21.243813, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SUCCEEDED" + } + ], + "duration": 2.297007, + "exception": null, + "id": "autogen_plot1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_for_task1_V", + "status": "SUCCEEDED" + } + ], + "duration": 1.976225, + "exception": null, + "id": "autogen_plot2", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "curves": [ + { + "id": "autogen_curve_for_task1_vk", + "status": "SUCCEEDED" + } + ], + "duration": 1.959338, + "exception": null, + "id": "autogen_plot3", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000560", + "duration": 3.857735, + "exception": null, + "id": "task1", + "output": "", + "simulatorDetails": [ + { + "key": "methodName", + "value": "lsoda" + }, + { + "key": "parameters", + "value": null + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + }, + "gillespy2": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6735fcafb678b3883bb72756", + "download": "https://api.biosimulations.org/results/6735fcafb678b3883bb72756/download", + "logs": "https://api.biosimulations.org/logs/6735fcafb678b3883bb72756?includeOutput=true", + "log_yml": { + "duration": 0.185009, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "ginsim": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6735fcb15a60072d20f5cf8f", + "download": "https://api.biosimulations.org/results/6735fcb15a60072d20f5cf8f/download", + "logs": "https://api.biosimulations.org/logs/6735fcb15a60072d20f5cf8f?includeOutput=true", + "log_yml": { + "duration": 0.177393, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "libsbmlsim": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6735fcb30d09353e8f10cf55", + "download": "https://api.biosimulations.org/results/6735fcb30d09353e8f10cf55/download", + "logs": "https://api.biosimulations.org/logs/6735fcb30d09353e8f10cf55?includeOutput=true", + "log_yml": { + "duration": 0.183238, + "exception": { + "message": "`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n - The SED-ML file at location `./BIOMD0000000138_url.sedml` is invalid.\n - Simulation `auto_ten_seconds` is invalid.\n - Algorithm has an invalid KiSAO id `KISAO_0000694`.", + "type": "ValueError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "masspy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6735fcb5b678b3883bb7275f", + "download": "https://api.biosimulations.org/results/6735fcb5b678b3883bb7275f/download", + "logs": "https://api.biosimulations.org/logs/6735fcb5b678b3883bb7275f?includeOutput=true", + "log_yml": { + "duration": 1.461313, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n \t`(model, errors) = validate_sbml_model(filename)`\n If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.955101, + "exception": { + "message": "The SED document did not execute successfully:\n\n Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n \t`(model, errors) = validate_sbml_model(filename)`\n If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .", + "type": "SedmlExecutionError" + }, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 3 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (3):\r\n autogen_plot1: 1 curves\r\n autogen_plot2: 1 curves\r\n autogen_plot3: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 4 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot1`\r\n `autogen_plot2`\r\n `autogen_plot3`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 4 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 3: `autogen_plot2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 4: `autogen_plot3` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_c", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vca", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_Cm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gcal", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gsk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ga", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_va", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sa", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_taun", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_tauh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_lambda", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kc", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ks", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ff", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_alpha", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phih", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phif", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phical", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cinf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ica", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_isk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ibk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_n", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_h", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_V", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cell", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SKIPPED" + } + ], + "duration": 