Closed biosimulators-daemon closed 3 years ago
Thank you @biosimulators-daemon 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 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 from the "Artifacts" section at the bottom of this page.
The specifications of your simulator is valid!
Executed 63 test cases
Passed 26 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
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-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 37 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: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
(4.9 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:
cli.CliDisplaysHelpInline
(2.8 s)Test that a command-line interface provides inline help.
Warnings:
Command-line interface should support the `-h` option for displaying help inline.
The command-line interface displayed the following when executed with `-h`:
Invalid arguments: [-h, , , , , ]
Command-line interface should support the `--help` option for displaying help inline.
The command-line interface displayed the following when executed with `--help`:
Invalid arguments: [--help, , , , , ]
Log:
cli.CliDisplaysVersionInformationInline
(2.4 s)Test that a command-line interface provides version information inline.
Warnings:
Command-line interface should support the `-v` option for displaying version information inline.
The command-line interface displayed the following when executed with `-v`:
Invalid arguments: [-v, , , , , ]
Command-line interface should support the `--version` option for displaying version information inline.
The command-line interface displayed the following when executed with `--version`:
Invalid arguments: [--version, , , , , ]
Log:
docker_image.HasBioContainersLabels
(0.8 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
(0.8 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
(17.4 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
Jun 03, 2021 3:02:17 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_a2b21d78-5151-44c8-91cf-a0a7e14f28751514997849180412665
Python 3.6.9
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/temp3267105013983615852.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@b09fac1
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 3.6.9
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` (30.3 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
Jun 03, 2021 3:02:34 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_63ee66a2-9a05-482a-9e9a-e6ca7a0db5d29100852918851960687
Python 3.6.9
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/temp3622613446624970326.xml
/tmp/out/simulation_1.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@759de304
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 3.6.9
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
(71.5 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
Jun 03, 2021 3:04:25 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_45c5ed7a-1c52-46ac-a585-360bfded7c4c4942041319717329495
Python 3.6.9
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/temp8221945342343788938.xml
Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp6585530979215563289.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/temp8489257197551134340.xml
Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson
Succesful model import: SBML file /tmp/temp4803599954544509539.xml
/tmp/out/simulation.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@67f63d26
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@7c40ffef
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@433d9680
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_stochastic' Task 'tsk_1_0'.
-----------------------------------------------------------------------------------------------------
cbit.vcell.solver.stoch.GibsonSolver@1f992a3a
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 3.6.9
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
(50.4 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
Jun 03, 2021 3:03:05 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_bb3e0bcc-654c-4d75-8d29-4175ca6ee1926248975108313667153
Python 3.6.9
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/temp2663252565428851586.xml
Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp6241559689758881316.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@60a7e509
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@53c99b09
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 3.6.9
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
(29.6 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
Jun 03, 2021 3:03:55 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_297e9d7f-6d74-474a-9321-b20eb96fd6525482799180212616433
Python 3.6.9
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/temp6447980767447717926.xml
Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson
Succesful model import: SBML file /tmp/temp965379960086287054.xml
cbit.vcell.solver.stoch.GibsonSolver@42435b98
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@cb0f763
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 3.6.9
HDF conversion successful
Archiving resultant PDF files to `plots.zip`.
Archiving resultant CSV files to `reports.zip`.
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
(12.9 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
Jun 03, 2021 3:01:25 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_1d05abc1-5ad7-48e8-845d-a275f0de23e12460255175602288818
Python 3.6.9
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/temp3656025301138217000.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@273c947f
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
-----------------------------------------------------------------------------------------------------
Generating report `report`.
Python 3.6.9
HDF conversion successful
No PDF files found, skipping archiving `plots.zip` files
Archiving resultant CSV files to `reports.zip`.
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
(13.0 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
Jun 03, 2021 3:01:37 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_398aedaf-922c-4b24-881d-c85c03cb5a6b1424363097032498521
Python 3.6.9
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/temp4615875546501577937.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@273c947f
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
-----------------------------------------------------------------------------------------------------
Generating report `report`.
Python 3.6.9
HDF conversion successful
No PDF files found, skipping archiving `plots.zip` files
Archiving resultant CSV files to `reports.zip`.
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
(12.9 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
Jun 03, 2021 3:01:51 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_ab256294-0131-4c2b-a0f6-43859eee91be7413604024632584888
Python 3.6.9
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/temp1569131467873588086.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@273c947f
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
-----------------------------------------------------------------------------------------------------
Generating report `report`.
Python 3.6.9
HDF conversion successful
No PDF files found, skipping archiving `plots.zip` files
Archiving resultant CSV files to `reports.zip`.
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
(13.0 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
Jun 03, 2021 3:02:04 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_06c1ab66-51a6-4800-a75b-86e744f7f5d5416933645255689275
Python 3.6.9
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/temp7324750608683820298.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@273c947f
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
-----------------------------------------------------------------------------------------------------
Generating report `report`.
Python 3.6.9
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: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
(3.7 s)Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1
).
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_vcell/vcell:7.4.0.07' could not execute the archive:
Unknown error
Log:
VCell CLI input archive /tmp/in/archive.omex
Jun 03, 2021 2:56:33 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_6a5fb408-7585-4f15-a676-946bcbbbd0e4156659653519746940
Python 3.6.9
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:448)
at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:685)
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
(3.7 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/biosimulators/biosimulators_vcell/vcell:7.4.0.07' could not execute the archive:
Unknown error
Log:
VCell CLI input archive /tmp/in/archive.omex
Jun 03, 2021 2:56:36 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_6793efa3-7118-4b63-8615-5c86ebf873382886803786902678581
Python 3.6.9
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:448)
at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:685)
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
(13.1 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
Jun 03, 2021 2:57:42 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_6a127018-1f01-4823-a551-1085e35671dc833957126588421961
Python 3.6.9
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/temp7737356279155811068.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@b09fac1
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
Generating report report
.
Python 3.6.9
HDF conversion successful
No PDF files found, skipping archiving plots.zip
files
Archiving resultant CSV files to reports.zip
.
### `sedml.SimulatorSupportsComputeModelChanges` (14.2 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
Jun 03, 2021 2:58:08 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_47e35af0-ee21-482a-afe0-8e2bc5b37f263753850772382366764
Python 3.6.9
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/temp1479630363435892724.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@3b0ca5e1
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
Generating report report
.
Python 3.6.9
HDF conversion successful
No PDF files found, skipping archiving plots.zip
files
Archiving resultant CSV files to reports.zip
.
### `sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes` (16.4 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/tmpwqmt__o2/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
Jun 03, 2021 2:58:22 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_b92f3a93-65b6-45ad-be79-59d2db9d94393838741914330311443
Python 3.6.9
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/temp8608665594270171265.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@2c0f7678
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@5f574cc2
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.
Generating report report__copy_2
.
Python 3.6.9
Traceback (most recent call last):
File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 355, in
'genPlotPdfs': gen_plot_pdfs,
File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire
component_trace = _Fire(component, args, parsed_flag_args, context, name)
File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire
target=component.name)
File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
component = fn(*varargs, **kwargs)
File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 165, in exec_sed_doc
data_set_results[data_set.id] = data_set_df.loc[data_set.label, :].to_numpy(dtype ='float64')
File "/usr/local/lib/python3.6/dist-packages/pandas/core/base.py", line 846, in to_numpy
result = np.asarray(self._values, dtype=dtype)
File "/usr/local/lib/python3.6/dist-packages/numpy/core/_asarray.py", line 83, in asarray
return array(a, dtype, copy=False, order=order)
ValueError: could not convert string to float: 'NaN.9'
HDF conversion failed
No PDF files found, skipping archiving plots.zip
files
Archiving resultant CSV files to reports.zip
.
### `sedml.SimulatorSupportsDataSetsWithDifferentShapes` (16.5 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/tmpclimc69a/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
Jun 03, 2021 2:58:38 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_7ad56793-a243-47ed-adb8-6dc29840baa46769243163835779159
Python 3.6.9
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/temp6801442261111420624.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@62df0ff3
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@6134ac4a
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/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 355, in
'genPlotPdfs': gen_plot_pdfs,
File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire
component_trace = _Fire(component, args, parsed_flag_args, context, name)
File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire
target=component.name)
File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
component = fn(*varargs, **kwargs)
File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 305, in gen_plot_pdfs
report_frames = get_report_dataframes(all_report_dataref, result_out_dir)
File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 281, in get_report_dataframes
report_frames[report] = pd.read_csv(os.path.join(result_out_dir, report + ".csv")).T.reset_index()
File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 460, in _read
data = parser.read(nrows)
File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 1198, in read
ret = self._engine.read(nrows)
File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 2157, in read
data = self._reader.read(nrows)
File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader.read
File "pandas/_libs/parsers.pyx", line 862, in pandas._libs.parsers.TextReader._read_low_memory
File "pandas/_libs/parsers.pyx", line 918, in pandas._libs.parsers.TextReader._read_rows
File "pandas/_libs/parsers.pyx", line 905, in pandas._libs.parsers.TextReader._tokenize_rows
File "pandas/_libs/parsers.pyx", line 2042, in pandas._libs.parsers.raise_parser_error
pandas.errors.ParserError: Error tokenizing data. C error: Expected 12 fields in line 5, saw 22
Python 3.6.9
Traceback (most recent call last):
File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 355, in
'genPlotPdfs': gen_plot_pdfs,
File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire
component_trace = _Fire(component, args, parsed_flag_args, context, name)
File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire
target=component.name)
File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
component = fn(*varargs, **kwargs)
File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 145, in exec_sed_doc
data_set_df = pd.read_csv(report_filename).transpose()
File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 460, in _read
data = parser.read(nrows)
File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 1198, in read
ret = self._engine.read(nrows)
File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 2157, in read
data = self._reader.read(nrows)
File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader.read
File "pandas/_libs/parsers.pyx", line 862, in pandas._libs.parsers.TextReader._read_low_memory
File "pandas/_libs/parsers.pyx", line 918, in pandas._libs.parsers.TextReader._read_rows
File "pandas/_libs/parsers.pyx", line 905, in pandas._libs.parsers.TextReader._tokenize_rows
File "pandas/_libs/parsers.pyx", line 2042, 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` (14.4 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
Jun 03, 2021 2:58:55 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_cd736ca0-bd32-488e-8738-792e27f02dbb466818018482707058
Python 3.6.9
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/temp5019995266278276063.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@488b50ec
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
Generating report report
.
Python 3.6.9
HDF conversion successful
No PDF files found, skipping archiving plots.zip
files
Archiving resultant CSV files to reports.zip
.
### `sedml.SimulatorSupportsRepeatedTasksWithChanges` (6.8 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/tmp9lpcl4we/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
Jun 03, 2021 2:59:52 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_172f4688-3765-468f-8204-72f1a8df22991665420454893648850
Python 3.6.9
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_172f4688-3765-468f-8204-72f1a8df22991665420454893648850/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
Jun 03, 2021 2:59:56 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_46cbdbba-8270-4f53-83eb-6f970d42d5c8549941968615130995
Python 3.6.9
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_46cbdbba-8270-4f53-83eb-6f970d42d5c8549941968615130995/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` (6.8 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/tmpyptoq2hm/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
Jun 03, 2021 2:59:59 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_5cec1ed9-bbcc-4460-9e05-b7f556fd68de5786117796277307717
Python 3.6.9
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_5cec1ed9-bbcc-4460-9e05-b7f556fd68de5786117796277307717/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
Jun 03, 2021 3:00:03 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_9ead6fd4-a749-4739-bf41-bc3df5c6a2da2815203941005377476
Python 3.6.9
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_9ead6fd4-a749-4739-bf41-bc3df5c6a2da2815203941005377476/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` (3.4 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/tmpzqv5ouda/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
Jun 03, 2021 3:00:06 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_f368d526-d98d-4679-b474-1c007ca5f73f6698781018066830103
Python 3.6.9
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_f368d526-d98d-4679-b474-1c007ca5f73f6698781018066830103/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` (3.3 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/tmpy4rkzewc/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
Jun 03, 2021 3:00:09 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_40c18aac-acc8-4d23-aed7-6612a83a13a85669794037703447244
Python 3.6.9
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_40c18aac-acc8-4d23-aed7-6612a83a13a85669794037703447244/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` (3.2 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/tmpwx8mm0xj/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
Jun 03, 2021 3:00:13 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_94f7a54f-8732-4d43-ade9-0018eaa67bf53274485899552172477
Python 3.6.9
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_94f7a54f-8732-4d43-ade9-0018eaa67bf53274485899552172477/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` (3.3 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/tmpshslylcm/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
Jun 03, 2021 3:00:16 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_61fc3a35-96d9-44d7-85c9-cfcf070fbd824951127481021463257
Python 3.6.9
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_61fc3a35-96d9-44d7-85c9-cfcf070fbd824951127481021463257/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` (3.3 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/tmpiirhha0k/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
Jun 03, 2021 3:00:19 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_419bc1a4-b115-4582-a067-19081ac7b9ed3727780809273260695
Python 3.6.9
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_419bc1a4-b115-4582-a067-19081ac7b9ed3727780809273260695/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.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks` (3.4 s)
Test that a simulator supports nested repeated tasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp076y1v9o/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
Jun 03, 2021 3:00:23 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_510be3d9-c05d-46e3-b4ec-bcbfd4a5d1783695548560026207282
Python 3.6.9
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_510be3d9-c05d-46e3-b4ec-bcbfd4a5d1783695548560026207282/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.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes` (3.3 s)
Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their ``order`` attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes.
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpyegspevd/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
Jun 03, 2021 3:00:26 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_30847a77-d97b-4ff0-8408-0f778dab5c533538125043546602135
Python 3.6.9
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_30847a77-d97b-4ff0-8408-0f778dab5c533538125043546602135/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.SimulatorSupportsRepeatedTasksWithVectorRanges` (3.3 s)
Test that a simulator supports repeated tasks over vector ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmph1y104a5/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
Jun 03, 2021 3:00:29 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
TempPath Created: /tmp/vcell_temp_31b4d7b3-fc25-48f6-8789-4dd4a0cb6f2f1500334535016602888
Python 3.6.9
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_31b4d7b3-fc25-48f6-8789-4dd4a0cb6f2f1500334535016602888/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.SimulatorSupportsSubstitutingAlgorithms` (13.2 s)
Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.SAME_METHOD`. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.NONE`.
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected
Log:
VCell CLI input archive /tmp/in/archive.omex
Jun 03, 2021 3:00:33 PM java.util.prefs.FileSystemPrefer ...
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: 7.4.0.07 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_VCell/f83976f5c767369f31a7fa1b2e7f5dc52fa2a628/biosimulators.json specificationsPatch: version: 7.4.0.07 image: url: ghcr.io/biosimulators/biosimulators_vcell/vcell:7.4.0.07 validateImage: true commitSimulator: true