diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md index 1cf019a..e4cedfa 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) | Error (R) | Error (L) | Type (R) | d1 (R) | d1 (L) | -|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------|:------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------| -| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
| ✅ PASS | ✅ PASS | | | | plot | plot | -| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
| ⚠ XFAIL | ⚠ XFAIL |
DetailsThe 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`).
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```
|
CAEECombineArchiveExecutionError
| plot | plot | -| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
| ⚠ XFAIL | ⚠ XFAIL |
DetailsThe 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).
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```
|
CAEECombineArchiveExecutionError
| plot | plot | -| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2
| ⚠ XFAIL | ⚠ XFAIL |
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```
|
MNFEModuleNotFoundError
| | | -| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
| ❌ FAIL | ❌ FAIL |
DetailsThe 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
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```
|
CAEECombineArchiveExecutionError
| plot | plot | -| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
| ❌ FAIL | ❌ FAIL |
DetailsThe 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
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```
|
CAEECombineArchiveExecutionError
| plot | plot | -| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi
| ✅ PASS | ✅ PASS | | | | plot | plot | -| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2
| ✅ PASS | ✅ PASS | | | | plot | plot | -| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
| ⚠ XFAIL | ⚠ XFAIL |
DetailsThe 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
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```
|
CAEECombineArchiveExecutionError
| plot | plot | -| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim
| ✅ PASS | ✅ PASS | | | | plot | plot | -| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
| ❌ FAIL | ❌ FAIL |
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```
|
CAEECombineArchiveExecutionError
| plot | plot | -| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne
| ⚠ XFAIL | ⚠ XFAIL |
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```
|
MNFEModuleNotFoundError
| | | -| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
| ⚠ XFAIL | ⚠ XFAIL |
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```
|
MNFEModuleNotFoundError
| | | -| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
| ⚠ XFAIL | ⚠ XFAIL |
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```
|
MNFEModuleNotFoundError
| | | -| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
| ⚠ XFAIL | ⚠ XFAIL |
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```
|
MNFEModuleNotFoundError
| | | -| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
| ❌ FAIL | ❌ FAIL |
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Model at /tmp/tmp1bq_quiv/./LEMS_NML2_Ex9_FN.sbml could not be imported:

File /tmp/tmp1bq_quiv/./LEMS_NML2_Ex9_FN.sbml.xml does not exist
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```
|
CAEECombineArchiveExecutionError
| plot | plot | -| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
| ⚠ XFAIL | ⚠ XFAIL |
DetailsThe 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`).
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```
|
CAEECombineArchiveExecutionError
| plot | plot | -| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldyn
| ⚠ XFAIL | ⚠ XFAIL |
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```
|
MNFEModuleNotFoundError
| | | -| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium
| ✅ PASS | ✅ PASS | | | | plot | plot | -| 19 |
vcellhttps://github.com/virtualcell/vcell
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
| | ❌ FAIL | |
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```
| | | | -| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
| ⚠ XFAIL | ⚠ XFAIL |
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```
|
MNFEModuleNotFoundError
| | | \ No newline at end of file +| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------| +| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
|
❌ FAILview
download
logs

ERROR MESSAGE:
Reached maximum number of steps

|
❌ FAILERROR MESSAGE:
Reached maximum number of steps

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

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

view
download
logs

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

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

The SED document did not execute successfully:

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

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

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

view
download
logs

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

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

The SED document did not execute successfully:

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

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

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

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

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

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

The SED document did not execute successfully:

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

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

The SED document did not execute successfully:

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

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

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

The SED document did not execute successfully:

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

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

The SED document did not execute successfully:

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

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

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

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

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

view
download
logs

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

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

The SED document did not execute successfully:

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

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

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

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

The SED document did not execute successfully:

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

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

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

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

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

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

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

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

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

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

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

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

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

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

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

The SED document did not execute successfully:

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


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

The SED document did not execute successfully:

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


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

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

view
download
logs

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

The SED document did not execute successfully:

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

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

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

The SED document did not execute successfully:

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

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

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

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

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

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

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

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

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

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

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/SBML/tests/results_local.json b/SBML/tests/results_local.json new file mode 100644 index 0000000..adada99 --- /dev/null +++ b/SBML/tests/results_local.json @@ -0,0 +1,1265 @@ +{ + "amici": { + "exception_message": "", + "log_yml": { + "duration": 14.539468, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 14.02876, + "exception": null, + "location": "tmp873033", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp873033:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp873033 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SUCCEEDED" + }, + { + "id": "curve_W", + "status": "SUCCEEDED" + } + ], + "duration": 0.673566, + "exception": null, + "id": "d1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SUCCEEDED" + }, + { + "id": "ex9_V", + "status": "SUCCEEDED" + }, + { + "id": "ex9_W", + "status": "SUCCEEDED" + } + ], + "duration": 0.256373, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000496", + "duration": 13.028354, + "exception": null, + "id": "sim1_net1", + "output": "2024-11-01 14:26:12.406 - amici.swig_wrappers - ERROR - [OTHER] AMICI simulation failed: Reached maximum number of steps 10000 before reaching tout at t=99.66.\r\n2024-11-01 14:26:12.406 - amici.swig_wrappers - DEBUG - [BACKTRACE] The previous error occurred at:\r\n2 0x7fdf59c6ea8b /usr/local/lib/python3.11/site-packages/amici/_amici.cpython-311-x86_64-linux-gnu.so(+0xb5a8b) [0x7fdf59c6ea8b]\r\n3 0x7fdf59d62262 amici::Solver::run(double) const + 34\r\n4 0x7fdf59d9a5d0 amici::ForwardProblem::workForwardProblem() + 1728\r\n5 0x7fdf59d4e763 amici::runAmiciSimulation(amici::Solver&, amici::ExpData const*, amici::Model&, bool) + 435\r\n6 0x7fdf59cf8280 /usr/local/lib/python3.11/site-packages/amici/_amici.cpython-311-x86_64-linux-gnu.so(+0x13f\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/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1", + "log_yml": { + "duration": 0.062713, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "bionetgen": { + "exception_message": "Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1", + "log_yml": { + "duration": 0.75498, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Language for model `net1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.|$)` such as `urn:sedml:language:bngl`).", + "type": "CombineArchiveExecutionError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `net1` has warnings.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'I' 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 `./tmp727758` has warnings.\r\n - Model `net1` has warnings.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'I' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 0.41883, + "exception": { + "message": "The SED document did not execute successfully:\n\n Language for model `net1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.|$)` such as `urn:sedml:language:bngl`).", + "type": "SedmlExecutionError" + }, + "location": "tmp727758", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp727758:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp727758 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SKIPPED" + }, + { + "id": "curve_W", + "status": "SKIPPED" + } + ], + "duration": 0.251054, + "exception": null, + "id": "d1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SKIPPED" + }, + { + "id": "ex9_V", + "status": "SKIPPED" + }, + { + "id": "ex9_W", + "status": "SKIPPED" + } + ], + "duration": 0.061473, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.025634, + "exception": { + "message": "Language for model `net1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.|$)` such as `urn:sedml:language:bngl`).", + "type": "ValueError" + }, + "id": "sim1_net1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "boolnet": { + "exception_message": "Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1", + "log_yml": { + "duration": 0.816403, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Simulation `sim1` is invalid.\n - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).", + "type": "CombineArchiveExecutionError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `net1` may be invalid.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` 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 '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully 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 'I' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SEC' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of 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 \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'W' 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 `./tmp713633` may be invalid.\r\n - Model `net1` may be invalid.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` 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 '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully 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 'I' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SEC' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of 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 \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'W' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 0.471202, + "exception": { + "message": "The SED document did not execute successfully:\n\n Simulation `sim1` is invalid.\n - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).", + "type": "SedmlExecutionError" + }, + "location": "tmp713633", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp713633:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp713633 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SKIPPED" + }, + { + "id": "curve_W", + "status": "SKIPPED" + } + ], + "duration": 0.272143, + "exception": null, + "id": "d1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SKIPPED" + }, + { + "id": "ex9_V", + "status": "SKIPPED" + }, + { + "id": "ex9_W", + "status": "SKIPPED" + } + ], + "duration": 0.067113, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.032377, + "exception": { + "message": "Simulation `sim1` is invalid.\n - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).", + "type": "ValueError" + }, + "id": "sim1_net1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cbmpy": { + "exception_message": "Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.933566, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n UniformTimeCourseSimulation `sim1` is not supported.\n - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:\n - SteadyStateSimulation", + "type": "CombineArchiveExecutionError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `net1` has warnings.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'I' 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 `./tmp270883` has warnings.\r\n - Model `net1` has warnings.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'I' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 0.461954, + "exception": { + "message": "The SED document did not execute successfully:\n\n UniformTimeCourseSimulation `sim1` is not supported.\n - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:\n - SteadyStateSimulation", + "type": "SedmlExecutionError" + }, + "location": "tmp270883", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp270883:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp270883 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SKIPPED" + }, + { + "id": "curve_W", + "status": "SKIPPED" + } + ], + "duration": 0.27073, + "exception": null, + "id": "d1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SKIPPED" + }, + { + "id": "ex9_V", + "status": "SKIPPED" + }, + { + "id": "ex9_W", + "status": "SKIPPED" + } + ], + "duration": 0.061414, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.028861, + "exception": { + "message": "UniformTimeCourseSimulation `sim1` is not supported.\n - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:\n - SteadyStateSimulation", + "type": "ValueError" + }, + "id": "sim1_net1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "cobrapy": { + "exception_message": "Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1", + "log_yml": { + "duration": 1.11712, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n UniformTimeCourseSimulation `sim1` is not supported.\n - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:\n - SteadyStateSimulation", + "type": "CombineArchiveExecutionError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `net1` has warnings.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'I' 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 `./tmp380384` has warnings.\r\n - Model `net1` has warnings.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'I' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 0.511567, + "exception": { + "message": "The SED document did not execute successfully:\n\n UniformTimeCourseSimulation `sim1` is not supported.\n - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:\n - SteadyStateSimulation", + "type": "SedmlExecutionError" + }, + "location": "tmp380384", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp380384:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp380384 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SKIPPED" + }, + { + "id": "curve_W", + "status": "SKIPPED" + } + ], + "duration": 0.256911, + "exception": null, + "id": "d1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SKIPPED" + }, + { + "id": "ex9_V", + "status": "SKIPPED" + }, + { + "id": "ex9_W", + "status": "SKIPPED" + } + ], + "duration": 0.098905, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.029987, + "exception": { + "message": "UniformTimeCourseSimulation `sim1` is not supported.\n - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:\n - SteadyStateSimulation", + "type": "ValueError" + }, + "id": "sim1_net1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "copasi": { + "exception_message": "", + "log_yml": { + "duration": 2.862886, + "exception": null, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `net1` has warnings.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'I' 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 `./tmp778931` has warnings.\r\n - Model `net1` has warnings.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'I' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 1.873996, + "exception": null, + "location": "tmp778931", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp778931:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp778931 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SUCCEEDED" + }, + { + "id": "curve_W", + "status": "SUCCEEDED" + } + ], + "duration": 0.876977, + "exception": null, + "id": "d1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SUCCEEDED" + }, + { + "id": "ex9_V", + "status": "SUCCEEDED" + }, + { + "id": "ex9_W", + "status": "SUCCEEDED" + } + ], + "duration": 0.499028, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000560", + "duration": 0.180886, + "exception": null, + "id": "sim1_net1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `DISPLAY__d1_W_fnPop1_0_W` has warnings.\r\n - XPath could not be validated.\r\n- Variable `DISPLAY__d1_V_fnPop1_0_V` has warnings.\r\n - XPath could not be validated.\r\n- Variable `OUTPUT__of1_V_fnPop1_0_V` has warnings.\r\n - XPath could not be validated.\r\n- Variable `OUTPUT__of1_W_fnPop1_0_W` 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 `net1` may be invalid.\r\n - The model file `/tmp/tmpdxlb6qj2/./LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'I' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.10/site-packages/kisao/utils.py:518: AlgorithmSubstitutedWarning: \u001b[33m'LSODA/LSODAR hybrid method' (KISAO_0000560) will be substituted for 'CVODE' (KISAO_0000019) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "simulatorDetails": [ + { + "key": "methodName", + "value": "lsoda" + }, + { + "key": "parameters", + "value": null + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "gillespy2": { + "exception_message": "", + "log_yml": { + "duration": 1.39855, + "exception": null, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `net1` has warnings.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'I' 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 `./tmp567968` has warnings.\r\n - Model `net1` has warnings.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'I' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 1.149878, + "exception": null, + "location": "tmp567968", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp567968:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp567968 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SUCCEEDED" + }, + { + "id": "curve_W", + "status": "SUCCEEDED" + } + ], + "duration": 0.654028, + "exception": null, + "id": "d1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SUCCEEDED" + }, + { + "id": "ex9_V", + "status": "SUCCEEDED" + }, + { + "id": "ex9_W", + "status": "SUCCEEDED" + } + ], + "duration": 0.267502, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000088", + "duration": 0.149073, + "exception": null, + "id": "sim1_net1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `OUTPUT__of1_W_fnPop1_0_W` has warnings.\r\n - XPath could not be validated.\r\n- Variable `OUTPUT__of1_V_fnPop1_0_V` has warnings.\r\n - XPath could not be validated.\r\n- Variable `DISPLAY__d1_W_fnPop1_0_W` has warnings.\r\n - XPath could not be validated.\r\n- Variable `DISPLAY__d1_V_fnPop1_0_V` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/kisao/utils.py:477: AlgorithmSubstitutedWarning: \u001b[33m'LSODA' (KISAO_0000088) will be substituted for 'CVODE'' (KISAO_0000019) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "simulatorDetails": [ + { + "key": "method", + "value": "gillespy2.solvers.numpy.ode_solver.ODESolver" + }, + { + "key": "arguments", + "value": { + "integrator": "lsoda" + } + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "ginsim": { + "exception_message": "Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1", + "log_yml": { + "duration": 0.849976, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Simulation `sim1` is invalid.\n - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:\n Output start time: 0.0\n Output end time: 200.0\n Number of steps: 20000", + "type": "CombineArchiveExecutionError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `net1` may be invalid.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` 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 '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully 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 'I' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SEC' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of 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 \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'W' 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 `./tmp946431` may be invalid.\r\n - Model `net1` may be invalid.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` 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 '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully 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 'I' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SEC' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of 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 \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'W' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 0.628725, + "exception": { + "message": "The SED document did not execute successfully:\n\n Simulation `sim1` is invalid.\n - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:\n Output start time: 0.0\n Output end time: 200.0\n Number of steps: 20000", + "type": "SedmlExecutionError" + }, + "location": "tmp946431", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp946431:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp946431 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SKIPPED" + }, + { + "id": "curve_W", + "status": "SKIPPED" + } + ], + "duration": 0.32766, + "exception": null, + "id": "d1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SKIPPED" + }, + { + "id": "ex9_V", + "status": "SKIPPED" + }, + { + "id": "ex9_W", + "status": "SKIPPED" + } + ], + "duration": 0.06087, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.026721, + "exception": { + "message": "Simulation `sim1` is invalid.\n - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:\n Output start time: 0.0\n Output end time: 200.0\n Number of steps: 20000", + "type": "ValueError" + }, + "id": "sim1_net1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "libsbmlsim": { + "exception_message": "", + "log_yml": { + "duration": 5.083417, + "exception": null, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `net1` may be invalid.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` 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 '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully 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 'I' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SEC' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of 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 \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'W' 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 `./tmp87798` may be invalid.\r\n - Model `net1` may be invalid.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` 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 '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully 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 'I' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SEC' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of 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 \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'W' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 4.80478, + "exception": null, + "location": "tmp87798", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp87798:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp87798 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SUCCEEDED" + }, + { + "id": "curve_W", + "status": "SUCCEEDED" + } + ], + "duration": 0.879194, + "exception": null, + "id": "d1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SUCCEEDED" + }, + { + "id": "ex9_V", + "status": "SUCCEEDED" + }, + { + "id": "ex9_W", + "status": "SUCCEEDED" + } + ], + "duration": 0.310704, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000086", + "duration": 3.29071, + "exception": null, + "id": "sim1_net1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `OUTPUT__of1_W_fnPop1_0_W` may be invalid.\r\n - XPath could not be validated.\r\n- Variable `DISPLAY__d1_V_fnPop1_0_V` may be invalid.\r\n - XPath could not be validated.\r\n- Variable `OUTPUT__of1_V_fnPop1_0_V` may be invalid.\r\n - XPath could not be validated.\r\n- Variable `DISPLAY__d1_W_fnPop1_0_W` may be invalid.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `net1` may be invalid.\r\n - The model file `/tmp/tmpijizwxs3/./LEMS_NML2_Ex9_FN.sbml` 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 '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully 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 'I' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SEC' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of 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 \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'W' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/kisao/utils.py:477: AlgorithmSubstitutedWarning: \u001b[33m'Fehlberg method' (KISAO_0000086) will be substituted for 'CVODE'' (KISAO_0000019) at substitution policy 'SIMILAR_VARIABLES'.\u001b[0m\r\n warnings.warn(termcolor.colored(msg, 'yellow'), AlgorithmSubstitutedWarning)\r\n", + "simulatorDetails": [ + { + "key": "method", + "value": "simulateSBMLFromFile" + }, + { + "key": "arguments", + "value": { + "dt": 0.0001, + "method": 51, + "print_amount": 0, + "print_interval": 100, + "sim_time": 200.0, + "use_lazy_method": 0 + } + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "masspy": { + "exception_message": "Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1", + "log_yml": { + "duration": 1.477645, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n \t`(model, errors) = validate_sbml_model(filename)`\n If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .", + "type": "CombineArchiveExecutionError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `net1` has warnings.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'I' 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 `./tmp447344` has warnings.\r\n - Model `net1` has warnings.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'I' does not have a 'units' attribute.\u001b[0m\r\n", + "sedDocuments": [ + { + "duration": 0.756498, + "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": "tmp447344", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp447344:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp447344 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SKIPPED" + }, + { + "id": "curve_W", + "status": "SKIPPED" + } + ], + "duration": 0.317979, + "exception": null, + "id": "d1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mIllogicalVizWarning\u001b[0m: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mIllogicalVizWarning\u001b[0m: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mIllogicalVizWarning\u001b[0m: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mIllogicalVizWarning\u001b[0m: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SKIPPED" + }, + { + "id": "ex9_V", + "status": "SKIPPED" + }, + { + "id": "ex9_W", + "status": "SKIPPED" + } + ], + "duration": 0.076109, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.055729, + "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": "sim1_net1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33m- Variable `OUTPUT__of1_W_fnPop1_0_W` has warnings.\r\n - XPath could not be validated.\r\n- Variable `DISPLAY__d1_V_fnPop1_0_V` has warnings.\r\n - XPath could not be validated.\r\n- Variable `OUTPUT__of1_V_fnPop1_0_V` has warnings.\r\n - XPath could not be validated.\r\n- Variable `DISPLAY__d1_W_fnPop1_0_W` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31 \u001b[1;31mBioSimulatorsWarning\u001b[0m: \u001b[33mModel `net1` may be invalid.\r\n - The model file `/tmp/tmpw762zeum/./LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'I' does not have a 'units' attribute.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mSBML model is written as Level 2 Version 2, will attempt to convert the SBML model from Level 2 Version 2 to Level 3 Version 1 before parsing\u001b[0m\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "netpyne": { + "exception_message": "Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1", + "log_yml": { + "duration": 0.044627, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "neuron": { + "exception_message": "Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1", + "log_yml": { + "duration": 0.0335, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "opencor": { + "exception_message": "Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1", + "log_yml": { + "duration": 0.052168, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pyneuroml": { + "exception_message": "Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1", + "log_yml": { + "duration": 0.050431, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "pysces": { + "exception_message": "Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1", + "log_yml": { + "duration": 2.667261, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n :\n Unable to generate Stoichiometric Matrix! model has:\n 0 reactions\n 0 species\n what did you have in mind?\n ", + "type": "CombineArchiveExecutionError" + }, + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `net1` has warnings.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'I' 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 `./tmp924087` has warnings.