0.066305, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SKIPPED" + } + ], + "duration": 0.319888, + "exception": null, + "id": "autogen_plot1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_for_task1_V", + "status": "SKIPPED" + } + ], + "duration": 0.123432, + "exception": null, + "id": "autogen_plot2", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_for_task1_vk", + "status": "SKIPPED" + } + ], + "duration": 0.138534, + "exception": null, + "id": "autogen_plot3", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.083005, + "exception": { + "message": "Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n\t`(model, errors) = validate_sbml_model(filename)`\nIf the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .", + "type": "MassSBMLError" + }, + "id": "task1", + "output": "\u001b[93mWARNING:\u001b[0m \u001b[93mModel does not contain SBML fbc package\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mModel does not contain SBML groups package\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'model_0000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'model_0000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + } + }, + "netpyne": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6735fcb7b678b3883bb72762", + "download": "https://api.biosimulations.org/results/6735fcb7b678b3883bb72762/download", + "logs": "https://api.biosimulations.org/logs/6735fcb7b678b3883bb72762?includeOutput=true", + "log_yml": { + "duration": 0.051625, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "neuron": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6735fcb9b678b3883bb72767", + "download": "https://api.biosimulations.org/results/6735fcb9b678b3883bb72767/download", + "logs": "https://api.biosimulations.org/logs/6735fcb9b678b3883bb72767?includeOutput=true", + "log_yml": { + "duration": 0.06773, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "opencor": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6735fcbab678b3883bb7276f", + "download": "https://api.biosimulations.org/results/6735fcbab678b3883bb7276f/download", + "logs": "https://api.biosimulations.org/logs/6735fcbab678b3883bb7276f?includeOutput=true", + "log_yml": { + "duration": 0.031996, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmptvny277r/./BIOMD0000000138_url.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "pyneuroml": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6735fcbdb678b3883bb72777", + "download": "https://api.biosimulations.org/results/6735fcbdb678b3883bb72777/download", + "logs": "https://api.biosimulations.org/logs/6735fcbdb678b3883bb72777?includeOutput=true", + "log_yml": { + "duration": 0.052296, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "pysces": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6735fcbf0d09353e8f10cf76", + "download": "https://api.biosimulations.org/results/6735fcbf0d09353e8f10cf76/download", + "logs": "https://api.biosimulations.org/logs/6735fcbf0d09353e8f10cf76?includeOutput=true", + "log_yml": { + "duration": 8.88908, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n :'PysMod' object has no attribute 'lambda'", + "type": "CombineArchiveExecutionError" + }, + "output": "libtk8.6.so: cannot open shared object file: No such file or directory\r\n\r\nPySCeS defaults to matplotlib's TKagg backend if not specified in the user configuration file, set \"matplotlib_backend = \" \r\nMatplotlib interface loaded (pysces.plt.m)\r\nPitcon routines available\r\nNLEQ2 routines available\r\nSBML support available\r\nYou are using NumPy (2.1.2) with SciPy (1.14.1)\r\nAssimulo CVode available\r\nRateChar is available\r\nParallel scanner is available\r\n\r\nPySCeS environment\r\n******************\r\npysces.model_dir = /home/FCAM/crbmapi/Pysces/psc\r\npysces.output_dir = /home/FCAM/crbmapi/Pysces\r\n\r\n\r\n***********************************************************************\r\n* Welcome to PySCeS (1.2.2) - Python Simulator for Cellular Systems *\r\n* http://pysces.sourceforge.net *\r\n* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2024 *\r\n* Triple-J Group for Molecular Cell Physiology *\r\n* Stellenbosch University, ZA and VU University Amsterdam, NL *\r\n* PySCeS is distributed under the PySCeS (BSD style) licence, see *\r\n* LICENCE.txt (supplied with this release) for details *\r\n* Please cite PySCeS