Closed gmarupilla closed 3 years ago
The validation/submission of your simulator failed.
- 'NoneType' object has no attribute 'get'
The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.
If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.
Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.
The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators
(without the backticks).
The validation/submission of your simulator failed.
- 'NoneType' object has no attribute 'get'
The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.
If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.
Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.
The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators
(without the backticks).
The validation/submission of your simulator failed.
- while scanning a simple key
- in "<unicode string>", line 5, column 1:
- https://raw.githubusercontent.co ...
- ^
- could not find expected ':'
- in "<unicode string>", line 6, column 1:
- specificationsPatch:
- ^
The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.
If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.
Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.
The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators
(without the backticks).
Thank you @gmarupilla for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.
The specifications of your simulator is valid!
Executed 67 test cases
Passed 28 test cases:
cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
docker_image.SingularityImageExecutesSimulationsSuccessfully
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 0 test cases
Skipped 39 test cases:
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsComputeModelChanges
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
sedml.SimulatorSupportsDataSetsWithDifferentShapes
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsRepeatedTasksWithChanges
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
sedml.SimulatorSupportsSubstitutingAlgorithms
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
cli.CliDescribesSupportedEnvironmentVariablesInline
(1.6 s)Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.
The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
- 'ALGORITHM_SUBSTITUTION_POLICY'
If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.
Note, support for these environment variables is optional. Simulation tools are not required to support these variables.
Log:
docker_image.HasBioContainersLabels
(0.5 s)Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
The Docker image should have the following BioContainers labels:
extra.identifiers.biotools
Log:
docker_image.HasOciLabels
(0.5 s)Test that a Docker image has Open Container Initiative (OCI) labels with metadata about the image
Warnings:
The Docker image should have the following Open Container Initiative (OCI) labels:
org.opencontainers.image.created
org.opencontainers.image.revision
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
(11.5 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000019
Warnings:
Unexpected reports were produced:
BIOMD0000000912_sim.sedml/Figure_1
Plots were not produced:
BIOMD0000000912_sim.sedml/plot_1
Extra plots were produced:
BIOMD0000000912_sim.sedml/Figure_1
Log:
VCell CLI input archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex
Jul 03, 2021 1:50:34 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_9faf9a46-5c37-4c60-87c3-6b63fb58119e2353093029874331590
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 1 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp4011345425759625795.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@71b1a49c
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations__BIOMD0000000912' Task 'Caravagna2010'.
Ignoring unsupported output Figure_1
while CSV generation.
Generating report report
.
Python 3.8.10
HDF conversion successful
Archiving resultant PDF files to plots.zip
.
Archiving resultant CSV files to reports.zip
.
### `published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg` (22.1 s)
Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000086
Warnings:
Unexpected reports were produced:
simulation_1.sedml/Figure_3a
simulation_1.sedml/Figure_3b
simulation_1.sedml/Figure_3c
simulation_1.sedml/Figure_3d
Plots were not produced:
simulation.sedml/Figure_3a
simulation.sedml/Figure_3b
simulation.sedml/Figure_3c
simulation.sedml/Figure_3d
Extra plots were produced:
simulation_1.sedml/Figure_3a
simulation_1.sedml/Figure_3b
simulation_1.sedml/Figure_3c
simulation_1.sedml/Figure_3d
Log:
VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex
Jul 03, 2021 1:50:46 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_5e3a308c-8b67-45b9-8346-8181eafd20f25879143945446810406
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 4 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000086' matched to RungeKuttaFehlberg
Succesful model import: SBML file /tmp/temp8183972239076889573.xml
final tolerance=0.1 final threshold=0.060000000000000005, 552 remaining (keepAtMost=1000)
Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg__Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output `Figure_3a` while CSV generation.
Ignoring unsupported output `Figure_3b` while CSV generation.
Ignoring unsupported output `Figure_3c` while CSV generation.
Ignoring unsupported output `Figure_3d` while CSV generation.
Generating report `report`.
Python 3.8.10
HDF conversion successful
Archiving resultant PDF files to `plots.zip`.
Archiving resultant CSV files to `reports.zip`.
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
(21.1 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000019
Warnings:
Unexpected reports were produced:
simulation_1.sedml/Figure_3a
simulation_1.sedml/Figure_3b
simulation_1.sedml/Figure_3c
simulation_1.sedml/Figure_3d
Plots were not produced:
simulation.sedml/Figure_3a
simulation.sedml/Figure_3b
simulation.sedml/Figure_3c
simulation.sedml/Figure_3d
Extra plots were produced:
simulation_1.sedml/Figure_3a
simulation_1.sedml/Figure_3b
simulation_1.sedml/Figure_3c
simulation_1.sedml/Figure_3d
Log:
VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex
Jul 03, 2021 1:51:08 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_62aa06a6-1e34-4896-a0f0-7ea929a3a4642333980461687788882
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 4 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp6841360925640645947.xml
/tmp/out/simulation_1.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@53c99b09
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous__Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output `Figure_3a` while CSV generation.
Ignoring unsupported output `Figure_3b` while CSV generation.
Ignoring unsupported output `Figure_3c` while CSV generation.
Ignoring unsupported output `Figure_3d` while CSV generation.
Generating report `report`.
Python 3.8.10
HDF conversion successful
Archiving resultant PDF files to `plots.zip`.
Archiving resultant CSV files to `reports.zip`.
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
(50.3 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000027
Format: format_2585
Algorithm: KISAO_0000030
Warnings:
Unexpected reports were produced:
simulation.sedml/plot2d_Euler_default
simulation.sedml/plot2d_Euler_small_step_size
simulation.sedml/plot2d_Fig_1_c
simulation.sedml/plot2d_Fig_1a
simulation.sedml/plot2d_low_delta_R_det
simulation.sedml/plot2d_low_delta_R_stoch
Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex
Jul 03, 2021 1:52:26 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_6827a272-c5d1-4e6c-ae6b-03d90ad9af6c8907070664569507918
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 4 model(s), 6 simulation(s), 6 task(s), 6 report(s), 6 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file simulation.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp8586423608003350660.xml
Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp8383544676599209574.xml
Task (id='tsk_0_2') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler
Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler
Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson
Succesful model import: SBML file /tmp/temp5269120857949562349.xml
Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson
Succesful model import: SBML file /tmp/temp234843993908329079.xml
/tmp/out/simulation.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@1f9d4b0e
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_0'.