\r\n - Model `net1` has warnings.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'I' does not have a 'units' attribute.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 2.154212, + "exception": { + "message": "The SED document did not execute successfully:\n\n :\n Unable to generate Stoichiometric Matrix! model has:\n 0 reactions\n 0 species\n what did you have in mind?\n ", + "type": "SedmlExecutionError" + }, + "location": "tmp924087", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp924087:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp924087 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V2\r\n\r\n*******************************************************************\r\nIssues encountered in SBML translation (model processed anyway)\r\nSBML source: /tmp/tmpnulg_2g2.xml\r\n*******************************************************************\r\n\r\nNo free species!? ... help I'm confused! \r\n\r\n*******************************************************************\r\n\r\nWriting file: /tmp/tmpkg3wptnk.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpnulg_2g2.xml\r\nout: /tmp/tmpkg3wptnk.psc\r\nUsing model directory: /Pysces/psc\r\n/tmp/tmpkg3wptnk.psc loading ..... \r\nParsing file: /tmp/tmpkg3wptnk.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"I\" has been initialised but does not occur in a rate equation\r\nInfo: \"SEC\" 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\nInfo: \"W\" has been initialised but does not occur in a rate equation\r\n \r\n \u001b[31mfailed - \r\nUnable to generate Stoichiometric Matrix! model has:\r\n0 reactions\r\n0 species\r\nwhat did you have in mind?\r\n\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SKIPPED" + }, + { + "id": "curve_W", + "status": "SKIPPED" + } + ], + "duration": 0.586719, + "exception": null, + "id": "d1", + "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" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SKIPPED" + }, + { + "id": "ex9_V", + "status": "SKIPPED" + }, + { + "id": "ex9_W", + "status": "SKIPPED" + } + ], + "duration": 0.14359, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 1.098613, + "exception": { + "message": "\nUnable to generate Stoichiometric Matrix! model has:\n0 reactions\n0 species\nwhat did you have in mind?\n", + "type": "AssertionError" + }, + "id": "sim1_net1", + "output": "/usr/local/lib/python3.10/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `OUTPUT__of1_W_fnPop1_0_W` has warnings.\r\n - XPath could not be validated.\r\n- Variable `OUTPUT__of1_V_fnPop1_0_V` has warnings.\r\n - XPath could not be validated.\r\n- Variable `DISPLAY__d1_W_fnPop1_0_W` has warnings.\r\n - XPath could not be validated.\r\n- Variable `DISPLAY__d1_V_fnPop1_0_V` has warnings.\r\n - XPath could not be validated.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "rbapy": { + "exception_message": "Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1", + "log_yml": { + "duration": 0.650455, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Language for model `net1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.|$)` such as `urn:sedml:language:rba`).", + "type": "CombineArchiveExecutionError" + }, + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n - Model `net1` may be invalid.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` 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 '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully 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 'I' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SEC' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of 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 \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'W' 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 `./tmp268456` may be invalid.\r\n - Model `net1` may be invalid.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` 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 '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n \r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '0.08 * (V + (0.7 - 0.8 * W)) / SEC' cannot be fully 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 'I' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'SEC' does not have a 'units' attribute.\r\n \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of 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 \r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'W' does not have a 'units' attribute.\r\n \u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "sedDocuments": [ + { + "duration": 0.392611, + "exception": { + "message": "The SED document did not execute successfully:\n\n Language for model `net1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.|$)` such as `urn:sedml:language:rba`).", + "type": "SedmlExecutionError" + }, + "location": "tmp268456", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp268456:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp268456 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SKIPPED" + }, + { + "id": "curve_W", + "status": "SKIPPED" + } + ], + "duration": 0.230887, + "exception": null, + "id": "d1", + "output": "/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent x axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mCurves have inconsistent y axis scales. All curves will be plotted in linear scale.\u001b[0m\r\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SKIPPED" + }, + { + "id": "ex9_V", + "status": "SKIPPED" + }, + { + "id": "ex9_W", + "status": "SKIPPED" + } + ], + "duration": 0.046698, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.026157, + "exception": { + "message": "Language for model `net1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.|$)` such as `urn:sedml:language:rba`).", + "type": "ValueError" + }, + "id": "sim1_net1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + }, + "smoldyn": { + "exception_message": "Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.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": 2.355827, + "exception": null, + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33mThe SED document is potentially incorrect.\r\n - Model `net1` has warnings.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'I' 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 `./tmp732941` has warnings.\r\n - Model `net1` has warnings.\r\n - The model file `LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'I' does not have a 'units' attribute.\u001b[0m\r\n\r\n", + "sedDocuments": [ + { + "duration": 1.607307, + "exception": null, + "location": "tmp732941", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp732941:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp732941 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SUCCEEDED" + }, + { + "id": "curve_W", + "status": "SUCCEEDED" + } + ], + "duration": 0.75985, + "exception": null, + "id": "d1", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning:\r\n\r\n\u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n\r\n", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SUCCEEDED" + }, + { + "id": "ex9_V", + "status": "SUCCEEDED" + }, + { + "id": "ex9_W", + "status": "SUCCEEDED" + } + ], + "duration": 0.265557, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 0.193093, + "exception": null, + "id": "sim1_net1", + "output": "/usr/local/lib/python3.11/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\u001b[33m- Variable `DISPLAY__d1_W_fnPop1_0_W` has warnings.\r\n - XPath could not be validated.\r\n- Variable `OUTPUT__of1_W_fnPop1_0_W` has warnings.\r\n - XPath could not be validated.\r\n- Variable `OUTPUT__of1_V_fnPop1_0_V` has warnings.\r\n - XPath could not be validated.\r\n- Variable `DISPLAY__d1_V_fnPop1_0_V` 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 `net1` may be invalid.\r\n - The model file `/tmp/tmpn8bg7xgx/./LEMS_NML2_Ex9_FN.sbml` has warnings.\r\n - 2 warnings of type SBML unit consistency (99505). The following is the first warning at line 40, column 12:\r\n - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n The units of the expression '(V - pow(V, 3) / 3 - W + I) / SEC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n - 4 warnings of type Modeling practice (80701). The following is the first warning at line 32, column 12:\r\n - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n The with the id 'I' does not have a 'units' attribute.\u001b[0m\r\n\r\n", + "simulatorDetails": [ + { + "key": "method", + "value": "simulate" + }, + { + "key": "solver", + "value": "cvode" + }, + { + "key": "relative_tolerance", + "value": 1e-06 + }, + { + "key": "absolute_tolerance", + "value": 1e-12 + }, + { + "key": "stiff", + "value": true + }, + { + "key": "maximum_bdf_order", + "value": 5 + }, + { + "key": "maximum_adams_order", + "value": 12 + }, + { + "key": "maximum_num_steps", + "value": 20000 + }, + { + "key": "maximum_time_step", + "value": 0.0 + }, + { + "key": "minimum_time_step", + "value": 0.0 + }, + { + "key": "initial_time_step", + "value": 0.0 + }, + { + "key": "multiple_steps", + "value": false + }, + { + "key": "variable_step_size", + "value": false + }, + { + "key": "max_output_rows", + "value": 100000 + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": {} + }, + "vcell": { + "exception_message": "Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1", + "log_yml": { + "duration": 3, + "exception": null, + "output": "Processing tmp645125. Done", + "sedDocuments": [], + "skipReason": null, + "status": "SUCCEEDED" + }, + "detailed_error_log": { + "status": "FAIL", + "error_message": "Runtime Exception" + } + }, + "xpp": { + "exception_message": "Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1", + "log_yml": { + "duration": 0.061486, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + }, + "detailed_error_log": {} + } +} \ No newline at end of file diff --git a/SBML/tests/results_remote.json b/SBML/tests/results_remote.json new file mode 100644 index 0000000..67ba91e --- /dev/null +++ b/SBML/tests/results_remote.json @@ -0,0 +1,1358 @@ +{ + "amici": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672364ffb678b3883bb574ba", + "download": "https://api.biosimulations.org/results/672364ffb678b3883bb574ba/download", + "logs": "https://api.biosimulations.org/logs/672364ffb678b3883bb574ba?includeOutput=true", + "log_yml": { + "duration": 19.478039, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 19.098796, + "exception": null, + "location": "tmp395914", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp395914:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp395914 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SUCCEEDED" + }, + { + "id": "curve_W", + "status": "SUCCEEDED" + } + ], + "duration": 0.756623, + "exception": null, + "id": "d1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SUCCEEDED" + }, + { + "id": "ex9_V", + "status": "SUCCEEDED" + }, + { + "id": "ex9_W", + "status": "SUCCEEDED" + } + ], + "duration": 0.296161, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000496", + "duration": 17.966963, + "exception": null, + "id": "sim1_net1", + "output": "2024-10-31 07:08:08.154 - amici.swig_wrappers - ERROR - [OTHER] AMICI simulation failed: Reached maximum number of steps 10000 before reaching tout at t=99.66.\r\n2024-10-31 07:08:08.154 - amici.swig_wrappers - DEBUG - [BACKTRACE] The previous error occurred at:\r\n2 0x7ffff3462a8b /usr/local/lib/python3.11/site-packages/amici/_amici.cpython-311-x86_64-linux-gnu.so(+0xb5a8b) [0x7ffff3462a8b]\r\n3 0x7ffff3556262 amici::Solver::run(double) const + 34\r\n4 0x7ffff358e5d0 amici::ForwardProblem::workForwardProblem() + 1728\r\n5 0x7ffff3542763 amici::runAmiciSimulation(amici::Solver&, amici::ExpData const*, amici::Model&, bool) + 435\r\n6 0x7ffff34ec280 /usr/local/lib/python3.11/site-packages/amici/_amici.cpython-311-x86_64-linux-gnu.so(+0x13f\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" + } + }, + "brian2": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67236501b678b3883bb574bd", + "download": "https://api.biosimulations.org/results/67236501b678b3883bb574bd/download", + "logs": "https://api.biosimulations.org/logs/67236501b678b3883bb574bd?includeOutput=true", + "log_yml": { + "duration": 0.049725, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "bionetgen": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672365030d09353e8f0f21c1", + "download": "https://api.biosimulations.org/results/672365030d09353e8f0f21c1/download", + "logs": "https://api.biosimulations.org/logs/672365030d09353e8f0f21c1?includeOutput=true", + "log_yml": { + "duration": 0.56944, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Language for model `net1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.|$)` such as `urn:sedml:language:bngl`).", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.32309, + "exception": { + "message": "The SED document did not execute successfully:\n\n Language for model `net1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.|$)` such as `urn:sedml:language:bngl`).", + "type": "SedmlExecutionError" + }, + "location": "tmp908348", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp908348:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp908348 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SKIPPED" + }, + { + "id": "curve_W", + "status": "SKIPPED" + } + ], + "duration": 0.148064, + "exception": null, + "id": "d1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SKIPPED" + }, + { + "id": "ex9_V", + "status": "SKIPPED" + }, + { + "id": "ex9_W", + "status": "SKIPPED" + } + ], + "duration": 0.05807, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.026347, + "exception": { + "message": "Language for model `net1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.|$)` such as `urn:sedml:language:bngl`).", + "type": "ValueError" + }, + "id": "sim1_net1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + } + }, + "boolnet": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672365055a60072d20f42483", + "download": "https://api.biosimulations.org/results/672365055a60072d20f42483/download", + "logs": "https://api.biosimulations.org/logs/672365055a60072d20f42483?includeOutput=true", + "log_yml": { + "duration": 0.576474, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Simulation `sim1` is invalid.\n - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.331967, + "exception": { + "message": "The SED document did not execute successfully:\n\n Simulation `sim1` is invalid.\n - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).", + "type": "SedmlExecutionError" + }, + "location": "tmp444384", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp444384:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp444384 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SKIPPED" + }, + { + "id": "curve_W", + "status": "SKIPPED" + } + ], + "duration": 0.148167, + "exception": null, + "id": "d1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SKIPPED" + }, + { + "id": "ex9_V", + "status": "SKIPPED" + }, + { + "id": "ex9_W", + "status": "SKIPPED" + } + ], + "duration": 0.065588, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.028671, + "exception": { + "message": "Simulation `sim1` is invalid.\n - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).", + "type": "ValueError" + }, + "id": "sim1_net1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + } + }, + "cbmpy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67236507b678b3883bb574c0", + "download": "https://api.biosimulations.org/results/67236507b678b3883bb574c0/download", + "logs": "https://api.biosimulations.org/logs/67236507b678b3883bb574c0?includeOutput=true", + "log_yml": { + "duration": 0.63583, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n UniformTimeCourseSimulation `sim1` is not supported.\n - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:\n - SteadyStateSimulation", + "type": "CombineArchiveExecutionError" + }, + "output": "\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling *\r\n* http://cbmpy.sourceforge.net *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019 *\r\n* Dept. of Systems Bioinformatics *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project *\r\n* Distributed under the GNU GPL v 3.0 licence, see *\r\n* LICENCE (supplied with this release) for details *\r\n***********************************************************************\r\n\r\n", + "sedDocuments": [ + { + "duration": 0.30786, + "exception": { + "message": "The SED document did not execute successfully:\n\n UniformTimeCourseSimulation `sim1` is not supported.\n - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. 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Simulation must be an instance of one of the following:\n - SteadyStateSimulation", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.342356, + "exception": { + "message": "The SED document did not execute successfully:\n\n UniformTimeCourseSimulation `sim1` is not supported.\n - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:\n - SteadyStateSimulation", + "type": "SedmlExecutionError" + }, + "location": "tmp889066", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp889066:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp889066 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SKIPPED" + }, + { + "id": "curve_W", + "status": "SKIPPED" + } + ], + "duration": 0.170833, + "exception": null, + "id": "d1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SKIPPED" + }, + { + "id": "ex9_V", + "status": "SKIPPED" + }, + { + "id": "ex9_W", + "status": "SKIPPED" + } + ], + "duration": 0.05885, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.02883, + "exception": { + "message": "UniformTimeCourseSimulation `sim1` is not supported.\n - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. 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The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:\n Output start time: 0.0\n Output end time: 200.0\n Number of steps: 20000", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.35478, + "exception": { + "message": "The SED document did not execute successfully:\n\n Simulation `sim1` is invalid.\n - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:\n Output start time: 0.0\n Output end time: 200.0\n Number of steps: 20000", + "type": "SedmlExecutionError" + }, + "location": "tmp464659", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp464659:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp464659 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SKIPPED" + }, + { + "id": "curve_W", + "status": "SKIPPED" + } + ], + "duration": 0.175627, + "exception": null, + "id": "d1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SKIPPED" + }, + { + "id": "ex9_V", + "status": "SKIPPED" + }, + { + "id": "ex9_W", + "status": "SKIPPED" + } + ], + "duration": 0.06116, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.030889, + "exception": { + "message": "Simulation `sim1` is invalid.\n - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:\n Output start time: 0.0\n Output end time: 200.0\n Number of steps: 20000", + "type": "ValueError" + }, + "id": "sim1_net1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + } + }, + "libsbmlsim": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672365110d09353e8f0f21d1", + "download": "https://api.biosimulations.org/results/672365110d09353e8f0f21d1/download", + "logs": "https://api.biosimulations.org/logs/672365110d09353e8f0f21d1?includeOutput=true", + "log_yml": { + "duration": 9.430935, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 9.147262, + "exception": null, + "location": "tmp293345", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp293345:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp293345 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SUCCEEDED" + }, + { + "id": "curve_W", + "status": "SUCCEEDED" + } + ], + "duration": 1.069012, + "exception": null, + "id": "d1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SUCCEEDED" + }, + { + "id": "ex9_V", + "status": "SUCCEEDED" + }, + { + "id": "ex9_W", + "status": "SUCCEEDED" + } + ], + "duration": 0.462325, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000086", + "duration": 7.510757, + "exception": null, + "id": "sim1_net1", + "output": "", + "simulatorDetails": [ + { + "key": "method", + "value": "simulateSBMLFromFile" + }, + { + "key": "arguments", + "value": { + "dt": 0.0001, + "method": 51, + "print_amount": 0, + "print_interval": 100, + "sim_time": 200.0, + "use_lazy_method": 0 + } + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + }, + "masspy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672365125a60072d20f42493", + "download": "https://api.biosimulations.org/results/672365125a60072d20f42493/download", + "logs": "https://api.biosimulations.org/logs/672365125a60072d20f42493?includeOutput=true", + "log_yml": { + "duration": 2.548897, + "exception": null, + "output": "", + "sedDocuments": [ + { + "duration": 1.975757, + "exception": null, + "location": "tmp318145", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp318145:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp318145 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SUCCEEDED" + }, + { + "id": "curve_W", + "status": "SUCCEEDED" + } + ], + "duration": 1.190302, + "exception": null, + "id": "d1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SUCCEEDED" + }, + { + "id": "ex9_V", + "status": "SUCCEEDED" + }, + { + "id": "ex9_W", + "status": "SUCCEEDED" + } + ], + "duration": 0.460042, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 0.219986, + "exception": null, + "id": "sim1_net1", + "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 metabolites in model.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo reactions in model.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo compartments found in model. 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Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2024 *\r\n* Triple-J Group for Molecular Cell Physiology *\r\n* Stellenbosch University, ZA and VU University Amsterdam, NL *\r\n* PySCeS is distributed under the PySCeS (BSD style) licence, see *\r\n* LICENCE.txt (supplied with this release) for details *\r\n* Please cite PySCeS with: doi:10.1093/bioinformatics/bti046 *\r\n***********************************************************************\r\n", + "sedDocuments": [ + { + "duration": 1.570343, + "exception": { + "message": "The SED document did not execute successfully:\n\n :\n Unable to generate Stoichiometric Matrix! model has:\n 0 reactions\n 0 species\n what did you have in mind?\n ", + "type": "SedmlExecutionError" + }, + "location": "tmp334490", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp334490:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp334490 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V2\r\n\r\n*******************************************************************\r\nIssues encountered in SBML translation (model processed anyway)\r\nSBML source: /tmp/tmpyxj7t8de.xml\r\n*******************************************************************\r\n\r\nNo free species!? ... help I'm confused! \r\n\r\n*******************************************************************\r\n\r\nWriting file: /tmp/tmpcqqq_2ah.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpyxj7t8de.xml\r\nout: /tmp/tmpcqqq_2ah.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmpcqqq_2ah.psc loading ..... \r\nParsing file: /tmp/tmpcqqq_2ah.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"I\" has been initialised but does not occur in a rate equation\r\nInfo: \"SEC\" 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\nInfo: \"W\" has been initialised but does not occur in a rate equation\r\n \r\n \u001b[31mfailed - \r\nUnable to generate Stoichiometric Matrix! model has:\r\n0 reactions\r\n0 species\r\nwhat did you have in mind?\r\n\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SKIPPED" + }, + { + "id": "curve_W", + "status": "SKIPPED" + } + ], + "duration": 0.355719, + "exception": null, + "id": "d1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SKIPPED" + }, + { + "id": "ex9_V", + "status": "SKIPPED" + }, + { + "id": "ex9_W", + "status": "SKIPPED" + } + ], + "duration": 0.053872, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 1.084021, + "exception": { + "message": "\nUnable to generate Stoichiometric Matrix! model has:\n0 reactions\n0 species\nwhat did you have in mind?\n", + "type": "AssertionError" + }, + "id": "sim1_net1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + } + }, + "rbapy": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6723651cb678b3883bb57506", + "download": "https://api.biosimulations.org/results/6723651cb678b3883bb57506/download", + "logs": "https://api.biosimulations.org/logs/6723651cb678b3883bb57506?includeOutput=true", + "log_yml": { + "duration": 0.631232, + "exception": { + "message": "The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Language for model `net1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.|$)` such as `urn:sedml:language:rba`).", + "type": "CombineArchiveExecutionError" + }, + "output": "", + "sedDocuments": [ + { + "duration": 0.35197, + "exception": { + "message": "The SED document did not execute successfully:\n\n Language for model `net1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.|$)` such as `urn:sedml:language:rba`).", + "type": "SedmlExecutionError" + }, + "location": "tmp674654", + "output": "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n tmp674654:\r\n Tasks (1):\r\n sim1_net1\r\n Reports (1):\r\n ex9: 3 data sets\r\n Plots (1):\r\n d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp674654 ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `sim1_net1`\r\n Outputs:\r\n `d1`\r\n `ex9`\r\n Executing task 1: `sim1_net1`\r\n Executing simulation ... \u001b[31mfailed\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `d1` ... \u001b[36mqueued\u001b[0m\r\n Generating output 2: `ex9` ...", + "outputs": [ + { + "curves": [ + { + "id": "curve_V", + "status": "SKIPPED" + }, + { + "id": "curve_W", + "status": "SKIPPED" + } + ], + "duration": 0.173169, + "exception": null, + "id": "d1", + "output": "", + "skipReason": null, + "status": "SKIPPED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SKIPPED" + }, + { + "id": "ex9_V", + "status": "SKIPPED" + }, + { + "id": "ex9_W", + "status": "SKIPPED" + } + ], + "duration": 0.060541, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SKIPPED" + } + ], + "skipReason": null, + "status": "FAILED", + "tasks": [ + { + "algorithm": null, + "duration": 0.029105, + "exception": { + "message": "Language for model `net1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.|$)` such as `urn:sedml:language:rba`).", + "type": "ValueError" + }, + "id": "sim1_net1", + "output": "", + "simulatorDetails": null, + "skipReason": null, + "status": "FAILED" + } + ] + } + ], + "skipReason": null, + "status": "FAILED" + } + }, + "smoldyn": { + "response": 201, + "view": "https://api.biosimulations.org/runs/6723651e0d09353e8f0f2222", + "download": "https://api.biosimulations.org/results/6723651e0d09353e8f0f2222/download", + "logs": "https://api.biosimulations.org/logs/6723651e0d09353e8f0f2222?includeOutput=true", + "log_yml": { + "duration": 0.062326, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + }, + "tellurium": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672365200d09353e8f0f222c", + "download": 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"SUCCEEDED" + }, + { + "id": "curve_W", + "status": "SUCCEEDED" + } + ], + "duration": 0.872073, + "exception": null, + "id": "d1", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + }, + { + "dataSets": [ + { + "id": "ex9_time", + "status": "SUCCEEDED" + }, + { + "id": "ex9_V", + "status": "SUCCEEDED" + }, + { + "id": "ex9_W", + "status": "SUCCEEDED" + } + ], + "duration": 0.321507, + "exception": null, + "id": "ex9", + "output": "", + "skipReason": null, + "status": "SUCCEEDED" + } + ], + "skipReason": null, + "status": "SUCCEEDED", + "tasks": [ + { + "algorithm": "KISAO_0000019", + "duration": 0.165095, + "exception": null, + "id": "sim1_net1", + "output": "", + "simulatorDetails": [ + { + "key": "method", + "value": "simulate" + }, + { + "key": "solver", + "value": "cvode" + }, + { + "key": "relative_tolerance", + "value": 1e-06 + }, + { + "key": "absolute_tolerance", + "value": 1e-12 + }, + { + "key": "stiff", + "value": true + }, + { + "key": "maximum_bdf_order", + "value": 5 + }, + { + "key": "maximum_adams_order", + "value": 12 + }, + { + "key": "maximum_num_steps", + "value": 20000 + }, + { + "key": "maximum_time_step", + "value": 0.0 + }, + { + "key": "minimum_time_step", + "value": 0.0 + }, + { + "key": "initial_time_step", + "value": 0.0 + }, + { + "key": "multiple_steps", + "value": false + }, + { + "key": "variable_step_size", + "value": false + }, + { + "key": "max_output_rows", + "value": 100000 + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + ] + } + ], + "skipReason": null, + "status": "SUCCEEDED" + } + }, + "vcell": { + "response": 201, + "view": "https://api.biosimulations.org/runs/67236523b678b3883bb57531", + "download": "https://api.biosimulations.org/results/67236523b678b3883bb57531/download", + "logs": "https://api.biosimulations.org/logs/67236523b678b3883bb57531?includeOutput=true", + "log_yml": { + "duration": null, + "exception": null, + "output": null, + "sedDocuments": [], + "skipReason": null, + "status": "QUEUED" + } + }, + "xpp": { + "response": 201, + "view": "https://api.biosimulations.org/runs/672365250d09353e8f0f2240", + "download": "https://api.biosimulations.org/results/672365250d09353e8f0f2240/download", + "logs": "https://api.biosimulations.org/logs/672365250d09353e8f0f2240?includeOutput=true", + "log_yml": { + "duration": 0.060589, + "exception": { + "message": "No module named 'libsbml'", + "type": "ModuleNotFoundError" + }, + "output": "", + "sedDocuments": [], + "skipReason": null, + "status": "FAILED" + } + } +} \ No newline at end of file diff --git a/SBML/tests/test_biosimulators_local.py b/SBML/tests/test_biosimulators_local.py index 0f59f7a..d96c396 100644 --- a/SBML/tests/test_biosimulators_local.py +++ b/SBML/tests/test_biosimulators_local.py @@ -2,8 +2,7 @@ """ This script tests the compatibility of different biosimulation engines with a given SBML and SED-ML file. -It runs each engine and records the result (pass/fail) and any error messages encountered during the simulation. -The results are then displayed in a table and saved to a markdown file. +It runs each engine and saves a JSON file with the log.yml file (as a dict), and the d1 plot for each engine. """ import sys @@ -11,6 +10,7 @@ sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))) # to import utils import utils import argparse +import json # Save the current working directory cwd = os.getcwd() @@ -38,8 +38,15 @@ print('d1 plots will be saved in:', d1_plots_local_dir) -results_local = utils.run_biosimulators_locally(sedml_file_name=sedml_file_name, +engine_keys = list(utils.ENGINES.keys()) + +results_local = utils.run_biosimulators_locally(engine_keys, + sedml_file_name=sedml_file_name, sbml_file_name=sbml_file_name, d1_plots_local_dir=d1_plots_local_dir, test_folder=test_folder) + +results_local_path = os.path.join(path_to_sbml_folder, 'tests', 'results_local.json') +with open(results_local_path, 'w') as fp: + json.dump(results_local, fp, indent=4) \ No newline at end of file diff --git a/SBML/tests/test_biosimulators_remote.py b/SBML/tests/test_biosimulators_remote.py index 20896eb..d4227ec 100644 --- a/SBML/tests/test_biosimulators_remote.py +++ b/SBML/tests/test_biosimulators_remote.py @@ -2,8 +2,8 @@ """ This script tests the compatibility of different biosimulation engines with a given SBML and SED-ML file. -It runs each engine and records the result (pass/fail) and any error messages encountered during the simulation. -The results are then displayed in a table and saved to a markdown file. +It runs each engine and saves the d1 plots, and a JSON file containing the log.yml file (as dict) and the +links for accessing the remote results, for each engine. """ import sys @@ -11,6 +11,8 @@ sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))) # to import utils import utils import argparse +import json + # Save the current working directory cwd = os.getcwd() @@ -38,8 +40,14 @@ print('d1 plots will be saved in:', d1_plots_remote_dir) -results_remote = utils.run_biosimulators_remotely(sedml_file_name=sedml_file_name, +engine_keys = list(utils.ENGINES.keys()) + +results_remote = utils.run_biosimulators_remotely(engine_keys, sedml_file_name=sedml_file_name, sbml_file_name=sbml_file_name, d1_plots_remote_dir=d1_plots_remote_dir, test_folder=test_folder) + +results_remote_path = os.path.join(path_to_sbml_folder, 'tests', 'results_remote.json') +with open(results_remote_path, 'w') as fp: + json.dump(results_remote, fp, indent=4) \ No newline at end of file diff --git a/SBML/tests/test_compatibility_biosimulators.py b/SBML/tests/test_compatibility_biosimulators.py index 07bafd3..e712c0b 100644 --- a/SBML/tests/test_compatibility_biosimulators.py +++ b/SBML/tests/test_compatibility_biosimulators.py @@ -42,7 +42,10 @@ print('d1 plots will be saved in:', d1_plots_remote_dir, 'and', d1_plots_local_dir) -utils.run_biosimulators_remotely_and_locally(sedml_file_name, +engine_keys = list(utils.ENGINES.keys()) + +utils.run_biosimulators_remotely_and_locally(engine_keys, + sedml_file_name, sbml_file_name, d1_plots_remote_dir, d1_plots_local_dir, diff --git a/SBML/tests/test_creation_combined_results_table.py b/SBML/tests/test_creation_combined_results_table.py index 0db286c..6dd57d2 100644 --- a/SBML/tests/test_creation_combined_results_table.py +++ b/SBML/tests/test_creation_combined_results_table.py @@ -3,6 +3,7 @@ sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))) # to import utils import utils import argparse +import json engines = utils.ENGINES @@ -31,11 +32,18 @@ d1_plots_local_dir = os.path.join(test_folder, args.output_dir + '_local') d1_plots_remote_dir = os.path.join(test_folder, args.output_dir + '_remote') -results_local = {'amici': 'pass', 'brian2': ['other', "```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```"], 'bionetgen': ['other', "```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```"], 'boolnet': ['other', "```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```"], 'cbmpy': ['other', "```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```"], 'cobrapy': ['other', "```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```"], 'copasi': 'pass', 'gillespy2': 'pass', 'ginsim': ['other', "```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```"], 'libsbmlsim': 'pass', 'masspy': ['other', "```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```"], 'netpyne': ['other', "```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```"], 'neuron': ['other', "```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```"], 'opencor': ['other', "```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```"], 'pyneuroml': ['other', "```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```"], 'pysces': ['other', "```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```"], 'rbapy': ['other', "```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```"], 'smoldyn': ['other', "```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```"], 'tellurium': 'pass', 'vcell': ['other', "```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```"], 'xpp': ['other', "```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```"]} -results_remote = {'amici': ['pass', '', ''], 'brian2': ['FAIL', "No module named 'libsbml'", 'ModuleNotFoundError'], 'bionetgen': ['FAIL', 'The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Language for model `net1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\\.|$)` such as `urn:sedml:language:bngl`).', 'CombineArchiveExecutionError'], 'boolnet': ['FAIL', 'The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Simulation `sim1` is invalid.\n - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).', 'CombineArchiveExecutionError'], 'cbmpy': ['FAIL', 'The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n UniformTimeCourseSimulation `sim1` is not supported.\n - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:\n - SteadyStateSimulation', 'CombineArchiveExecutionError'], 'cobrapy': ['FAIL', 'The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n UniformTimeCourseSimulation `sim1` is not supported.\n - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:\n - SteadyStateSimulation', 'CombineArchiveExecutionError'], 'copasi': ['pass', '', ''], 'gillespy2': ['pass', '', ''], 'ginsim': ['FAIL', 'The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Simulation `sim1` is invalid.\n - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:\n Output start time: 0.0\n Output end time: 200.0\n Number of steps: 20000', 'CombineArchiveExecutionError'], 'libsbmlsim': ['pass', '', ''], 'masspy': ['FAIL', '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 .', 'CombineArchiveExecutionError'], 'netpyne': ['FAIL', "No module named 'libsbml'", 'ModuleNotFoundError'], 'neuron': ['FAIL', "No module named 'libsbml'", 'ModuleNotFoundError'], 'opencor': ['FAIL', "No module named 'libsbml'", 'ModuleNotFoundError'], 'pyneuroml': ['FAIL', "No module named 'libsbml'", 'ModuleNotFoundError'], 'pysces': ['FAIL', 'The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Model at /tmp/tmp1bq_quiv/./LEMS_NML2_Ex9_FN.sbml could not be imported:\n \n File /tmp/tmp1bq_quiv/./LEMS_NML2_Ex9_FN.sbml.xml does not exist', 'CombineArchiveExecutionError'], 'rbapy': ['FAIL', 'The COMBINE/OMEX did not execute successfully:\n\n The SED document did not execute successfully:\n \n Language for model `net1` is not supported.\n - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\\.|$)` such as `urn:sedml:language:rba`).', 'CombineArchiveExecutionError'], 'smoldyn': ['FAIL', "No module named 'libsbml'", 'ModuleNotFoundError'], 'tellurium': ['pass', '', ''], 'vcell': [None, '', ''], 'xpp': ['FAIL', "No module named 'libsbml'", 'ModuleNotFoundError']} +results_paths = { + "local": os.path.join(path_to_sbml_folder, 'tests', 'results_local.json'), + "remote": os.path.join(path_to_sbml_folder, 'tests', 'results_remote.json') +} -results_table = utils.create_combined_results_table(results_remote, - results_local, +results = {} +for key, path in results_paths.items(): + with open(path, 'r') as f: + results[key] = json.load(f) + +results_table = utils.create_combined_results_table(results["remote"], + results["local"], sedml_file_name, sbml_file_name, d1_plots_local_dir, diff --git a/test_suite/test_test_suite_compatibility_biosimulators.py b/test_suite/test_test_suite_compatibility_biosimulators.py index 1a1a590..a7b790e 100644 --- a/test_suite/test_test_suite_compatibility_biosimulators.py +++ b/test_suite/test_test_suite_compatibility_biosimulators.py @@ -134,7 +134,7 @@ def process_cases(args): os.path.basename(sbml_file_path), os.path.join(test_folder,'d1_plots_remote'), os.path.join(test_folder,'d1_plots_local'), - engines=engines, test_folder=test_folder) + test_folder=test_folder) if __name__ == "__main__": diff --git a/utils/__init__.py b/utils/__init__.py index e6dbf57..6b41d69 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -157,6 +157,7 @@ # (currently only tellurium) # key is the tag/category used to report the category, value is a regex matching the error message # see MarkdownTable.process_engine_outcomes +# TODO: use error categories in process_log_yml_dict error_categories=\ { "tellurium": @@ -366,8 +367,6 @@ def find_file_in_dir(file_name, directory): list_of_files.append(file_path) return list_of_files - -# write definition to create d1 plots dict def d1_plots_dict(d1_plots_path='d1_plots'): """ Create a dictionary with engine names as keys and d1 plot paths as values. @@ -379,16 +378,15 @@ def d1_plots_dict(d1_plots_path='d1_plots'): return d1_plots_dict - -def create_hyperlink(file_path, title=None): +def create_hyperlink(path, title=None): """ Create a hyperlink to a file or folder. If the path is None, return None. Title is the basename of the path. """ - if file_path: + if path: if title is None: - title = os.path.basename(file_path) - return f'{title}' + title = os.path.basename(path) + return f'{title}' else: return None @@ -435,11 +433,6 @@ def ansi_to_html(text): text = text.replace('The COMBINE/OMEX did not execute successfully:', 'The COMBINE/OMEX did not execute successfully:') return text -def display_error_message(error_message): - if error_message != None: - display_markdown(f'{error_message}', raw=True) - return error_message - def check_file_compatibility_test(engine, model_filepath, experiment_filepath): ''' Check if the file extensions suggest the file types are compatible with the engine. @@ -469,7 +462,7 @@ def collapsible_content(content, title='Details'): if content: return f'
{title}{content}
' else: - return None + return f'{title}' def get_filetypes(model_filepath, simulation_filepath): """ @@ -526,13 +519,11 @@ def run_biosimulators_remote(engine,sedml_filepath,sbml_filepath): "email": "", } - res = biosimulations.submit_simulation_archive(\ + results_urls = biosimulations.submit_simulation_archive(\ archive_file=omex_file_name,\ sim_dict=sim_dict) - - download_url = res["download"] - - return download_url + + return results_urls def get_remote_results(engine, download_link, output_dir='remote_results'): @@ -545,12 +536,7 @@ def get_remote_results(engine, download_link, output_dir='remote_results'): def rename_files_in_extract_dir(extract_dir, engine): - # find the log.yml file in the extracted directory log_yml_path = find_file_in_dir('log.yml', extract_dir)[0] - with open(log_yml_path) as f: - log_yml_dict = yaml.safe_load(f) - - # rename log.yml file to '{engine}_log.yml' new_file_name = f'{engine}_log.yml' root = os.path.dirname(log_yml_path) new_file_path = os.path.join(root, new_file_name) @@ -561,7 +547,7 @@ def rename_files_in_extract_dir(extract_dir, engine): return extract_dir -def run_biosimulators_docker(engine,sedml_filepath,sbml_filepath,output_dir='output',error_categories=error_categories,chown_outputs=True): +def run_biosimulators_docker(engine,sedml_filepath,sbml_filepath,output_dir='output',chown_outputs=True): ''' put the sedml and sbml file into an omex archive run it locally using a biosimulators docker @@ -570,14 +556,14 @@ def run_biosimulators_docker(engine,sedml_filepath,sbml_filepath,output_dir='out #put the sedml and sbml into a combine archive omex_filepath = create_omex(sedml_filepath,sbml_filepath) - error_str = None + log_yml_path = os.path.join(output_dir,"log.yml") + log_yml_dict = {} + exception_message = "" try: biosimulators_core(engine,omex_filepath,output_dir=output_dir) except Exception as e: - #capture the error as a string which won't break markdown tables - # error_str = safe_md_string(e) - error_str = str(e) + exception_message = str(e) #ensure outputs are owned by the user if 'getuid' in dir(os) and chown_outputs: @@ -585,23 +571,20 @@ def run_biosimulators_docker(engine,sedml_filepath,sbml_filepath,output_dir='out gid = os.getgid() os.system(f'sudo chown -R {uid}:{gid} {output_dir}') - if not error_str: return "pass" - - # #try to load the cleaner error message from the log.yml file - log_str = read_log_yml(os.path.join(os.path.dirname(omex_filepath),"log.yml")) - - if log_str: - error_str = str(log_str) - # if log_str: - # error_str = safe_md_string(log_str) + if os.path.exists(log_yml_path): + with open(log_yml_path) as f: + log_yml_dict = yaml.safe_load(f) - #categorise the error string - if engine in error_categories: - for tag in error_categories[engine]: - if re.search(error_categories[engine][tag],error_str): - return [tag,f"```{error_str}```"] + # to deal with vcell like cases where there is a log_yml with status SUCCEEDED but a detailedErrorLog.txt with "RuntimeError" + detailed_error_log_dict = {} + if os.path.exists(os.path.join(output_dir, 'detailedErrorLog.txt')): + with open(os.path.join(output_dir, 'detailedErrorLog.txt')) as f: + detailed_error_log = f.read() + if 'RuntimeException' in detailed_error_log: + detailed_error_log_dict['status'] = 'FAIL' + detailed_error_log_dict['error_message'] = "Runtime Exception" - return ["other",f"```{error_str}```"] + return {"exception_message":exception_message,"log_yml":log_yml_dict, "detailed_error_log":detailed_error_log_dict} def biosimulators_core(engine,omex_filepath,output_dir=None): ''' @@ -1043,40 +1026,6 @@ def download_file_from_link(engine, download_link, output_file='results.zip', ma print(f'Failed to download {engine} results.') raise HTTPError(f'Failed to download {engine} results.') -# unzip the file in file_path if it is a zip file and remove the zip file, replace with the unzipped folder -def unzip_file(file_path, output_dir=None): - """ - Unzip a file if it is a zip file. - - Parameters: - file_path (str): The path to the file to unzip. - output_dir (str): The directory to extract the contents of the zip file to. Defaults to None. - - Returns: - str: The path to the unzipped folder. - """ - - # If the file is a zip file, unzip it - if zipfile.is_zipfile(file_path): - # If the output directory is not specified, use the directory of the file - if output_dir is None: - output_dir = os.path.dirname(file_path) - - # Create a ZipFile object - with zipfile.ZipFile(file_path, 'r') as zip_ref: - # Extract the contents of the zip file - zip_ref.extractall(output_dir) - - # Remove the zip file - os.remove(file_path) - - # Get the name of the unzipped folder - unzipped_folder = os.path.join(output_dir, os.path.splitext(os.path.basename(file_path))[0]) - - return unzipped_folder - - return file_path - def create_results_table(results, sbml_filepath, sedml_filepath, output_dir): """ Create a markdown table of the results. @@ -1089,41 +1038,41 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir): pass_html = "✅ PASS" fail_html = "❌ FAIL" warning_html = "⚠ WARNING" - xfail_html = "❎" xfail_html = "⚠ XFAIL" - # Create a table of the results + for e in results.keys(): + results[e].update(process_log_yml_dict(results[e]["log_yml"])) + if "detailed_error_log" in results[e].keys(): + if results[e]["detailed_error_log"] != {}: + results[e]['status'] = results[e]["detailed_error_log"]['status'] + results[e]['error_message'] = results[e]["detailed_error_log"]['error_message'] + + links = ['view', 'download', 'logs'] + for e in results.keys(): + if any([l in results[e].keys() for l in links]): + results[e]['links'] = '
'.join([f'{create_hyperlink(results[e][k], title=k)}' for k in results[e].keys() if k in links]) + results_table = pd.DataFrame.from_dict(results).T - # if list is three elements - if results_table.shape[1] == 3: - results_table.columns = [PASS_FAIL, ERROR, TYPE] - elif results_table.shape[1] == 2: - results_table.columns = [PASS_FAIL, ERROR] + results_table.rename(columns={"status": PASS_FAIL, "error_message": ERROR, "exception_type": TYPE}, inplace=True) results_table.index.name = ENGINE results_table.reset_index(inplace=True) # Error results_table[ERROR] = results_table.apply(lambda x: None if x[PASS_FAIL] == x[ERROR] else x[ERROR], axis=1) - results_table[PASS_FAIL] = results_table[PASS_FAIL].replace('other', 'FAIL') - results_table[ERROR] = results_table[ERROR].apply(lambda x: ansi_to_html(x)) - results_table[ERROR] = results_table[ERROR].apply(lambda x: collapsible_content(x)) results_table[PASS_FAIL] = results_table[PASS_FAIL].apply(lambda x: f'{fail_html}' if x == 'FAIL' \ - else f'{pass_html}' if x == 'pass' else x) + else f'{pass_html}' if x == 'pass' + else f'{warning_html}' if x == 'WARNING' + else x) # d1 plot clickable link results_table[D1] = results_table[ENGINE].apply(lambda x: d1_plots_dict(output_dir).get(x, None)) results_table[D1] = results_table[D1].apply(lambda x: create_hyperlink(x,title='plot')) - if TYPE in results_table.columns: - results_table[TYPE] = results_table[TYPE].apply(lambda x: collapsible_content(x,"".join(re.findall(r'[A-Z]', x)))) - for e in ENGINES.keys(): compatibility_content = check_file_compatibility_test(e, sbml_filepath, sedml_filepath) - - print(e, compatibility_content[0] ) if compatibility_content[0] == 'pass': results_table.loc[results_table[ENGINE] == e, COMPAT] = collapsible_content(compatibility_content[1], title=f'{pass_html}') elif compatibility_content[0] == 'unsure': @@ -1134,64 +1083,106 @@ def create_results_table(results, sbml_filepath, sedml_filepath, output_dir): # add xfail to engines that do not support sbml sbml_incompatible_ENGINES = [e for e in ENGINES.keys() if 'sbml' not in ENGINES[e]['formats'][0]] for e in sbml_incompatible_ENGINES: - compatibility_content = check_file_compatibility_test(e, sbml_filepath, sedml_filepath) - results_table.loc[results_table[ENGINE] == e, COMPAT] = collapsible_content(compatibility_content[1], title=f'{xfail_html}') + compatibility = check_file_compatibility_test(e, sbml_filepath, sedml_filepath) + compatibility_content = f'EXPECTED FAIL

{compatibility[1]}' + results_table.loc[results_table[ENGINE] == e, COMPAT] = collapsible_content(compatibility_content, title=f'{xfail_html}') results_table.loc[results_table[ENGINE] == e, PASS_FAIL] = f'{xfail_html}' - - + + for e in results_table[ENGINE]: + links = "" + error_message = "" + error_type = "" + expected_fail = "" + + if results_table.loc[results_table[ENGINE] == e, PASS_FAIL].values[0] == f'{xfail_html}': + expected_fail = f'EXPECTED FAIL

' + if len(results_table.loc[results_table[ENGINE] == e, ERROR].values[0]) > 1: + error_message = f'ERROR MESSAGE:
{results_table.loc[results_table[ENGINE] == e, ERROR].values[0]}

' + if "links" in results_table.columns: + links = results_table.loc[results_table[ENGINE] == e, "links"].values[0] + links = f'{links}

' + if TYPE in results_table.columns: + if len(results_table.loc[results_table[ENGINE] == e, TYPE].values[0])>1: + error_type = f'ERROR TYPE:
{results_table.loc[results_table[ENGINE] == e, TYPE].values[0]}' + + links_error = f'{expected_fail}{links}{error_message}{error_type}' + results_table.loc[results_table[ENGINE] == e, "links_error"] = links_error + + # add links as collapsible content to pass / fail column + for e in results_table[ENGINE]: + title = results_table.loc[results_table[ENGINE] == e, PASS_FAIL].values[0] + content = results_table.loc[results_table[ENGINE] == e, "links_error"].values[0] + results_table.loc[results_table[ENGINE] == e, PASS_FAIL] = collapsible_content(content, title) + # add status message defined in ENGINES - results_table[ENGINE] = results_table[ENGINE].apply(lambda x: collapsible_content(f'{ENGINES[x]["url"]}
{ENGINES[x]["status"]}', x)) + results_table[ENGINE] = results_table[ENGINE].apply(lambda x: collapsible_content(f'{ENGINES[x]["url"]}
{ENGINES[x]["status"]}', x)) return results_table +def process_log_yml_dict(log_yml_dict): + status = "" + error_message = "" + exception_type = "" + + if log_yml_dict == {}: + return {"status":"FAIL", "error_message":"Error unknown. The log.yml containing error information was not found.","exception_type": ""} + + log_yml_str = str(log_yml_dict) + if log_yml_dict['status'] == 'SUCCEEDED': + status = 'pass' + # to deal with cases like amici where the d1 plot max x is half the expected value + pattern_max_number_of_steps = "simulation failed: Reached maximum number of steps" + pattern_match = re.search(pattern_max_number_of_steps, log_yml_str) + if pattern_match: + status = 'FAIL' + error_message = 'Reached maximum number of steps' + elif log_yml_dict['status'] == 'FAILED': + status = 'FAIL' + exception = log_yml_dict['exception'] + error_message = exception['message'] + exception_type = exception['type'] + # in the case of vcell the status is QUEUED + elif log_yml_dict['status'] == 'QUEUED': + status = 'FAIL' + error_message = 'status: QUEUED' + else: + status = None + + return {"status":status, "error_message":error_message,"exception_type": exception_type} + -def run_biosimulators_remotely(sedml_file_name, +def run_biosimulators_remotely(engine_keys, + sedml_file_name, sbml_file_name, d1_plots_remote_dir, test_folder='tests'): """ run with directory pointing towards the location of the sedml and sbml files""" + engines = {k: v for k, v in ENGINES.items() if k in engine_keys} + remote_output_dir = 'remote_results' remote_output_dir = os.path.join(test_folder, remote_output_dir) - download_links_dict = dict() - for e in ENGINES.keys(): - download_link = run_biosimulators_remote(e, sedml_file_name, sbml_file_name) - download_links_dict[e] = download_link - - extract_dir_dict = dict() results_remote = dict() - for e, link in download_links_dict.items(): + for e in engines.keys(): + results_remote[e] = run_biosimulators_remote(e, sedml_file_name, sbml_file_name) + results_remote[e]['response'] = results_remote[e]['response'].status_code + + extract_dir_dict = dict() + for e, link in results_remote.items(): try: - extract_dir = get_remote_results(e, link, remote_output_dir) + extract_dir = get_remote_results(e, link["download"], remote_output_dir) except HTTPError as emessage: results_remote[e] = ["FAIL", str(emessage), type(emessage).__name__] continue extract_dir_dict[e] = extract_dir for e, extract_dir in extract_dir_dict.items(): - status = "" - error_message = "" - exception_type = "" - log_yml_path = find_file_in_dir('log.yml', extract_dir)[0] - if not log_yml_path: - status = None - error_message = 'log.yml not found' - continue with open(log_yml_path) as f: log_yml_dict = yaml.safe_load(f) - if log_yml_dict['status'] == 'SUCCEEDED': - status = 'pass' - elif log_yml_dict['status'] == 'FAILED': - status = 'FAIL' - exception = log_yml_dict['exception'] - error_message = exception['message'] - exception_type = exception['type'] - else: - status = None - results_remote[e] = [status, error_message, exception_type] + results_remote[e]["log_yml"] = log_yml_dict file_paths = find_files(remote_output_dir, '.pdf') move_d1_files(file_paths, d1_plots_remote_dir) @@ -1203,21 +1194,23 @@ def run_biosimulators_remotely(sedml_file_name, return results_remote -def run_biosimulators_locally(sedml_file_name, +def run_biosimulators_locally(engine_keys, + sedml_file_name, sbml_file_name, d1_plots_local_dir, test_folder='tests'): + + engines = {k: v for k, v in ENGINES.items() if k in engine_keys} results_local = {} output_folder = 'local_results' local_output_dir = os.path.join(test_folder, output_folder) - for e in ENGINES.keys(): + for e in engines.keys(): print('Running ' + e) local_output_dir_e = os.path.abspath(os.path.join(local_output_dir, e)) print(local_output_dir_e) - record = run_biosimulators_docker(e, sedml_file_name, sbml_file_name, output_dir=local_output_dir_e) - results_local[e] = record + results_local[e] = run_biosimulators_docker(e, sedml_file_name, sbml_file_name, output_dir=local_output_dir_e) file_paths = find_files(local_output_dir, '.pdf') print('file paths:', file_paths) @@ -1230,8 +1223,6 @@ def run_biosimulators_locally(sedml_file_name, return results_local - - def create_combined_results_table(results_remote, results_local, sedml_file_name, @@ -1262,8 +1253,6 @@ def create_combined_results_table(results_remote, ENGINE, COMPAT, f"{PASS_FAIL}{suffix_remote}", f"{PASS_FAIL}{suffix_local}", - f"{ERROR}{suffix_remote}", f"{ERROR}{suffix_local}", - f"{TYPE}{suffix_remote}", f"{D1}{suffix_remote}", f"{D1}{suffix_local}" ] @@ -1282,18 +1271,21 @@ def create_combined_results_table(results_remote, return combined_results -def run_biosimulators_remotely_and_locally(sedml_file_name, +def run_biosimulators_remotely_and_locally(engine_keys, + sedml_file_name, sbml_file_name, d1_plots_remote_dir, d1_plots_local_dir, test_folder='tests'): - results_remote = run_biosimulators_remotely(sedml_file_name=sedml_file_name, + results_remote = run_biosimulators_remotely(engine_keys, + sedml_file_name=sedml_file_name, sbml_file_name=sbml_file_name, d1_plots_remote_dir=d1_plots_remote_dir, test_folder=test_folder) - results_local = run_biosimulators_locally(sedml_file_name=sedml_file_name, + results_local = run_biosimulators_locally(engine_keys, + sedml_file_name=sedml_file_name, sbml_file_name=sbml_file_name, d1_plots_local_dir=d1_plots_local_dir, test_folder=test_folder)