with: doi:10.1093/bioinformatics/bti046 *\r\n***********************************************************************\r\n", + "sedDocuments": [ + { + "duration": 8.562459, + "exception": { + "message": "The SED document did not execute successfully:\n\n :'PysMod' object has no attribute 'lambda'", + "type": "SedmlExecutionError" + }, + "location": "BIOMD0000000138_url.sedml", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 3 plots:\r\n BIOMD0000000138_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 44 data sets\r\n Plots (3):\r\n autogen_plot1: 1 curves\r\n autogen_plot2: 1 curves\r\n autogen_plot3: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n Found 1 tasks and 4 outputs:\r\n Tasks:\r\n `task1`\r\n Outputs:\r\n `autogen_plot1`\r\n `autogen_plot2`\r\n `autogen_plot3`\r\n `autogen_report_for_task1`\r\n Executing task 1: `task1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V1\r\nlambda is a reserved symbol, replacing with Lambda\r\n\r\n*******************************************************************\r\nIssues encountered in SBML translation (model processed anyway)\r\nSBML source: /tmp/tmpku3lpobu.xml\r\n*******************************************************************\r\n\r\nReserved symbol lambda replaced with Lambda \r\n\r\n*******************************************************************\r\n\r\nInfo: single compartment model: locating \"reaction_0000004\" in default compartment\r\nWriting file: /tmp/tmp2s4xbeay.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpku3lpobu.xml\r\nout: /tmp/tmp2s4xbeay.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmp2s4xbeay.psc loading ..... \r\nParsing file: /tmp/tmp2s4xbeay.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"vca\" has been initialised but does not occur in a rate equation\r\nInfo: \"vk\" has been initialised but does not occur in a rate equation\r\nInfo: \"Cm\" has been initialised but does not occur in a rate equation\r\nInfo: \"gk\" has been initialised but does not occur in a rate equation\r\nInfo: \"gcal\" has been initialised but does not occur in a rate equation\r\nInfo: \"gsk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ga\" has been initialised but does not occur in a rate equation\r\nInfo: \"gf\" has been initialised but does not occur in a rate equation\r\nInfo: \"vn\" has been initialised but does not occur in a rate equation\r\nInfo: \"va\" has been initialised but does not occur in a rate equation\r\nInfo: \"vm\" has been initialised but does not occur in a rate equation\r\nInfo: \"vh\" has been initialised but does not occur in a rate equation\r\nInfo: \"vf\" has been initialised but does not occur in a rate equation\r\nInfo: \"sn\" has been initialised but does not occur in a rate equation\r\nInfo: \"sa\" has been initialised but does not occur in a rate equation\r\nInfo: \"sm\" has been initialised but does not occur in a rate equation\r\nInfo: \"sh\" has been initialised but does not occur in a rate equation\r\nInfo: \"sf\" has been initialised but does not occur in a rate equation\r\nInfo: \"taun\" has been initialised but does not occur in a rate equation\r\nInfo: \"tauh\" has been initialised but does not occur in a rate equation\r\nInfo: \"Lambda\" has been initialised but does not occur in a rate equation\r\nInfo: \"ks\" has been initialised but does not occur in a rate equation\r\nInfo: \"phik\" has been initialised but does not occur in a rate equation\r\nInfo: \"phia\" has been initialised but does not occur in a rate equation\r\nInfo: \"phih\" has been initialised but does not occur in a rate equation\r\nInfo: \"phif\" has been initialised but does not occur in a rate equation\r\nInfo: \"phical\" has been initialised but does not occur in a rate equation\r\nInfo: \"cinf\" has been initialised but does not occur in a rate equation\r\nInfo: \"isk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ibk\" has been initialised but does not occur in a rate equation\r\nInfo: \"ikdr\" has been initialised but does not occur in a rate equation\r\nInfo: \"ia\" has been initialised but does not occur in a rate equation\r\nInfo: \"ik\" has been initialised but does not occur in a rate equation\r\nInfo: \"n\" has been initialised but does not occur in a rate equation\r\nInfo: \"h\" has been initialised but does not occur in a rate equation\r\nInfo: \"V\" has been initialised but does not occur in a rate equation\r\n \r\nCalculating L matrix . . . . . . . done.\r\nCalculating K matrix . . . . . . . no flux conservation\r\n done.\r\n \r\n\r\nAssignment rule(s) detected.\r\nRate rule(s) detected.\r\nINFO: RateRules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nINFO: Assignment Rules detected and Assimulo installed,\r\nswitching to CVODE (mod.mode_integrator='CVODE').