-----------------------------------------------------------------------------------------------------
Solver status: 3
Solver message: simulation failed at time=1.3: consider using smaller default or max time step.
values are:
A = NaN
C = Infinity
PrmA = Infinity
PrmA_bound = -Infinity
PrmR = Infinity
PrmR_bound = -Infinity
R = -Infinity
Failed execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_2'.
-----------------------------------------------------------------------------------------------------
final tolerance=0.1 final threshold=0.09, 885 remaining (keepAtMost=1000)
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_3'.
-----------------------------------------------------------------------------------------------------
/tmp/out/simulation.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@7730ef88
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic_0' Task 'tsk_0_1'.
-----------------------------------------------------------------------------------------------------
cbit.vcell.solver.stoch.GibsonSolver@2b08772d
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_stochastic' Task 'tsk_1_0'.
-----------------------------------------------------------------------------------------------------
cbit.vcell.solver.stoch.GibsonSolver@7d4d8579
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_stochastic_0' Task 'tsk_1_1'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output `plot2d_Fig_1a` while CSV generation.
Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation.
Ignoring unsupported output `plot2d_Euler_default` while CSV generation.
Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation.
Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation.
Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation.
Generating report `report_Fig_1a`.
Generating report `report_low_delta_R_det`.
Generating report `report_Euler_default`.
Generating report `report_Euler_small_step_size`.
Generating report `report_Fig_1_c`.
Generating report `report_low_delta_R_stoch`.
Python 3.8.10
HDF conversion successful
Archiving resultant PDF files to `plots.zip`.
Archiving resultant CSV files to `reports.zip`.
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
(35.2 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000030
Warnings:
Unexpected reports were produced:
simulation.sedml/Figure_2ab
simulation.sedml/plot2d_Euler_default
simulation.sedml/plot2d_Euler_small_step_size
simulation.sedml/plot2d_Fig_1a
simulation.sedml/plot2d_low_delta_R_det
Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex
Jul 03, 2021 1:51:29 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_7f4a422a-023b-43b5-91bc-44525e1992476346925845275593143
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 2 model(s), 4 simulation(s), 4 task(s), 4 report(s), 5 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file simulation.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp6443679598117253815.xml
Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp2228148413737813089.xml
Task (id='tsk_0_2') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler
Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler
/tmp/out/simulation.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@1860f3be
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic' Task 'tsk_0_0'.
-----------------------------------------------------------------------------------------------------
Solver status: 3
Solver message: simulation failed at time=1.3: consider using smaller default or max time step.
values are:
A = NaN
C = Infinity
PrmA = Infinity
PrmA_bound = -Infinity
PrmR = Infinity
PrmR_bound = -Infinity
R = -Infinity
Failed execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic' Task 'tsk_0_2'.
-----------------------------------------------------------------------------------------------------
final tolerance=0.1 final threshold=0.09, 885 remaining (keepAtMost=1000)
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic' Task 'tsk_0_3'.
-----------------------------------------------------------------------------------------------------
/tmp/out/simulation.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@93824eb
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic_0' Task 'tsk_0_1'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output `Figure_2ab` while CSV generation.
Ignoring unsupported output `plot2d_Fig_1a` while CSV generation.
Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation.
Ignoring unsupported output `plot2d_Euler_default` while CSV generation.
Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation.
Generating report `report_Fig_1a`.
Generating report `report_low_delta_R_det`.
Generating report `report_Euler_default`.
Generating report `report_Euler_small_step_size`.
Python 3.8.10
HDF conversion successful
Archiving resultant PDF files to `plots.zip`.
Archiving resultant CSV files to `reports.zip`.
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
(20.9 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000027
Warnings:
Unexpected reports were produced:
simulation.sedml/plot2d_Fig_1_c
simulation.sedml/plot2d_low_delta_R_stoch
Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex
Jul 03, 2021 1:52:05 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_e5bb462e-bd40-4a07-b60a-73ed8f9df4ec109679894031255139
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 2 model(s), 2 simulation(s), 2 task(s), 2 report(s), 2 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file simulation.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson
Succesful model import: SBML file /tmp/temp8668246185335589010.xml
Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson
Succesful model import: SBML file /tmp/temp3826319189979384707.xml
cbit.vcell.solver.stoch.GibsonSolver@178270b2
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM__ODE_stochastic' Task 'tsk_1_0'.
-----------------------------------------------------------------------------------------------------
cbit.vcell.solver.stoch.GibsonSolver@6e0f7aad
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM__ODE_stochastic_0' Task 'tsk_1_1'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation.
Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation.
Generating report `report_Fig_1_c`.
Generating report `report_low_delta_R_stoch`.
Python 3.8.10
HDF conversion successful
Archiving resultant PDF files to `plots.zip`.
Archiving resultant CSV files to `reports.zip`.
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
(9.2 s)Test that simulator logs the execution of COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.
More information: https://biosimulators.org/conventions/status
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:49:58 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_b6a372f7-c3ec-48f4-9a5d-8d0234413f102052270678797719402
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp504125951608237700.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@77e2a6e2
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
-----------------------------------------------------------------------------------------------------
Generating report `report`.
Python 3.8.10
HDF conversion successful
No PDF files found, skipping archiving `plots.zip` files
Archiving resultant CSV files to `reports.zip`.
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
(9.1 s)Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.
More information: https://biosimulators.org/conventions/status
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:50:07 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_6cac110a-fc44-4720-b923-3337f66c67535034365064132343460
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp2603611414224677003.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@77e2a6e2
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
-----------------------------------------------------------------------------------------------------
Generating report `report`.
Python 3.8.10
HDF conversion successful
No PDF files found, skipping archiving `plots.zip` files
Archiving resultant CSV files to `reports.zip`.
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
(9.2 s)Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.
More information: https://biosimulators.org/conventions/status
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:50:16 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_1d764c57-6db0-48e7-ad14-0ef04b2665993992907903586177545
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp3109108527525431784.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@77e2a6e2
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
-----------------------------------------------------------------------------------------------------
Generating report `report`.