\r\n\r\nCVODE time for 100001 points: 6.472142934799194\r\nRateRules evaluated and added to mod.data_sim.\r\n \u001b[31mfailed - 'PysMod' object has no attribute 'lambda'\u001b[0m\r\n Generating 4 outputs ...\r\n Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `autogen_plot1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 3: `autogen_plot2` ... \u001b[36mqueued\u001b[0m\r\n Generating output 4: `autogen_plot3` ...", + "outputs": [ + { + "dataSets": [ + { + "id": "autogen_time_for_task1", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_c", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vca", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_Cm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gcal", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gsk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ga", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_gf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_va", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_vf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sn", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sa", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sm", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_sf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_taun", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_tauh", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_lambda", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_kc", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ks", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ff", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_alpha", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phih", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phif", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_phical", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cinf", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ica", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_isk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ibk", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ikdr", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ia", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_ik", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_n", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_h", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_V", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_cell", + "status": "SKIPPED" + }, + { + "id": "autogen_task1_reaction_0000004", + "status": "SKIPPED" + } + ], + "duration": 0.074844, + "exception": null, + "id": "autogen_report_for_task1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_task1_c", + "status": "SKIPPED" + } + ], + "duration": 0.279991, + "exception": null, + "id": "autogen_plot1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "curves": [ + { + "id": "autogen_curve_for_task1_V", + "status": "SKIPPED" + } + ], + "duration": 0.109229, + "exception": null, + "id": 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"skipReason": null, + "status": "QUEUED" + } + ], + "skipReason": null, + "status": "QUEUED", + "tasks": [ + { + "algorithm": null, + "duration": null, + "exception": null, + "id": "task1", + "output": null, + "simulatorDetails": null, + "skipReason": null, + "status": "QUEUED" + } + ] + } + ], + "skipReason": null, + "status": "QUEUED" + } + }, + "xpp": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6735fccab678b3883bb727b2", + "download": "https://api.biosimulations.org/results/6735fccab678b3883bb727b2/download", + "logs": "https://api.biosimulations.org/logs/6735fccab678b3883bb727b2?includeOutput=true", + "log_yml": { + "duration": 0.045202, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + } +} \ No newline at end of file diff --git a/BioModels/test_biomodels_compatibility_biosimulators.py b/BioModels/test_biomodels_compatibility_biosimulators.py new file mode 100644 index 00000000..9f30f049 --- /dev/null +++ b/BioModels/test_biomodels_compatibility_biosimulators.py @@ -0,0 +1,168 @@ +import re +import os +import urllib +import sys +import shutil + +sys.path.append("..") +import utils +engines = utils.ENGINES +API_URL: str = "https://www.ebi.ac.uk/biomodels" + +out_format="json" +max_count = 0 #0 for unlimited +tmp_dir = "tmplocalfiles" +suppress_stdout = True +suppress_stderr = True +fix_broken_ref = True +skip = {} + +def download_file(model_id,filename,output_file,cache): + ''' + request the given file and save it to disk + ''' + + qfilename = urllib.parse.quote_plus(filename) + + response = cache.do_request(f'{API_URL}/model/download/{model_id}?filename={qfilename}').content + + with open(output_file,"wb") as fout: + fout.write(response) + +def replace_model_xml(sedml_path,sbml_filename): + ''' + if the SEDML refers to a generic "model.xml" file + and the SBML file is not called this + replace the SEDML reference with the actual SBML filename + + method used assumes 'source="model.xml"' will only + occur in the SBML file reference + which was true at time of testing on current BioModels release + + returns True if the SBML reference already seemed valid + ''' + + if sbml_filename == "model.xml": return True + + with open(sedml_path,encoding='utf-8') as f: + data = f.read() + + if not 'source="model.xml"' in data: return True + + data = data.replace('source="model.xml"',f'source="{sbml_filename}"') + + with open(f'{sedml_path}',"w",encoding="utf-8") as fout: + fout.write(data) + + return False + +def download_sbml_file(model_id,info,cache): + sbml_file = info['files']['main'][0]['name'] + try: + download_file(model_id,sbml_file,sbml_file,cache) + except Exception as e: + raise Exception(f"Error downloading {sbml_file} for {model_id}: {e}") + + return sbml_file + +def download_sedml_file(model_id,info,cache,sbml_file): + + if not 'additional' in info['files']: + print(f"no additional files for {model_id}") + + sedml_file = [] + for file_info in info['files']['additional']: + pattern = 'SED[-]?ML' + target = f"{file_info['name']}|{file_info['description']}".upper() + if re.search(pattern,target): + sedml_file.append(file_info['name']) + sedml_file = sedml_file[0] + + try: + download_file(model_id,sedml_file,sedml_file,cache) + except Exception as e: + print(f"Error downloading {sedml_file} for {model_id}: {e}") + + #if the sedml file contains a generic 'source="model.xml"' replace it with the sbml filename + if fix_broken_ref: + replace_model_xml(sedml_file,sbml_file) + + return sedml_file + +def main(): + ''' + download the BioModel model files, run various validation steps + report the results as a markdown table README file with a summary row at the top + ''' + + #mode="off" to disable caching, "store" to wipe and store fresh results, "reuse" to use the stored cache + cache = utils.RequestCache(mode="store",direc="cache") + count = 0 + starting_dir = os.getcwd() + + model_ids = cache.do_request(f"{API_URL}/model/identifiers?format={out_format}").json()['models'] + if biomodel_id_list != None: + model_ids = biomodel_id_list + + + for model_id in model_ids: + + if max_count > 0 and count >= max_count: break + count += 1 + print(f"\r{model_id} {count}/{len(model_ids)} ",end='') + + #BIOMD ids should be the curated models + if not 'BIOMD' in model_id: + continue + if count in skip or model_id in skip: + continue + + info = cache.do_request(f"{API_URL}/{model_id}?format={out_format}").json() + + tmp_model_dir = os.path.join(starting_dir,tmp_dir,model_id) + os.makedirs(tmp_model_dir,exist_ok=True) + os.chdir(tmp_model_dir) + + sbml_file = download_sbml_file(model_id,info,cache) + sbml_file_path = os.path.join(tmp_model_dir,sbml_file) + if not sbml_file: continue + sedml_file = download_sedml_file(model_id,info,cache,sbml_file) + sedml_file_path = os.path.join(tmp_model_dir,sedml_file) + if not sedml_file: continue + + print(f'\ntesting {sbml_file}...') + + new_subfolder = model_id + new_directory = os.path.join(starting_dir, new_subfolder) + os.makedirs(new_directory, exist_ok=True) + + new_sbml_file_path = os.path.join(new_directory, os.path.basename(sbml_file)) + new_sedml_file_path = os.path.join(new_directory, os.path.basename(sedml_file)) + + paths_exist = os.path.exists(new_sbml_file_path) and os.path.exists(new_sedml_file_path) + if use_original_files or not paths_exist: + print (f"Copying {sbml_file} and {sedml_file} to {starting_dir}/{new_subfolder}") + shutil.copy(sbml_file_path, new_sbml_file_path) + shutil.copy(sedml_file_path, new_sedml_file_path) + + os.chdir(new_directory) + print(f"Changed to {new_directory}") + + engine_ids = list(engines.keys()) + # engine_ids = engine_list if engine_list is not None else engine_ids + + test_folder = 'tests' + utils.run_biosimulators_remotely_and_locally(engine_ids, + os.path.basename(sedml_file_path), + os.path.basename(sbml_file_path), + os.path.join(test_folder,'d1_plots_remote'), + os.path.join(test_folder,'d1_plots_local'), + test_folder=test_folder) + + shutil.rmtree(tmp_model_dir) + + +if __name__ == "__main__": + use_original_files = False + biomodel_id_list = ["BIOMD0000000001","BIOMD0000000138"] + main() diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md index e41ce7f0..0a977f5d 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
| | | +|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatible with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