Python 3.8.10
HDF conversion successful
No PDF files found, skipping archiving `plots.zip` files
Archiving resultant CSV files to `reports.zip`.
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
(9.0 s)Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.
More information: https://biosimulators.org/conventions/status
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:50:25 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_203361ee-5dd5-4f61-bc52-b2fb20e949a4450625068230984547
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp2503078643282952717.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@77e2a6e2
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
-----------------------------------------------------------------------------------------------------
Generating report `report`.
Python 3.8.10
HDF conversion successful
No PDF files found, skipping archiving `plots.zip` files
Archiving resultant CSV files to `reports.zip`.
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_3972
Algorithm: KISAO_0000263
Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000263
Log:
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_3972
Algorithm: KISAO_0000019
Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000019
Log:
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_3240
Algorithm: KISAO_0000019
Reason for skip:
Case requires model formats format_3240 and simulation algorithms KISAO_0000019
Log:
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_9004
Algorithm: KISAO_0000019
Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000019
Log:
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_9004
Algorithm: KISAO_0000030
Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000030
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000088
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000088
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_000019
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_000019
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000496
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000496
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000560
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000560
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000029
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000029
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000437
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000437
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000449
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000449
Log:
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_9001
Algorithm: KISAO_0000057
Reason for skip:
Case requires model formats format_9001 and simulation algorithms KISAO_0000057
Log:
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
(2.5 s)Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1
).
Reason for skip:
The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.14' could not execute the archive:
Unknown error
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:46:31 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_bf44abf1-b9d9-4b6a-bd5a-12cca822431d1219239772316189735
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
[Fatal Error] :1:1: Content is not allowed in prolog.
[Fatal Error] :1:1: Content is not allowed in prolog.
java.lang.RuntimeException: Error importing from SBML : no SBML source.
at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:449)
at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:700)
at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:66)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:188)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection
Error importing from SBML : no SBML source.
Unable to initialize bioModel for the given selection
Error importing from SBML : no SBML source.
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
(2.6 s)Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1
) and inherit the changes of the model.
Reason for skip:
The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.14' could not execute the archive:
Unknown error
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:46:33 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_44f4ed63-abc7-4661-8fc2-3393fc40d64e3524806034515532154
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
[Fatal Error] :1:1: Content is not allowed in prolog.
[Fatal Error] :1:1: Content is not allowed in prolog.
java.lang.RuntimeException: Error importing from SBML : no SBML source.
at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:449)
at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:700)
at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:66)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:188)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection
Error importing from SBML : no SBML source.
Unable to initialize bioModel for the given selection
Error importing from SBML : no SBML source.
sedml.SimulatorProducesLinear3DPlots
(0.3 s)Test that a simulator produces linear 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing
Log:
sedml.SimulatorProducesLogarithmic3DPlots
(0.3 s)Test that a simulator produces logarithmic 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing
Log:
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
(9.4 s)Test that a simulator supports model changes that involve adding, replacing, and removing model elements.
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:47:19 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_900ceafd-1520-4d6c-b3b0-b4f8bed7d14d8218565582972024574
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp5526871555291675331.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@71b1a49c
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
Generating report report
.
Python 3.8.10
HDF conversion successful
No PDF files found, skipping archiving plots.zip
files
Archiving resultant CSV files to reports.zip
.
### `sedml.SimulatorSupportsComputeModelChanges` (10.1 s)
Test that a simulator supports compute model changes
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:47:38 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_d9f8985a-d376-4fd3-81a4-555d05557fc03933977229543564396
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp6928758899982039554.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@67207d8a
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
Generating report report
.
Python 3.8.10
HDF conversion successful
No PDF files found, skipping archiving plots.zip
files
Archiving resultant CSV files to reports.zip
.
### `sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes` (11.6 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpbv723jje/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:47:48 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_1c6ac474-5698-4a8b-9fb4-ff4adf716df2244885160077480599
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp8491499252315211528.xml
Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@2d83c5a5
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@18151a14
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.
Generating report report__copy_2
.
Python 3.8.10
Traceback (most recent call last):
File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 372, in
fire.Fire({
File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
component_trace = _Fire(component, args, parsed_flag_args, context, name)
File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
component, remaining_args = _CallAndUpdateTrace(
File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
component = fn(*varargs, **kwargs)
File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 176, in exec_sed_doc
data_set_results[data_set.id] = data_set_df.loc[data_set.label, :].to_numpy(
File "/usr/local/lib/python3.8/dist-packages/pandas/core/base.py", line 610, in to_numpy
result = np.asarray(self._values, dtype=dtype)
ValueError: could not convert string to float: 'NaN.1'
HDF conversion failed
No PDF files found, skipping archiving plots.zip
files
Archiving resultant CSV files to reports.zip
.
### `sedml.SimulatorSupportsDataSetsWithDifferentShapes` (11.7 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpf4f7_5do/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:48:00 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_e6271b2d-fdb8-4267-8f22-6de3190b84ed3484134780039858598
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp3452408655358101515.xml
Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@73e132e0
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@55a8dc49
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.
Generating report report
.
Traceback (most recent call last):
File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 372, in
fire.Fire({
File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
component_trace = _Fire(component, args, parsed_flag_args, context, name)
File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
component, remaining_args = _CallAndUpdateTrace(
File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
component = fn(*varargs, **kwargs)
File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 329, in gen_plot_pdfs
report_frames = get_report_dataframes(all_report_dataref, result_out_dir)
File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 298, in get_report_dataframes
report_frames[report] = pd.read_csv(os.path.join(
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 610, in read_csv
return _read(filepath_or_buffer, kwds)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 468, in _read
return parser.read(nrows)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 1057, in read
index, columns, col_dict = self._engine.read(nrows)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 2036, in read
data = self._reader.read(nrows)
File "pandas/_libs/parsers.pyx", line 756, in pandas._libs.parsers.TextReader.read
File "pandas/_libs/parsers.pyx", line 771, in pandas._libs.parsers.TextReader._read_low_memory
File "pandas/_libs/parsers.pyx", line 827, in pandas._libs.parsers.TextReader._read_rows
File "pandas/_libs/parsers.pyx", line 814, in pandas._libs.parsers.TextReader._tokenize_rows
File "pandas/_libs/parsers.pyx", line 1951, in pandas._libs.parsers.raise_parser_error
pandas.errors.ParserError: Error tokenizing data. C error: Expected 12 fields in line 5, saw 22
Python 3.8.10
Traceback (most recent call last):
File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 372, in
fire.Fire({
File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
component_trace = _Fire(component, args, parsed_flag_args, context, name)
File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
component, remaining_args = _CallAndUpdateTrace(
File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
component = fn(*varargs, **kwargs)
File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 156, in exec_sed_doc
data_set_df = pd.read_csv(report_filename).transpose()
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 610, in read_csv
return _read(filepath_or_buffer, kwds)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 468, in _read
return parser.read(nrows)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 1057, in read
index, columns, col_dict = self._engine.read(nrows)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 2036, in read
data = self._reader.read(nrows)
File "pandas/_libs/parsers.pyx", line 756, in pandas._libs.parsers.TextReader.read
File "pandas/_libs/parsers.pyx", line 771, in pandas._libs.parsers.TextReader._read_low_memory
File "pandas/_libs/parsers.pyx", line 827, in pandas._libs.parsers.TextReader._read_rows
File "pandas/_libs/parsers.pyx", line 814, in pandas._libs.parsers.TextReader._tokenize_rows
File "pandas/_libs/parsers.pyx", line 1951, in pandas._libs.parsers.raise_parser_error
pandas.errors.ParserError: Error tokenizing data. C error: Expected 12 fields in line 5, saw 22
HDF conversion failed
No PDF files found, skipping archiving plots.zip
files
Archiving resultant CSV files to reports.zip
.
### `sedml.SimulatorSupportsModelAttributeChanges` (10.3 s)
Test that a simulator supports changes to the attributes of model elements
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:48:12 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_694fa98a-c037-4f91-8838-3fbf972671db5299729891347726240
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp1598801345850138208.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@4f20a5e0
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
Generating report report
.
Python 3.8.10
HDF conversion successful
No PDF files found, skipping archiving plots.zip
files
Archiving resultant CSV files to reports.zip
.
### `sedml.SimulatorSupportsRepeatedTasksWithChanges` (4.7 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpn8n3qano/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:48:52 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_cdf73017-9494-4488-9939-a199d670c27b3027599203778123206
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
java.lang.NullPointerException
at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
SED-ML processing for /tmp/vcell_temp_cdf73017-9494-4488-9939-a199d670c27b3027599203778123206/BIOMD0000000912_sim.sedml failed with error: null
org.jlibsedml.XMLException
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
One or more errors encountered while executing archive /tmp/in/archive.omex
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:48:55 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_53be173a-0fc3-4c83-ac4e-e500185eb9081519938376516081702
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
java.lang.NullPointerException
at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
SED-ML processing for /tmp/vcell_temp_53be173a-0fc3-4c83-ac4e-e500185eb9081519938376516081702/BIOMD0000000912_sim.sedml failed with error: null
org.jlibsedml.XMLException
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
One or more errors encountered while executing archive /tmp/in/archive.omex
### `sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables` (4.7 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpj45ih7nw/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:48:57 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_6d7a0cb0-2dc5-42ea-bef3-6479995433222831260735198623525
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
java.lang.NullPointerException
at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
SED-ML processing for /tmp/vcell_temp_6d7a0cb0-2dc5-42ea-bef3-6479995433222831260735198623525/BIOMD0000000912_sim.sedml failed with error: null
org.jlibsedml.XMLException
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
One or more errors encountered while executing archive /tmp/in/archive.omex
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:48:59 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_3a53bfcf-c516-4d02-bb8c-1d9c727032496900126501198590858
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
java.lang.NullPointerException
at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
SED-ML processing for /tmp/vcell_temp_3a53bfcf-c516-4d02-bb8c-1d9c727032496900126501198590858/BIOMD0000000912_sim.sedml failed with error: null
org.jlibsedml.XMLException
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
One or more errors encountered while executing archive /tmp/in/archive.omex
### `sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges` (2.4 s)
Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpqr0kd2dy/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:49:02 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_6e8eb3aa-d32c-41f4-8619-d7195d33fefa6717852815953337992
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
java.lang.NullPointerException
at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
SED-ML processing for /tmp/vcell_temp_6e8eb3aa-d32c-41f4-8619-d7195d33fefa6717852815953337992/BIOMD0000000912_sim.sedml failed with error: null
org.jlibsedml.XMLException
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
One or more errors encountered while executing archive /tmp/in/archive.omex
### `sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges` (2.3 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpi9n8y4c3/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:49:04 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_de0ed57d-c76c-4a0c-b669-ba69c7178f061706415233759311178
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
java.lang.NullPointerException
at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
SED-ML processing for /tmp/vcell_temp_de0ed57d-c76c-4a0c-b669-ba69c7178f061706415233759311178/BIOMD0000000912_sim.sedml failed with error: null
org.jlibsedml.XMLException
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
One or more errors encountered while executing archive /tmp/in/archive.omex
### `sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges` (2.3 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp1izycqfm/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:49:07 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_35356cd0-c3df-4f3b-8c80-cfc151a004717218003392427551576
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
java.lang.NullPointerException
at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
SED-ML processing for /tmp/vcell_temp_35356cd0-c3df-4f3b-8c80-cfc151a004717218003392427551576/BIOMD0000000912_sim.sedml failed with error: null
org.jlibsedml.XMLException
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
One or more errors encountered while executing archive /tmp/in/archive.omex
### `sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks` (2.3 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpxj4196sk/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:49:09 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_618dec4e-f20f-4cce-a682-e4dbccfa8c45150158483734736619
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
java.lang.NullPointerException
at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
SED-ML processing for /tmp/vcell_temp_618dec4e-f20f-4cce-a682-e4dbccfa8c45150158483734736619/BIOMD0000000912_sim.sedml failed with error: null
org.jlibsedml.XMLException
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
One or more errors encountered while executing archive /tmp/in/archive.omex
### `sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges` (2.3 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpsg91nhf8/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 1:49:11 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_cb6bfb65-4d54-46d8-a9b1-787ebffe8af65126606056496845983
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
java.lang.NullPointerException
at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
...
The image for your simulator is valid!
A member of the BioSimulators team will review your submission and publish your image before final committment to the registry.
Thank you @gmarupilla for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.
The specifications of your simulator is valid!
Executed 67 test cases
Passed 28 test cases:
cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
docker_image.SingularityImageExecutesSimulationsSuccessfully
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 0 test cases
Skipped 39 test cases:
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsComputeModelChanges
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
sedml.SimulatorSupportsDataSetsWithDifferentShapes
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsRepeatedTasksWithChanges
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
sedml.SimulatorSupportsSubstitutingAlgorithms
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
cli.CliDescribesSupportedEnvironmentVariablesInline
(1.5 s)Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.
The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
- 'ALGORITHM_SUBSTITUTION_POLICY'
If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.
Note, support for these environment variables is optional. Simulation tools are not required to support these variables.
Log:
docker_image.HasBioContainersLabels
(0.2 s)Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
The Docker image should have the following BioContainers labels:
extra.identifiers.biotools
Log:
docker_image.HasOciLabels
(0.2 s)Test that a Docker image has Open Container Initiative (OCI) labels with metadata about the image
Warnings:
The Docker image should have the following Open Container Initiative (OCI) labels:
org.opencontainers.image.created
org.opencontainers.image.revision
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
(13.1 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000019
Warnings:
Unexpected reports were produced:
BIOMD0000000912_sim.sedml/Figure_1
Plots were not produced:
BIOMD0000000912_sim.sedml/plot_1
Extra plots were produced:
BIOMD0000000912_sim.sedml/Figure_1
Log:
VCell CLI input archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex
Jul 03, 2021 2:47:47 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_c5ee576f-e42d-4def-963f-66199183f0b44983631964960357499
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 1 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp5377820954710510644.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@71b1a49c
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations__BIOMD0000000912' Task 'Caravagna2010'.
Ignoring unsupported output Figure_1
while CSV generation.
Generating report report
.
Python 3.8.10
HDF conversion successful
Archiving resultant PDF files to plots.zip
.
Archiving resultant CSV files to reports.zip
.
### `published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg` (26.3 s)
Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000086
Warnings:
Unexpected reports were produced:
simulation_1.sedml/Figure_3a
simulation_1.sedml/Figure_3b
simulation_1.sedml/Figure_3c
simulation_1.sedml/Figure_3d
Plots were not produced:
simulation.sedml/Figure_3a
simulation.sedml/Figure_3b
simulation.sedml/Figure_3c
simulation.sedml/Figure_3d
Extra plots were produced:
simulation_1.sedml/Figure_3a
simulation_1.sedml/Figure_3b
simulation_1.sedml/Figure_3c
simulation_1.sedml/Figure_3d
Log:
VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex
Jul 03, 2021 2:48:00 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_3bd4ea0d-12a5-46da-ba5a-eba78fdb28d81238025338850184332
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 4 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000086' matched to RungeKuttaFehlberg
Succesful model import: SBML file /tmp/temp8269468102278799043.xml
final tolerance=0.1 final threshold=0.060000000000000005, 552 remaining (keepAtMost=1000)
Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg__Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output `Figure_3a` while CSV generation.
Ignoring unsupported output `Figure_3b` while CSV generation.
Ignoring unsupported output `Figure_3c` while CSV generation.
Ignoring unsupported output `Figure_3d` while CSV generation.
Generating report `report`.
Python 3.8.10
HDF conversion successful
Archiving resultant PDF files to `plots.zip`.
Archiving resultant CSV files to `reports.zip`.
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
(24.7 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000019
Warnings:
Unexpected reports were produced:
simulation_1.sedml/Figure_3a
simulation_1.sedml/Figure_3b
simulation_1.sedml/Figure_3c
simulation_1.sedml/Figure_3d
Plots were not produced:
simulation.sedml/Figure_3a
simulation.sedml/Figure_3b
simulation.sedml/Figure_3c
simulation.sedml/Figure_3d
Extra plots were produced:
simulation_1.sedml/Figure_3a
simulation_1.sedml/Figure_3b
simulation_1.sedml/Figure_3c
simulation_1.sedml/Figure_3d
Log:
VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex
Jul 03, 2021 2:48:26 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_0a136f55-e48a-41d7-98a4-5ca2a74cef073907431865287659039
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 4 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp3493234162633038144.xml
/tmp/out/simulation_1.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@53c99b09
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous__Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output `Figure_3a` while CSV generation.
Ignoring unsupported output `Figure_3b` while CSV generation.
Ignoring unsupported output `Figure_3c` while CSV generation.
Ignoring unsupported output `Figure_3d` while CSV generation.
Generating report `report`.
Python 3.8.10
HDF conversion successful
Archiving resultant PDF files to `plots.zip`.
Archiving resultant CSV files to `reports.zip`.
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
(60.1 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000027
Format: format_2585
Algorithm: KISAO_0000030
Warnings:
Unexpected reports were produced:
simulation.sedml/plot2d_Euler_default
simulation.sedml/plot2d_Euler_small_step_size
simulation.sedml/plot2d_Fig_1_c
simulation.sedml/plot2d_Fig_1a
simulation.sedml/plot2d_low_delta_R_det
simulation.sedml/plot2d_low_delta_R_stoch
Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex
Jul 03, 2021 2:49:56 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_48e272dc-d36b-4863-a288-c68b3ebcd5f91577650612854825711
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 4 model(s), 6 simulation(s), 6 task(s), 6 report(s), 6 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file simulation.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp4835017010108005798.xml
Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp8701814922218427910.xml
Task (id='tsk_0_2') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler
Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler
Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson
Succesful model import: SBML file /tmp/temp4002369895259870513.xml
Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson
Succesful model import: SBML file /tmp/temp2414655692466891520.xml
/tmp/out/simulation.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@1f9d4b0e
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_0'.
-----------------------------------------------------------------------------------------------------
Solver status: 3
Solver message: simulation failed at time=1.3: consider using smaller default or max time step.
values are:
A = NaN
C = Infinity
PrmA = Infinity
PrmA_bound = -Infinity
PrmR = Infinity
PrmR_bound = -Infinity
R = -Infinity
Failed execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_2'.
-----------------------------------------------------------------------------------------------------
final tolerance=0.1 final threshold=0.09, 885 remaining (keepAtMost=1000)
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_3'.
-----------------------------------------------------------------------------------------------------
/tmp/out/simulation.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@66f5a02e
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic_0' Task 'tsk_0_1'.
-----------------------------------------------------------------------------------------------------
cbit.vcell.solver.stoch.GibsonSolver@78a8978a
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_stochastic' Task 'tsk_1_0'.
-----------------------------------------------------------------------------------------------------
cbit.vcell.solver.stoch.GibsonSolver@159424e2
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_stochastic_0' Task 'tsk_1_1'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output `plot2d_Fig_1a` while CSV generation.
Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation.
Ignoring unsupported output `plot2d_Euler_default` while CSV generation.
Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation.
Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation.
Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation.
Generating report `report_Fig_1a`.
Generating report `report_low_delta_R_det`.
Generating report `report_Euler_default`.
Generating report `report_Euler_small_step_size`.
Generating report `report_Fig_1_c`.
Generating report `report_low_delta_R_stoch`.
Python 3.8.10
HDF conversion successful
Archiving resultant PDF files to `plots.zip`.
Archiving resultant CSV files to `reports.zip`.
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
(41.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000030
Warnings:
Unexpected reports were produced:
simulation.sedml/Figure_2ab
simulation.sedml/plot2d_Euler_default
simulation.sedml/plot2d_Euler_small_step_size
simulation.sedml/plot2d_Fig_1a
simulation.sedml/plot2d_low_delta_R_det
Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex
Jul 03, 2021 2:48:51 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_02ae93e8-2d99-4fcc-8956-27743ee2e04e4533636117417778607
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 2 model(s), 4 simulation(s), 4 task(s), 4 report(s), 5 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file simulation.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp4373693094120886631.xml
Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp3854756596844255917.xml
Task (id='tsk_0_2') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler
Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler
/tmp/out/simulation.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@1860f3be
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic' Task 'tsk_0_0'.
-----------------------------------------------------------------------------------------------------
Solver status: 3
Solver message: simulation failed at time=1.3: consider using smaller default or max time step.
values are:
A = NaN
C = Infinity
PrmA = Infinity
PrmA_bound = -Infinity
PrmR = Infinity
PrmR_bound = -Infinity
R = -Infinity
Failed execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic' Task 'tsk_0_2'.
-----------------------------------------------------------------------------------------------------
final tolerance=0.1 final threshold=0.09, 885 remaining (keepAtMost=1000)
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic' Task 'tsk_0_3'.
-----------------------------------------------------------------------------------------------------
/tmp/out/simulation.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@7af52ec7
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic_0' Task 'tsk_0_1'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output `Figure_2ab` while CSV generation.
Ignoring unsupported output `plot2d_Fig_1a` while CSV generation.
Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation.
Ignoring unsupported output `plot2d_Euler_default` while CSV generation.
Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation.
Generating report `report_Fig_1a`.
Generating report `report_low_delta_R_det`.
Generating report `report_Euler_default`.
Generating report `report_Euler_small_step_size`.
Python 3.8.10
HDF conversion successful
Archiving resultant PDF files to `plots.zip`.
Archiving resultant CSV files to `reports.zip`.
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
(24.2 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000027
Warnings:
Unexpected reports were produced:
simulation.sedml/plot2d_Fig_1_c
simulation.sedml/plot2d_low_delta_R_stoch
Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex
Jul 03, 2021 2:49:32 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_d3f11fb4-3457-4af0-85c9-46d72b609ccc7101228591929324252
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 2 model(s), 2 simulation(s), 2 task(s), 2 report(s), 2 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file simulation.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson
Succesful model import: SBML file /tmp/temp3682302998013122867.xml
Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson
Succesful model import: SBML file /tmp/temp8682192694551817540.xml
cbit.vcell.solver.stoch.GibsonSolver@178270b2
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM__ODE_stochastic' Task 'tsk_1_0'.
-----------------------------------------------------------------------------------------------------
cbit.vcell.solver.stoch.GibsonSolver@15fb7a32
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM__ODE_stochastic_0' Task 'tsk_1_1'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation.
Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation.
Generating report `report_Fig_1_c`.
Generating report `report_low_delta_R_stoch`.
Python 3.8.10
HDF conversion successful
Archiving resultant PDF files to `plots.zip`.
Archiving resultant CSV files to `reports.zip`.
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
(10.4 s)Test that simulator logs the execution of COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.
More information: https://biosimulators.org/conventions/status
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:47:05 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_248c9001-457e-4fec-8373-8777c717c7e15031358420438498571
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp3364724191462071292.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@77e2a6e2
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
-----------------------------------------------------------------------------------------------------
Generating report `report`.
Python 3.8.10
HDF conversion successful
No PDF files found, skipping archiving `plots.zip` files
Archiving resultant CSV files to `reports.zip`.
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
(10.5 s)Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.
More information: https://biosimulators.org/conventions/status
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:47:15 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_7067b1af-70d5-4936-821d-91f6e043c9fc4315264737624446413
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp3246684957460087224.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@77e2a6e2
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
-----------------------------------------------------------------------------------------------------
Generating report `report`.
Python 3.8.10
HDF conversion successful
No PDF files found, skipping archiving `plots.zip` files
Archiving resultant CSV files to `reports.zip`.
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
(10.3 s)Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.
More information: https://biosimulators.org/conventions/status
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:47:26 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_fb547784-9ab8-408c-9d02-ce2849a90fb61666253770330844669
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp6604291614595049683.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@77e2a6e2
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
-----------------------------------------------------------------------------------------------------
Generating report `report`.
Python 3.8.10
HDF conversion successful
No PDF files found, skipping archiving `plots.zip` files
Archiving resultant CSV files to `reports.zip`.
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
(10.6 s)Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.
More information: https://biosimulators.org/conventions/status
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:47:36 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_6b4ef30c-f9a3-4100-82bc-7c48e8d0afe86335007625603098163
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp8458038989198758338.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@77e2a6e2
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
-----------------------------------------------------------------------------------------------------
Generating report `report`.
Python 3.8.10
HDF conversion successful
No PDF files found, skipping archiving `plots.zip` files
Archiving resultant CSV files to `reports.zip`.
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_3972
Algorithm: KISAO_0000263
Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000263
Log:
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_3972
Algorithm: KISAO_0000019
Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000019
Log:
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_3240
Algorithm: KISAO_0000019
Reason for skip:
Case requires model formats format_3240 and simulation algorithms KISAO_0000019
Log:
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_9004
Algorithm: KISAO_0000019
Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000019
Log:
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_9004
Algorithm: KISAO_0000030
Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000030
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000088
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000088
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_000019
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_000019
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000496
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000496
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000560
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000560
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000029
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000029
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000437
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000437
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000449
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000449
Log:
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_9001
Algorithm: KISAO_0000057
Reason for skip:
Case requires model formats format_9001 and simulation algorithms KISAO_0000057
Log:
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
(2.7 s)Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1
).
Reason for skip:
The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.14' could not execute the archive:
Unknown error
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:43:11 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_f84ffac8-7278-4224-9bd5-5ed557d609e44582871903981045730
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
[Fatal Error] :1:1: Content is not allowed in prolog.
[Fatal Error] :1:1: Content is not allowed in prolog.
java.lang.RuntimeException: Error importing from SBML : no SBML source.
at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:449)
at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:700)
at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:66)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:188)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection
Error importing from SBML : no SBML source.
Unable to initialize bioModel for the given selection
Error importing from SBML : no SBML source.
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
(2.8 s)Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1
) and inherit the changes of the model.
Reason for skip:
The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.14' could not execute the archive:
Unknown error
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:43:14 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_fdbdf4cc-9e66-4ca7-8eae-8d8c2bf7b45a43127485615975458
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
[Fatal Error] :1:1: Content is not allowed in prolog.
[Fatal Error] :1:1: Content is not allowed in prolog.
java.lang.RuntimeException: Error importing from SBML : no SBML source.
at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:449)
at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:700)
at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:66)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:188)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection
Error importing from SBML : no SBML source.
Unable to initialize bioModel for the given selection
Error importing from SBML : no SBML source.
sedml.SimulatorProducesLinear3DPlots
(0.4 s)Test that a simulator produces linear 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing
Log:
sedml.SimulatorProducesLogarithmic3DPlots
(0.4 s)Test that a simulator produces logarithmic 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing
Log:
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
(10.4 s)Test that a simulator supports model changes that involve adding, replacing, and removing model elements.
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:44:06 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_04703fbf-4abf-4cfb-86cf-b070b5fcbfbb2335725844858544801
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp2512969967552597353.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@71b1a49c
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
Generating report report
.
Python 3.8.10
HDF conversion successful
No PDF files found, skipping archiving plots.zip
files
Archiving resultant CSV files to reports.zip
.
### `sedml.SimulatorSupportsComputeModelChanges` (11.5 s)
Test that a simulator supports compute model changes
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:44:27 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_3792c5fc-e02a-419d-9da9-c7ad3ca9bf9c7500771520050261646
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp6770789603215485308.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@67207d8a
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
Generating report report
.
Python 3.8.10
HDF conversion successful
No PDF files found, skipping archiving plots.zip
files
Archiving resultant CSV files to reports.zip
.
### `sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes` (13.8 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpgwp0vzp1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:44:39 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_2b6582cc-95c6-48b1-856e-679be09153f87928150321097858934
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp7193236838086361649.xml
Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@2d83c5a5
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@18151a14
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.
Generating report report__copy_2
.
Python 3.8.10
Traceback (most recent call last):
File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 372, in
fire.Fire({
File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
component_trace = _Fire(component, args, parsed_flag_args, context, name)
File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
component, remaining_args = _CallAndUpdateTrace(
File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
component = fn(*varargs, **kwargs)
File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 176, in exec_sed_doc
data_set_results[data_set.id] = data_set_df.loc[data_set.label, :].to_numpy(
File "/usr/local/lib/python3.8/dist-packages/pandas/core/base.py", line 610, in to_numpy
result = np.asarray(self._values, dtype=dtype)
ValueError: could not convert string to float: 'NaN.1'
HDF conversion failed
No PDF files found, skipping archiving plots.zip
files
Archiving resultant CSV files to reports.zip
.
### `sedml.SimulatorSupportsDataSetsWithDifferentShapes` (13.4 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp7x2djg6b/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:44:53 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_b7518a2e-32d8-4560-bd0e-919a3163e4944644695996497250327
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp579021980847083980.xml
Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@73e132e0
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@55a8dc49
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.
Generating report report
.
Traceback (most recent call last):
File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 372, in
fire.Fire({
File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
component_trace = _Fire(component, args, parsed_flag_args, context, name)
File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
component, remaining_args = _CallAndUpdateTrace(
File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
component = fn(*varargs, **kwargs)
File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 329, in gen_plot_pdfs
report_frames = get_report_dataframes(all_report_dataref, result_out_dir)
File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 298, in get_report_dataframes
report_frames[report] = pd.read_csv(os.path.join(
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 610, in read_csv
return _read(filepath_or_buffer, kwds)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 468, in _read
return parser.read(nrows)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 1057, in read
index, columns, col_dict = self._engine.read(nrows)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 2036, in read
data = self._reader.read(nrows)
File "pandas/_libs/parsers.pyx", line 756, in pandas._libs.parsers.TextReader.read
File "pandas/_libs/parsers.pyx", line 771, in pandas._libs.parsers.TextReader._read_low_memory
File "pandas/_libs/parsers.pyx", line 827, in pandas._libs.parsers.TextReader._read_rows
File "pandas/_libs/parsers.pyx", line 814, in pandas._libs.parsers.TextReader._tokenize_rows
File "pandas/_libs/parsers.pyx", line 1951, in pandas._libs.parsers.raise_parser_error
pandas.errors.ParserError: Error tokenizing data. C error: Expected 12 fields in line 5, saw 22
Python 3.8.10
Traceback (most recent call last):
File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 372, in
fire.Fire({
File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
component_trace = _Fire(component, args, parsed_flag_args, context, name)
File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
component, remaining_args = _CallAndUpdateTrace(
File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
component = fn(*varargs, **kwargs)
File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 156, in exec_sed_doc
data_set_df = pd.read_csv(report_filename).transpose()
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 610, in read_csv
return _read(filepath_or_buffer, kwds)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 468, in _read
return parser.read(nrows)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 1057, in read
index, columns, col_dict = self._engine.read(nrows)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 2036, in read
data = self._reader.read(nrows)
File "pandas/_libs/parsers.pyx", line 756, in pandas._libs.parsers.TextReader.read
File "pandas/_libs/parsers.pyx", line 771, in pandas._libs.parsers.TextReader._read_low_memory
File "pandas/_libs/parsers.pyx", line 827, in pandas._libs.parsers.TextReader._read_rows
File "pandas/_libs/parsers.pyx", line 814, in pandas._libs.parsers.TextReader._tokenize_rows
File "pandas/_libs/parsers.pyx", line 1951, in pandas._libs.parsers.raise_parser_error
pandas.errors.ParserError: Error tokenizing data. C error: Expected 12 fields in line 5, saw 22
HDF conversion failed
No PDF files found, skipping archiving plots.zip
files
Archiving resultant CSV files to reports.zip
.
### `sedml.SimulatorSupportsModelAttributeChanges` (11.9 s)
Test that a simulator supports changes to the attributes of model elements
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:45:06 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_21aef178-97e1-42e1-b206-bd7834ffd6e44276726985851909294
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s)
Successful translation: SED-ML file BIOMD0000000912_sim.sedml
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.
User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.
Succesful model import: SBML file /tmp/temp4309714689105680819.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@4f20a5e0
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
Generating report report
.
Python 3.8.10
HDF conversion successful
No PDF files found, skipping archiving plots.zip
files
Archiving resultant CSV files to reports.zip
.
### `sedml.SimulatorSupportsRepeatedTasksWithChanges` (4.9 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpy_bbdfxk/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:45:53 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_18318e00-8af7-43be-9b68-104e23cb4525551042468208609388
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
java.lang.NullPointerException
at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
SED-ML processing for /tmp/vcell_temp_18318e00-8af7-43be-9b68-104e23cb4525551042468208609388/BIOMD0000000912_sim.sedml failed with error: null
org.jlibsedml.XMLException
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
One or more errors encountered while executing archive /tmp/in/archive.omex
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:45:56 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_4ebce5fa-07bf-43b9-996b-9150dd3588096758372409516535710
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
java.lang.NullPointerException
at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
SED-ML processing for /tmp/vcell_temp_4ebce5fa-07bf-43b9-996b-9150dd3588096758372409516535710/BIOMD0000000912_sim.sedml failed with error: null
org.jlibsedml.XMLException
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
One or more errors encountered while executing archive /tmp/in/archive.omex
### `sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables` (4.9 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpmbdodx61/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:45:58 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_75400e31-6ea3-495c-9769-64717aaf82c62731654245571645858
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
java.lang.NullPointerException
at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
SED-ML processing for /tmp/vcell_temp_75400e31-6ea3-495c-9769-64717aaf82c62731654245571645858/BIOMD0000000912_sim.sedml failed with error: null
org.jlibsedml.XMLException
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
One or more errors encountered while executing archive /tmp/in/archive.omex
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:46:01 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_0926d1aa-6dbf-48d7-868f-ba36ae67dec52560794483319304852
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
java.lang.NullPointerException
at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
SED-ML processing for /tmp/vcell_temp_0926d1aa-6dbf-48d7-868f-ba36ae67dec52560794483319304852/BIOMD0000000912_sim.sedml failed with error: null
org.jlibsedml.XMLException
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
One or more errors encountered while executing archive /tmp/in/archive.omex
### `sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges` (2.4 s)
Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmps2un_9p0/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:46:03 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_4d2cd7bf-f9c1-4038-86b8-e0fbfdf593803725698290282127952
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
java.lang.NullPointerException
at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
SED-ML processing for /tmp/vcell_temp_4d2cd7bf-f9c1-4038-86b8-e0fbfdf593803725698290282127952/BIOMD0000000912_sim.sedml failed with error: null
org.jlibsedml.XMLException
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
One or more errors encountered while executing archive /tmp/in/archive.omex
### `sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges` (2.4 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpm21k5o1h/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:46:06 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_ff6a702a-ae29-45a0-86fa-e3b62a12bb64689867479419162420
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
java.lang.NullPointerException
at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
SED-ML processing for /tmp/vcell_temp_ff6a702a-ae29-45a0-86fa-e3b62a12bb64689867479419162420/BIOMD0000000912_sim.sedml failed with error: null
org.jlibsedml.XMLException
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
One or more errors encountered while executing archive /tmp/in/archive.omex
### `sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges` (2.4 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp0mxh24f8/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:46:08 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_c6690c6f-91d5-4253-998c-19849c8efe0a103810295799950409
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
java.lang.NullPointerException
at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
SED-ML processing for /tmp/vcell_temp_c6690c6f-91d5-4253-998c-19849c8efe0a103810295799950409/BIOMD0000000912_sim.sedml failed with error: null
org.jlibsedml.XMLException
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
One or more errors encountered while executing archive /tmp/in/archive.omex
### `sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks` (2.4 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpnkcb3ge5/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:46:11 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_853d61d7-39cd-4ac0-bbbd-9e9cada475625059839111660672082
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
java.lang.NullPointerException
at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
SED-ML processing for /tmp/vcell_temp_853d61d7-39cd-4ac0-bbbd-9e9cada475625059839111660672082/BIOMD0000000912_sim.sedml failed with error: null
org.jlibsedml.XMLException
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)
at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)
One or more errors encountered while executing archive /tmp/in/archive.omex
### `sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges` (2.4 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp_n58fuov/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
VCell CLI input archive /tmp/in/archive.omex
Jul 03, 2021 2:46:13 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_5b113604-dc25-4349-b397-9c3fe2320f653254334928173696920
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
SED-ML version level not supported, import may fail
java.lang.NullPointerException
at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
...
The image for your simulator is valid!
Your submission was committed to the BioSimulators registry. Thank you!
Future submissions of subsequent versions of VCell to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.
id: vcell version: 7.4.0.14 specificationsUrl: https://raw.githubusercontent.com/virtualcell/vcell/master/biosimulators.json specificationsPatch: version: 7.4.0.14 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.14 validateImage: true commitSimulator: true