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

The SED document did not execute successfully:

Language for model `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 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 `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 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 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 | +|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatible with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

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

The SED document did not execute successfully:

Simulation `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
| | | +|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatible with netpyne.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

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

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatible with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

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

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatible with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

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

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatible with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | |
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.

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

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatible with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

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

The SED document did not execute successfully:

Language for model `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 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 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 +|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatible with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/utils/__init__.py b/utils/__init__.py index 1b7e4eaf..7fad17b0 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -461,17 +461,21 @@ def check_file_compatibility_test(engine, model_filepath, experiment_filepath): if file_extensions in engine_filetypes_tuple_list: file_types = [TYPES[i] for i in file_extensions] return 'pass', (f"The file extensions {file_extensions} suggest the input file types are '{file_types}'. {compatible_filetypes} are compatible with {engine}.") + if 'xml' in file_extensions: - if 'sbml' in model_filepath and 'sedml' not in model_filepath: - if 'sbml' in experiment_filepath and 'sedml' in experiment_filepath: - file_types = ('sbml', 'sedml') - if file_types in engine_filetypes_tuple_list: - return 'pass', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {[TYPES[i] for i in file_types]} which is compatible with {engine}.

{compatible_filetypes} are compatible with {engine}.") - else: - return 'unsure', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {[TYPES[i] for i in file_types]} which is not compatible with {engine}.

{compatible_filetypes} are compatible with {engine}.") + model_sbml = 'sbml' in model_filepath + model_sedml = 'sedml' in model_filepath + experiment_sbml = 'sbml' in experiment_filepath + experiment_sedml = 'sedml' in experiment_filepath + + if model_sbml and experiment_sbml and experiment_sedml and not model_sedml: + file_types = [TYPES[i] for i in ('sbml', 'sedml') ] + return 'pass', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {file_types} which is compatible with {engine}.

{compatible_filetypes} are compatible with {engine}.") + else: + return 'unsure', (f"The file extensions {file_extensions} suggest the input file types may be compatible with {engine}.

{compatible_filetypes} are compatible with {engine}.") else: - return 'unsure', (f"The file extensions {file_extensions} suggest the input file types may not be compatibe with {engine}.

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

{compatible_filetypes} are compatible with {engine}.") + def collapsible_content(content, title='Details'): """ @@ -1018,14 +1022,14 @@ def safe_md_string(value): import time -def download_file_from_link(engine, download_link, output_file='results.zip', max_wait_time=120, wait_time=2): +def download_file_from_link(engine, download_link, output_file='results.zip', max_wait_time=600, wait_time=2): """ Function to download a file from a given URL. Parameters: download_link (str): The URL of the file to download. output_file (str): The name of the file to save the download as. Defaults to 'results.zip'. - max_wait_time (int): The maximum time to wait for the file to be ready to download. Defaults to 120 seconds. + max_wait_time (int): The maximum time to wait for the file to be ready to download. Defaults to 300 seconds. wait_time (int): The time to wait between checks if the file is ready to download. Defaults to 2 seconds. Returns: @@ -1035,23 +1039,16 @@ def download_file_from_link(engine, download_link, output_file='results.zip', ma start_time = time.time() while True: - # Check status of download_link response = requests.get(download_link) - - # If status is not 404 or max_wait_time has passed, break the loop if response.status_code != 404 or time.time() - start_time > max_wait_time: break - - # Wait for wait_time seconds before checking again time.sleep(wait_time) - # If status == 200 then download the results if response.status_code == 200: print(f'Downloading {engine} results...') with requests.get(download_link, stream=True) as r: with open(output_file, 'wb') as f: shutil.copyfileobj(r.raw, f) - # filepath where the file is downloaded filepath = os.path.abspath(output_file) return filepath else: