Closed vcdaemon closed 3 years ago
Thank you @vcdaemon 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 73 test cases
Passed 29 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/Elowitz-Nature-2000-Repressilator
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.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 0 test cases
Skipped 44 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/Elowitz-Nature-2000-Repressilator
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
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:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsComputeModelChanges
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'
- 'BUNDLE_OUTPUTS'
- 'COLLECT_COMBINE_ARCHIVE_RESULTS'
- 'COLLECT_SED_DOCUMENT_RESULTS'
- 'DEBUG'
- 'H5_REPORTS_PATH'
- 'KEEP_INDIVIDUAL_OUTPUTS'
- 'LOG_PATH'
- 'OMEX_METADATA_INPUT_FORMAT'
- 'OMEX_METADATA_OUTPUT_FORMAT'
- 'OMEX_METADATA_SCHEMA'
- 'PLOTS_PATH'
- 'REPORTS_PATH'
- 'REPORT_FORMATS'
- 'SAVE_PLOT_DATA'
- 'VALIDATE_IMAGES'
- 'VALIDATE_OMEX_MANIFESTS'
- 'VALIDATE_OMEX_METADATA'
- 'VALIDATE_RESULTS'
- 'VALIDATE_SEDML'
- 'VALIDATE_SEDML_MODELS'
- 'VERBOSE'
- 'VIZ_FORMATS'
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
(2.9 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`:
usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]
Command-line interface should support the `--help` option for displaying help inline.
The command-line interface displayed the following when executed with `--help`:
usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]
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`:
usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]
Command-line interface should support the `--version` option for displaying version information inline.
The command-line interface displayed the following when executed with `--version`:
usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]
Log:
docker_image.DeclaresSupportedEnvironmentVariables
(0.3 s)Test if a Docker image declares the environment variables that is supports
Warnings:
Docker images for simulation tools should declare the environment variables that they support.
The Docker image does not declare the following standard environment variables recognized by BioSimulators:
- 'BUNDLE_OUTPUTS'
- 'COLLECT_COMBINE_ARCHIVE_RESULTS'
- 'COLLECT_SED_DOCUMENT_RESULTS'
- 'DEBUG'
- 'H5_REPORTS_PATH'
- 'KEEP_INDIVIDUAL_OUTPUTS'
- 'LOG_PATH'
- 'OMEX_METADATA_INPUT_FORMAT'
- 'OMEX_METADATA_OUTPUT_FORMAT'
- 'OMEX_METADATA_SCHEMA'
- 'PLOTS_PATH'
- 'REPORTS_PATH'
- 'REPORT_FORMATS'
- 'SAVE_PLOT_DATA'
- 'VALIDATE_IMAGES'
- 'VALIDATE_OMEX_MANIFESTS'
- 'VALIDATE_OMEX_METADATA'
- 'VALIDATE_RESULTS'
- 'VALIDATE_SEDML'
- 'VALIDATE_SEDML_MODELS'
- 'VERBOSE'
- 'VIZ_FORMATS'
If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.
Note, support for these environment variables is optional. Simulation tools are not required to support these variables.
Log:
docker_image.HasBioContainersLabels
(0.3 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
(18.8 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_bottom_left
Log:
Oct 14, 2021 3:35:55 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_89a4398b-10bd-4e97-94e9-cb0999a4aa3d2813573605395207918
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
-----------------------------------------------------------------------------------------------------
name: BIOMD0000000912_sim
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]
UniformTimeCourse [initialTime=0.0, numberOfPoints=5000, outputEndTime=1000.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]
Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]
DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=time, getId()=data_gen_time]
DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=T, getId()=data_gen_T]
DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=E, getId()=data_gen_E]
DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=I, getId()=data_gen_I]
Plot2D [listOfCurves=[Curve [id=plot_1_T_time, logX=false, logY=false, name=T, xDataReference=data_gen_time, yDataReference=data_gen_T], Curve [id=plot_1_E_time, logX=false, logY=false, name=E, xDataReference=data_gen_time, yDataReference=data_gen_E], Curve [id=plot_1_I_time, logX=false, logY=false, name=I, xDataReference=data_gen_time, yDataReference=data_gen_I]], name=Figure 1 bottom, left]
org.jlibsedml.Report@c84c5553
org.jlibsedml.Report@6ca13e92
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/temp873453695920575961.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@325f7fa9
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations__BIOMD0000000912' Task 'Caravagna2010'.
Running simulation BIOMD0000000912_task_Caravagna2010, 232 ms
Ran 1 simulations for 1 biomodels.
Ignoring unsupported output Figure_1_bottom_left
while CSV generation.
Generating report report
.
Generating report __plot__Figure_1_bottom_left
.
report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv
HDF conversion successful
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: np.float
is a deprecated alias for the builtin float
. To silence this warning, use float
by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64
here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: np.float
is a deprecated alias for the builtin float
. To silence this warning, use float
by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64
here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: np.float
is a deprecated alias for the builtin float
. To silence this warning, use float
by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64
here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
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` (38.8 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
Log:
Oct 14, 2021 3:36:14 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_90ad1b8c-f9c9-43b1-9ff6-229fa46e3ba01045195953976933252
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
-----------------------------------------------------------------------------------------------------
name: simulation_1
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Model [id=Ciliberto2003_Morphogenesis, name=Ciliberto2003_Morphogenesis_Checkpoint, language=urn:sedml:language:sbml, src=BIOMD0000000297_url.xml]
UniformTimeCourse [initialTime=0.0, numberOfPoints=200, outputEndTime=140.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000086], getId()=simulation_1]
Task [modelReference=Ciliberto2003_Morphogenesis, name=simulation 1, simulationReference=simulation_1, getId()=task_1]
DataGenerator [math=org.jmathml.ASTRootNode@1c481ff2, name=time, getId()=data_gen_time]
DataGenerator [math=org.jmathml.ASTRootNode@72437d8d, name=Trim, getId()=data_gen_Trim]
DataGenerator [math=org.jmathml.ASTRootNode@1b955cac, name=Clb, getId()=data_gen_Clb]
DataGenerator [math=org.jmathml.ASTRootNode@676cf48, name=Sic, getId()=data_gen_Sic]
DataGenerator [math=org.jmathml.ASTRootNode@5a1de7fb, name=PTrim, getId()=data_gen_PTrim]
DataGenerator [math=org.jmathml.ASTRootNode@335b5620, name=PClb, getId()=data_gen_PClb]
DataGenerator [math=org.jmathml.ASTRootNode@29a0cdb, name=SBF, getId()=data_gen_SBF]
DataGenerator [math=org.jmathml.ASTRootNode@32a68f4f, name=IE, getId()=data_gen_IE]
DataGenerator [math=org.jmathml.ASTRootNode@73194df, name=Cdc20a, getId()=data_gen_Cdc20a]
DataGenerator [math=org.jmathml.ASTRootNode@6eb2384f, name=Cdc20, getId()=data_gen_Cdc20]
DataGenerator [math=org.jmathml.ASTRootNode@3c9c0d96, name=Cdh1, getId()=data_gen_Cdh1]
DataGenerator [math=org.jmathml.ASTRootNode@3a4621bd, name=Swe1, getId()=data_gen_Swe1]
DataGenerator [math=org.jmathml.ASTRootNode@31dadd46, name=Swe1M, getId()=data_gen_Swe1M]
DataGenerator [math=org.jmathml.ASTRootNode@4ed5eb72, name=PSwe1, getId()=data_gen_PSwe1]
DataGenerator [math=org.jmathml.ASTRootNode@12f9af83, name=PSwe1M, getId()=data_gen_PSwe1M]
DataGenerator [math=org.jmathml.ASTRootNode@19b93fa8, name=Mih1a, getId()=data_gen_Mih1a]
DataGenerator [math=org.jmathml.ASTRootNode@7e6ef134, name=Mcm, getId()=data_gen_Mcm]
DataGenerator [math=org.jmathml.ASTRootNode@1f010bf0, name=BE, getId()=data_gen_BE]
DataGenerator [math=org.jmathml.ASTRootNode@40db2a24, name=Cln, getId()=data_gen_Cln]
DataGenerator [math=org.jmathml.ASTRootNode@10cf09e8, name=mass, getId()=data_gen_mass]
DataGenerator [math=org.jmathml.ASTRootNode@1921ad94, name=Swe1T, getId()=data_gen_Swe1T]
Plot2D [listOfCurves=[Curve [id=curve_Figure_3a_Sic, logX=false, logY=false, name=Sic1, xDataReference=data_gen_time, yDataReference=data_gen_Sic], Curve [id=curve_Figure_3a_SBF, logX=false, logY=false, name=SBF, xDataReference=data_gen_time, yDataReference=data_gen_SBF], Curve [id=curve_Figure_3a_Clb, logX=false, logY=false, name=Clb2, xDataReference=data_gen_time, yDataReference=data_gen_Clb], Curve [id=curve_Figure_3a_Cln, logX=false, logY=false, name=Cln, xDataReference=data_gen_time, yDataReference=data_gen_Cln]], name=Figure 3a]
Plot2D [listOfCurves=[Curve [id=curve_Figure_3b_Cdc20a, logX=false, logY=false, name=Activated Cdc20, xDataReference=data_gen_time, yDataReference=data_gen_Cdc20a], Curve [id=curve_Figure_3b_Cdh1, logX=false, logY=false, name=Cdh1, xDataReference=data_gen_time, yDataReference=data_gen_Cdh1], Curve [id=curve_Figure_3b_Clb, logX=false, logY=false, name=Clb2, xDataReference=data_gen_time, yDataReference=data_gen_Clb], Curve [id=curve_Figure_3b_IE, logX=false, logY=false, name=Intermediary enzyme, xDataReference=data_gen_time, yDataReference=data_gen_IE]], name=Figure 3b]
Plot2D [listOfCurves=[Curve [id=curve_Figure_3c_Swe1, logX=false, logY=false, name=Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1], Curve [id=curve_Figure_3c_Swe1M, logX=false, logY=false, name=Modified Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1M], Curve [id=curve_Figure_3c_Swe1T, logX=false, logY=false, name=Total Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1T], Curve [id=curve_Figure_3c_PSwe1M, logX=false, logY=false, name=Phosphorylated, modified Swe1, xDataReference=data_gen_time, yDataReference=data_gen_PSwe1M]], name=Figure 3c]
Plot2D [listOfCurves=[Curve [id=curve_Figure_3d_mass, logX=false, logY=false, name=Mass, xDataReference=data_gen_time, yDataReference=data_gen_mass]], name=Figure 3d]
org.jlibsedml.Report@c84c5553
org.jlibsedml.Report@49f8ba87
org.jlibsedml.Report@49f8ba88
org.jlibsedml.Report@49f8ba89
org.jlibsedml.Report@49f8ba8a
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/temp3854971086453074288.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'.
Running simulation task_1_simulation 1, 1098 ms
-----------------------------------------------------------------------------------------------------
Ran 1 simulations for 1 biomodels.
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`.
Generating report `__plot__Figure_3a`.
Generating report `__plot__Figure_3b`.
Generating report `__plot__Figure_3c`.
Generating report `__plot__Figure_3d`.
report : /tmp/out/./simulation_1.sedml/report.csv
HDF conversion successful
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
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
(38.0 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
Log:
Oct 14, 2021 3:36:53 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_4af8902e-c70a-4efe-9cbb-69fd48be4a68423429995834310295
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
-----------------------------------------------------------------------------------------------------
name: simulation_1
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Model [id=Ciliberto2003_Morphogenesis, name=Ciliberto2003_Morphogenesis_Checkpoint, language=urn:sedml:language:sbml, src=BIOMD0000000297_url.xml]
UniformTimeCourse [initialTime=0.0, numberOfPoints=200, outputEndTime=140.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=simulation_1]
Task [modelReference=Ciliberto2003_Morphogenesis, name=simulation 1, simulationReference=simulation_1, getId()=task_1]
DataGenerator [math=org.jmathml.ASTRootNode@1c481ff2, name=time, getId()=data_gen_time]
DataGenerator [math=org.jmathml.ASTRootNode@72437d8d, name=Trim, getId()=data_gen_Trim]
DataGenerator [math=org.jmathml.ASTRootNode@1b955cac, name=Clb, getId()=data_gen_Clb]
DataGenerator [math=org.jmathml.ASTRootNode@676cf48, name=Sic, getId()=data_gen_Sic]
DataGenerator [math=org.jmathml.ASTRootNode@5a1de7fb, name=PTrim, getId()=data_gen_PTrim]
DataGenerator [math=org.jmathml.ASTRootNode@335b5620, name=PClb, getId()=data_gen_PClb]
DataGenerator [math=org.jmathml.ASTRootNode@29a0cdb, name=SBF, getId()=data_gen_SBF]
DataGenerator [math=org.jmathml.ASTRootNode@32a68f4f, name=IE, getId()=data_gen_IE]
DataGenerator [math=org.jmathml.ASTRootNode@73194df, name=Cdc20a, getId()=data_gen_Cdc20a]
DataGenerator [math=org.jmathml.ASTRootNode@6eb2384f, name=Cdc20, getId()=data_gen_Cdc20]
DataGenerator [math=org.jmathml.ASTRootNode@3c9c0d96, name=Cdh1, getId()=data_gen_Cdh1]
DataGenerator [math=org.jmathml.ASTRootNode@3a4621bd, name=Swe1, getId()=data_gen_Swe1]
DataGenerator [math=org.jmathml.ASTRootNode@31dadd46, name=Swe1M, getId()=data_gen_Swe1M]
DataGenerator [math=org.jmathml.ASTRootNode@4ed5eb72, name=PSwe1, getId()=data_gen_PSwe1]
DataGenerator [math=org.jmathml.ASTRootNode@12f9af83, name=PSwe1M, getId()=data_gen_PSwe1M]
DataGenerator [math=org.jmathml.ASTRootNode@19b93fa8, name=Mih1a, getId()=data_gen_Mih1a]
DataGenerator [math=org.jmathml.ASTRootNode@7e6ef134, name=Mcm, getId()=data_gen_Mcm]
DataGenerator [math=org.jmathml.ASTRootNode@1f010bf0, name=BE, getId()=data_gen_BE]
DataGenerator [math=org.jmathml.ASTRootNode@40db2a24, name=Cln, getId()=data_gen_Cln]
DataGenerator [math=org.jmathml.ASTRootNode@10cf09e8, name=mass, getId()=data_gen_mass]
DataGenerator [math=org.jmathml.ASTRootNode@1921ad94, name=Swe1T, getId()=data_gen_Swe1T]
Plot2D [listOfCurves=[Curve [id=curve_Figure_3a_Sic, logX=false, logY=false, name=Sic1, xDataReference=data_gen_time, yDataReference=data_gen_Sic], Curve [id=curve_Figure_3a_SBF, logX=false, logY=false, name=SBF, xDataReference=data_gen_time, yDataReference=data_gen_SBF], Curve [id=curve_Figure_3a_Clb, logX=false, logY=false, name=Clb2, xDataReference=data_gen_time, yDataReference=data_gen_Clb], Curve [id=curve_Figure_3a_Cln, logX=false, logY=false, name=Cln, xDataReference=data_gen_time, yDataReference=data_gen_Cln]], name=Figure 3a]
Plot2D [listOfCurves=[Curve [id=curve_Figure_3b_Cdc20a, logX=false, logY=false, name=Activated Cdc20, xDataReference=data_gen_time, yDataReference=data_gen_Cdc20a], Curve [id=curve_Figure_3b_Cdh1, logX=false, logY=false, name=Cdh1, xDataReference=data_gen_time, yDataReference=data_gen_Cdh1], Curve [id=curve_Figure_3b_Clb, logX=false, logY=false, name=Clb2, xDataReference=data_gen_time, yDataReference=data_gen_Clb], Curve [id=curve_Figure_3b_IE, logX=false, logY=false, name=Intermediary enzyme, xDataReference=data_gen_time, yDataReference=data_gen_IE]], name=Figure 3b]
Plot2D [listOfCurves=[Curve [id=curve_Figure_3c_Swe1, logX=false, logY=false, name=Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1], Curve [id=curve_Figure_3c_Swe1M, logX=false, logY=false, name=Modified Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1M], Curve [id=curve_Figure_3c_Swe1T, logX=false, logY=false, name=Total Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1T], Curve [id=curve_Figure_3c_PSwe1M, logX=false, logY=false, name=Phosphorylated, modified Swe1, xDataReference=data_gen_time, yDataReference=data_gen_PSwe1M]], name=Figure 3c]
Plot2D [listOfCurves=[Curve [id=curve_Figure_3d_mass, logX=false, logY=false, name=Mass, xDataReference=data_gen_time, yDataReference=data_gen_mass]], name=Figure 3d]
org.jlibsedml.Report@c84c5553
org.jlibsedml.Report@49f8ba87
org.jlibsedml.Report@49f8ba88
org.jlibsedml.Report@49f8ba89
org.jlibsedml.Report@49f8ba8a
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/temp6715071080615597744.xml
/tmp/out/simulation_1.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@50ab56e2
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous__Ciliberto2003_Morphogenesis' Task 'simulation 1'.
Running simulation task_1_simulation 1, 188 ms
-----------------------------------------------------------------------------------------------------
Ran 1 simulations for 1 biomodels.
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`.
Generating report `__plot__Figure_3a`.
Generating report `__plot__Figure_3b`.
Generating report `__plot__Figure_3c`.
Generating report `__plot__Figure_3d`.
report : /tmp/out/./simulation_1.sedml/report.csv
HDF conversion successful
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
Archiving resultant PDF files to `plots.zip`.
Archiving resultant CSV files to `reports.zip`.
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
(19.2 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000019
Warnings:
Unexpected reports were produced:
simulation.sedml/Figure_1c
Log:
Oct 14, 2021 3:37:31 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/Elowitz-Nature-2000-Repressilator.omex
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_96d4be60-f1d7-4809-823a-0ffd9bbd3d3e1190408632388309143
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 simulation.sedml
-----------------------------------------------------------------------------------------------------
name: simulation
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Model [id=model, name=null, language=urn:sedml:language:sbml, src=BIOMD0000000012_url.xml]
UniformTimeCourse [initialTime=0.0, numberOfPoints=600, outputEndTime=1000.0, outputStartTime=400.0, Algorithm [kisaoID=KISAO:0000019], getId()=simulation]
Task [modelReference=model, name=null, simulationReference=simulation, getId()=task]
DataGenerator [math=org.jmathml.ASTRootNode@78641d23, name=time, getId()=data_gen_time]
DataGenerator [math=org.jmathml.ASTRootNode@74589991, name=LacI protein, getId()=data_gen_px]
DataGenerator [math=org.jmathml.ASTRootNode@146dfe6, name=TetR protein, getId()=data_gen_py]
DataGenerator [math=org.jmathml.ASTRootNode@4716be8b, name=cI protein, getId()=data_gen_pz]
DataGenerator [math=org.jmathml.ASTRootNode@1fc32e4f, name=LacI mRNA, getId()=data_gen_x]
DataGenerator [math=org.jmathml.ASTRootNode@2f67b837, name=TetR mRNA, getId()=data_gen_y]
DataGenerator [math=org.jmathml.ASTRootNode@1869fbd2, name=cI mRNA, getId()=data_gen_z]
Plot2D [listOfCurves=[Curve [id=Figure_1c_laci_protein, logX=false, logY=false, name=LacI protein, xDataReference=data_gen_time, yDataReference=data_gen_px], Curve [id=Figure_1c_tetr_protein, logX=false, logY=false, name=TetR protein, xDataReference=data_gen_time, yDataReference=data_gen_py], Curve [id=Figure_1c_ci_protein, logX=false, logY=false, name=cI protein, xDataReference=data_gen_time, yDataReference=data_gen_pz]], name=Figure 1c]
org.jlibsedml.Report@c84c5553
org.jlibsedml.Report@49f8ba4b
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') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp8252578738778708431.xml
/tmp/out/simulation.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@4e17913b
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'Elowitz-Nature-2000-Repressilator__model' Task 'task'.
Running simulation task_task, 189 ms
-----------------------------------------------------------------------------------------------------
Ran 1 simulations for 1 biomodels.
Ignoring unsupported output `Figure_1c` while CSV generation.
Generating report `report`.
Generating report `__plot__Figure_1c`.
report : /tmp/out/simulation.sedml/report.csv
HDF conversion successful
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:415: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
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
(103.9 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:
Oct 14, 2021 3:39:12 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_2b2413f1-050a-4c1d-be8c-274927932bdb9029932550554609793
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
-----------------------------------------------------------------------------------------------------
name: simulation
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Model [id=ODE_deterministic, name=ODE deterministic, language=urn:sedml:language:sbml, src=model_ODE_deterministic.xml]
Model [id=ODE_deterministic_0, name=ODE deterministic modified, language=urn:sedml:language:sbml, src=model_ODE_deterministic.xml]
Model [id=ODE_stochastic, name=ODE stochastic, language=urn:sedml:language:sbml, src=model_ODE_stochastic.xml]
Model [id=ODE_stochastic_0, name=ODE stochastic modified, language=urn:sedml:language:sbml, src=model_ODE_stochastic.xml]
UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019 AlgorithmParameter [kisaoID=KISAO:0000211 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000209 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000467 value=1.0] ], getId()=Fig_1a]
UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019 AlgorithmParameter [kisaoID=KISAO:0000211 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000209 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000467 value=1.0] ], getId()=low_delta_R_det]
UniformTimeCourse [initialTime=0.0, numberOfPoints=1000, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000030 AlgorithmParameter [kisaoID=KISAO:0000483 value=0.1] ], getId()=Euler_default]
UniformTimeCourse [initialTime=0.0, numberOfPoints=1000, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000030 AlgorithmParameter [kisaoID=KISAO:0000483 value=0.001] ], getId()=Euler_small_step_size]
UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000027], getId()=Fig_1_c]
UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000027], getId()=low_delta_R_stoch]
Task [modelReference=ODE_deterministic, name=tsk_0_0, simulationReference=Fig_1a, getId()=tsk_0_0]
Task [modelReference=ODE_deterministic_0, name=tsk_0_1, simulationReference=low_delta_R_det, getId()=tsk_0_1]
Task [modelReference=ODE_deterministic, name=tsk_0_2, simulationReference=Euler_default, getId()=tsk_0_2]
Task [modelReference=ODE_deterministic, name=tsk_0_3, simulationReference=Euler_small_step_size, getId()=tsk_0_3]
Task [modelReference=ODE_stochastic, name=tsk_1_0, simulationReference=Fig_1_c, getId()=tsk_1_0]
Task [modelReference=ODE_stochastic_0, name=tsk_1_1, simulationReference=low_delta_R_stoch, getId()=tsk_1_1]
DataGenerator [math=org.jmathml.ASTRootNode@495fac5f, name=time_tsk_0_0, getId()=time_tsk_0_0]
DataGenerator [math=org.jmathml.ASTRootNode@76012793, name=dataGen_tsk_0_0_mRNA_R, getId()=dataGen_tsk_0_0_mRNA_R]
DataGenerator [math=org.jmathml.ASTRootNode@635572a7, name=dataGen_tsk_0_0_A, getId()=dataGen_tsk_0_0_A]
DataGenerator [math=org.jmathml.ASTRootNode@79d94571, name=dataGen_tsk_0_0_R, getId()=dataGen_tsk_0_0_R]
DataGenerator [math=org.jmathml.ASTRootNode@4dd02341, name=dataGen_tsk_0_0_PrmA, getId()=dataGen_tsk_0_0_PrmA]
DataGenerator [math=org.jmathml.ASTRootNode@3212a8d7, name=dataGen_tsk_0_0_PrmR, getId()=dataGen_tsk_0_0_PrmR]
DataGenerator [math=org.jmathml.ASTRootNode@7a1a3478, name=dataGen_tsk_0_0_C, getId()=dataGen_tsk_0_0_C]
DataGenerator [math=org.jmathml.ASTRootNode@495b0487, name=dataGen_tsk_0_0_PrmA_bound, getId()=dataGen_tsk_0_0_PrmA_bound]
DataGenerator [math=org.jmathml.ASTRootNode@55dfcc6, name=dataGen_tsk_0_0_PrmR_bound, getId()=dataGen_tsk_0_0_PrmR_bound]
DataGenerator [math=org.jmathml.ASTRootNode@222eb8aa, name=dataGen_tsk_0_0_mRNA_A_, getId()=dataGen_tsk_0_0_mRNA_A_]
DataGenerator [math=org.jmathml.ASTRootNode@93cf163, name=time_tsk_0_1, getId()=time_tsk_0_1]
DataGenerator [math=org.jmathml.ASTRootNode@1852a3ff, name=dataGen_tsk_0_1_mRNA_R, getId()=dataGen_tsk_0_1_mRNA_R]
DataGenerator [math=org.jmathml.ASTRootNode@7203c7ff, name=dataGen_tsk_0_1_A, getId()=dataGen_tsk_0_1_A]
DataGenerator [math=org.jmathml.ASTRootNode@25bfcafd, name=dataGen_tsk_0_1_R, getId()=dataGen_tsk_0_1_R]
DataGenerator [math=org.jmathml.ASTRootNode@4b6690c0, name=dataGen_tsk_0_1_PrmA, getId()=dataGen_tsk_0_1_PrmA]
DataGenerator [math=org.jmathml.ASTRootNode@46268f08, name=dataGen_tsk_0_1_PrmR, getId()=dataGen_tsk_0_1_PrmR]
DataGenerator [math=org.jmathml.ASTRootNode@2a76840c, name=dataGen_tsk_0_1_C, getId()=dataGen_tsk_0_1_C]
DataGenerator [math=org.jmathml.ASTRootNode@71454b9d, name=dataGen_tsk_0_1_PrmA_bound, getId()=dataGen_tsk_0_1_PrmA_bound]
DataGenerator [math=org.jmathml.ASTRootNode@eda25e5, name=dataGen_tsk_0_1_PrmR_bound, getId()=dataGen_tsk_0_1_PrmR_bound]
DataGenerator [math=org.jmathml.ASTRootNode@7cf6a5f9, name=dataGen_tsk_0_1_mRNA_A_, getId()=dataGen_tsk_0_1_mRNA_A_]
DataGenerator [math=org.jmathml.ASTRootNode@623e088f, name=time_tsk_0_2, getId()=time_tsk_0_2]
DataGenerator [math=org.jmathml.ASTRootNode@39fcbef6, name=dataGen_tsk_0_2_mRNA_R, getId()=dataGen_tsk_0_2_mRNA_R]
DataGenerator [math=org.jmathml.ASTRootNode@66565121, name=dataGen_tsk_0_2_A, getId()=dataGen_tsk_0_2_A]
DataGenerator [math=org.jmathml.ASTRootNode@2fc6f97f, name=dataGen_tsk_0_2_R, getId()=dataGen_tsk_0_2_R]
DataGenerator [math=org.jmathml.ASTRootNode@3d2ee678, name=dataGen_tsk_0_2_PrmA, getId()=dataGen_tsk_0_2_PrmA]
DataGenerator [math=org.jmathml.ASTRootNode@6179e425, name=dataGen_tsk_0_2_PrmR, getId()=dataGen_tsk_0_2_PrmR]
DataGenerator [math=org.jmathml.ASTRootNode@35f26e72, name=dataGen_tsk_0_2_C, getId()=dataGen_tsk_0_2_C]
DataGenerator [math=org.jmathml.ASTRootNode@2d6764b2, name=dataGen_tsk_0_2_PrmA_bound, getId()=dataGen_tsk_0_2_PrmA_bound]
DataGenerator [math=org.jmathml.ASTRootNode@67304a40, name=dataGen_tsk_0_2_PrmR_bound, getId()=dataGen_tsk_0_2_PrmR_bound]
DataGenerator [math=org.jmathml.ASTRootNode@49c6c24f, name=dataGen_tsk_0_2_mRNA_A_, getId()=dataGen_tsk_0_2_mRNA_A_]
DataGenerator [math=org.jmathml.ASTRootNode@6fe1b4fb, name=time_tsk_0_3, getId()=time_tsk_0_3]
DataGenerator [math=org.jmathml.ASTRootNode@79351f41, name=dataGen_tsk_0_3_mRNA_R, getId()=dataGen_tsk_0_3_mRNA_R]
DataGenerator [math=org.jmathml.ASTRootNode@1c32386d, name=dataGen_tsk_0_3_A, getId()=dataGen_tsk_0_3_A]
DataGenerator [math=org.jmathml.ASTRootNode@6399551e, name=dataGen_tsk_0_3_R, getId()=dataGen_tsk_0_3_R]
DataGenerator [math=org.jmathml.ASTRootNode@13d73fa, name=dataGen_tsk_0_3_PrmA, getId()=dataGen_tsk_0_3_PrmA]
DataGenerator [math=org.jmathml.ASTRootNode@5023bb8b, name=dataGen_tsk_0_3_PrmR, getId()=dataGen_tsk_0_3_PrmR]
DataGenerator [math=org.jmathml.ASTRootNode@5d5f10b2, name=dataGen_tsk_0_3_C, getId()=dataGen_tsk_0_3_C]
DataGenerator [math=org.jmathml.ASTRootNode@74c79fa2, name=dataGen_tsk_0_3_PrmA_bound, getId()=dataGen_tsk_0_3_PrmA_bound]
DataGenerator [math=org.jmathml.ASTRootNode@1e0f9063, name=dataGen_tsk_0_3_PrmR_bound, getId()=dataGen_tsk_0_3_PrmR_bound]
DataGenerator [math=org.jmathml.ASTRootNode@53bd8fca, name=dataGen_tsk_0_3_mRNA_A_, getId()=dataGen_tsk_0_3_mRNA_A_]
DataGenerator [math=org.jmathml.ASTRootNode@7642df8f, name=time_tsk_1_0, getId()=time_tsk_1_0]
DataGenerator [math=org.jmathml.ASTRootNode@3e30646a, name=dataGen_tsk_1_0_mRNA_R, getId()=dataGen_tsk_1_0_mRNA_R]
DataGenerator [math=org.jmathml.ASTRootNode@5cde6747, name=dataGen_tsk_1_0_A, getId()=dataGen_tsk_1_0_A]
DataGenerator [math=org.jmathml.ASTRootNode@63a270c9, name=dataGen_tsk_1_0_R, getId()=dataGen_tsk_1_0_R]
DataGenerator [math=org.jmathml.ASTRootNode@37c7595, name=dataGen_tsk_1_0_PrmA, getId()=dataGen_tsk_1_0_PrmA]
DataGenerator [math=org.jmathml.ASTRootNode@3ed242a4, name=dataGen_tsk_1_0_PrmR, getId()=dataGen_tsk_1_0_PrmR]
DataGenerator [math=org.jmathml.ASTRootNode@1199fe66, name=dataGen_tsk_1_0_C, getId()=dataGen_tsk_1_0_C]
DataGenerator [math=org.jmathml.ASTRootNode@614df0a4, name=dataGen_tsk_1_0_PrmA_bound, getId()=dataGen_tsk_1_0_PrmA_bound]
DataGenerator [math=org.jmathml.ASTRootNode@1fdf1c5, name=dataGen_tsk_1_0_PrmR_bound, getId()=dataGen_tsk_1_0_PrmR_bound]
DataGenerator [math=org.jmathml.ASTRootNode@2d96543c, name=dataGen_tsk_1_0_mRNA_A_, getId()=dataGen_tsk_1_0_mRNA_A_]
DataGenerator [math=org.jmathml.ASTRootNode@73a2e526, name=time_tsk_1_1, getId()=time_tsk_1_1]
DataGenerator [math=org.jmathml.ASTRootNode@7d64e326, name=dataGen_tsk_1_1_mRNA_R, getId()=dataGen_tsk_1_1_mRNA_R]
DataGenerator [math=org.jmathml.ASTRootNode@13f95696, name=dataGen_tsk_1_1_A, getId()=dataGen_tsk_1_1_A]
DataGenerator [math=org.jmathml.ASTRootNode@cd1d761, name=dataGen_tsk_1_1_R, getId()=dataGen_tsk_1_1_R]
DataGenerator [math=org.jmathml.ASTRootNode@68be8808, name=dataGen_tsk_1_1_PrmA, getId()=dataGen_tsk_1_1_PrmA]
DataGenerator [math=org.jmathml.ASTRootNode@32193bea, name=dataGen_tsk_1_1_PrmR, getId()=dataGen_tsk_1_1_PrmR]
DataGenerator [math=org.jmathml.ASTRootNode@6b8d96d9, name=dataGen_tsk_1_1_C, getId()=dataGen_tsk_1_1_C]
DataGenerator [math=org.jmathml.ASTRootNode@69653e16, name=dataGen_tsk_1_1_PrmA_bound, getId()=dataGen_tsk_1_1_PrmA_bound]
DataGenerator [math=org.jmathml.ASTRootNode@758705fa, name=dataGen_tsk_1_1_PrmR_bound, getId()=dataGen_tsk_1_1_PrmR_bound]
DataGenerator [math=org.jmathml.ASTRootNode@ebaa6cb, name=dataGen_tsk_1_1_mRNA_A_, getId()=dataGen_tsk_1_1_mRNA_A_]
Plot2D [listOfCurves=[Curve [id=plot2d_Fig_1a_curve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_mRNA_R], Curve [id=plot2d_Fig_1a_curve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_A], Curve [id=plot2d_Fig_1a_curve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_R], Curve [id=plot2d_Fig_1a_curve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmA], Curve [id=plot2d_Fig_1a_curve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmR], Curve [id=plot2d_Fig_1a_curve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_C], Curve [id=plot2d_Fig_1a_curve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmA_bound], Curve [id=plot2d_Fig_1a_curve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmR_bound], Curve [id=plot2d_Fig_1a_curve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_mRNA_A_]], name=ODE deterministicplots]
Plot2D [listOfCurves=[Curve [id=plot2d_low_delta_R_detcurve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_mRNA_R], Curve [id=plot2d_low_delta_R_detcurve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_A], Curve [id=plot2d_low_delta_R_detcurve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_R], Curve [id=plot2d_low_delta_R_detcurve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmA], Curve [id=plot2d_low_delta_R_detcurve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmR], Curve [id=plot2d_low_delta_R_detcurve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_C], Curve [id=plot2d_low_delta_R_detcurve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmA_bound], Curve [id=plot2d_low_delta_R_detcurve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmR_bound], Curve [id=plot2d_low_delta_R_detcurve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_mRNA_A_]], name=ODE deterministicplots]
Plot2D [listOfCurves=[Curve [id=plot2d_Euler_default_curve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_mRNA_R], Curve [id=plot2d_Euler_default_curve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_A], Curve [id=plot2d_Euler_default_curve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_R], Curve [id=plot2d_Euler_default_curve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmA], Curve [id=plot2d_Euler_default_curve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmR], Curve [id=plot2d_Euler_default_curve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_C], Curve [id=plot2d_Euler_default_curve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmA_bound], Curve [id=plot2d_Euler_default_curve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmR_bound], Curve [id=plot2d_Euler_default_curve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_mRNA_A_]], name=ODE deterministicplots]
Plot2D [listOfCurves=[Curve [id=plot2d_Euler_small_step_size_curve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_mRNA_R], Curve [id=plot2d_Euler_small_step_size_curve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_A], Curve [id=plot2d_Euler_small_step_size_curve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_R], Curve [id=plot2d_Euler_small_step_size_curve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_PrmA], Curve [id=plot2d_Euler_small_step_size_curve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_PrmR], Curve [id=plot2d_Euler_small_step_size_curve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_C], Curve [id=plot2d_Euler_small_step_size_curve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_PrmA_bound], Curve [id=plot2d_Euler_small_step_size_curve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_PrmR_bound], Curve [id=plot2d_Euler_small_step_size_curve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_mRNA_A_]], name=ODE deterministicplots]
Plot2D [listOfCurves=[Curve [id=plot2d_Fig_1_ccurve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_mRNA_R], Curve [id=plot2d_Fig_1_ccurve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_A], Curve [id=plot2d_Fig_1_ccurve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_R], Curve [id=plot2d_Fig_1_ccurve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_PrmA], Curve [id=plot2d_Fig_1_ccurve_4, logX=false, logY=false, name=curve_4, xData ...
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
(14.5 s)Test that simulator logs the execution of COMBINE/OMEX archives
Reason for skip:
The execution status report produced by the simulator is not valid:
load() missing 1 required positional argument: 'Loader'
Log:
Oct 14, 2021 3:34:57 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/archive.omex
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_c084048e-4989-4742-8213-97cf6f59fe157472210901806582979
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
-----------------------------------------------------------------------------------------------------
name: BIOMD0000000912_sim
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]
UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]
Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]
DataGenerator [math=org.jmathml.ASTRootNode@2c78d320, name=time, getId()=data_gen_time]
DataGenerator [math=org.jmathml.ASTRootNode@132e0cc, name=T, getId()=data_gen_T]
DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=E, getId()=data_gen_E]
DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=I, getId()=data_gen_I]
org.jlibsedml.Report@c84c5553
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/temp8086111508179903275.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@757f675c
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
Running simulation BIOMD0000000912_task_Caravagna2010, 103 ms
-----------------------------------------------------------------------------------------------------
Ran 1 simulations for 1 biomodels.
Generating report `report`.
report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv
HDF conversion successful
No PDF files found, skipping archiving `plots.zip` files
Archiving resultant CSV files to `reports.zip`.
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
(14.4 s)Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives
Reason for skip:
The execution status report produced by the simulator is not valid:
load() missing 1 required positional argument: 'Loader'
Log:
Oct 14, 2021 3:35:11 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/archive.omex
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_4470a289-68e9-4b26-a023-fed2723d7d743717328942117994241
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
-----------------------------------------------------------------------------------------------------
name: BIOMD0000000912_sim
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]
UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]
Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]
DataGenerator [math=org.jmathml.ASTRootNode@2c78d320, name=time, getId()=data_gen_time]
DataGenerator [math=org.jmathml.ASTRootNode@132e0cc, name=T, getId()=data_gen_T]
DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=E, getId()=data_gen_E]
DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=I, getId()=data_gen_I]
org.jlibsedml.Report@c84c5553
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/temp7016211203109970443.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@757f675c
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
Running simulation BIOMD0000000912_task_Caravagna2010, 111 ms
-----------------------------------------------------------------------------------------------------
Ran 1 simulations for 1 biomodels.
Generating report `report`.
report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv
HDF conversion successful
No PDF files found, skipping archiving `plots.zip` files
Archiving resultant CSV files to `reports.zip`.
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
(14.7 s)Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives
Reason for skip:
The execution status report produced by the simulator is not valid:
load() missing 1 required positional argument: 'Loader'
Log:
Oct 14, 2021 3:35:26 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/archive.omex
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_d1299a33-2486-4196-837c-ab1237b62a251014813867579097538
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
-----------------------------------------------------------------------------------------------------
name: BIOMD0000000912_sim
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]
UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]
Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]
DataGenerator [math=org.jmathml.ASTRootNode@2c78d320, name=time, getId()=data_gen_time]
DataGenerator [math=org.jmathml.ASTRootNode@132e0cc, name=T, getId()=data_gen_T]
DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=E, getId()=data_gen_E]
DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=I, getId()=data_gen_I]
org.jlibsedml.Report@c84c5553
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/temp6528206683117526591.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@757f675c
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
Running simulation BIOMD0000000912_task_Caravagna2010, 102 ms
-----------------------------------------------------------------------------------------------------
Ran 1 simulations for 1 biomodels.
Generating report `report`.
report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv
HDF conversion successful
No PDF files found, skipping archiving `plots.zip` files
Archiving resultant CSV files to `reports.zip`.
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
(14.7 s)Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives
Reason for skip:
The execution status report produced by the simulator is not valid:
load() missing 1 required positional argument: 'Loader'
Log:
Oct 14, 2021 3:35:41 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/archive.omex
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_61b04b24-0306-4b96-a0c2-8399c10367a61755933335631185923
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
-----------------------------------------------------------------------------------------------------
name: BIOMD0000000912_sim
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]
UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]
Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]
DataGenerator [math=org.jmathml.ASTRootNode@2c78d320, name=time, getId()=data_gen_time]
DataGenerator [math=org.jmathml.ASTRootNode@132e0cc, name=T, getId()=data_gen_T]
DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=E, getId()=data_gen_E]
DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=I, getId()=data_gen_I]
org.jlibsedml.Report@c84c5553
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/temp1447154212714301329.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@2617f816
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
Running simulation BIOMD0000000912_task_Caravagna2010, 105 ms
-----------------------------------------------------------------------------------------------------
Ran 1 simulations for 1 biomodels.
Generating report `report`.
report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv
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/Elowitz-Nature-2000-Repressilator
(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: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:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000019
Reason for skip:
Case requires model formats format_2585 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:rba/Escherichia-coli-K12-WT
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_9012
Algorithm: KISAO_0000669
Reason for skip:
Case requires model formats format_9012 and simulation algorithms KISAO_0000669
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:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
(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:
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
(0.0 s)Required model formats and simulation algorithms for SED tasks:
Format: format_9010
Algorithm: KISAO_0000019
Reason for skip:
Case requires model formats format_9010 and simulation algorithms KISAO_0000019
Log:
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
(7.0 s)Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1
).
Reason for skip:
Simulator did not produce the following reports:
- `BIOMD0000000912_sim.sedml/report`
Log:
Oct 14, 2021 3:28:47 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/archive.omex
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_a4089cc0-45f7-48bd-a736-e0d70649dd783176327734173947976
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
-----------------------------------------------------------------------------------------------------
name: BIOMD0000000912_sim
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=#__source__]
Model [id=__source__, name=null, language=urn:sedml:language:sbml, src=Caravagna2010.xml]
UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]
Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]
DataGenerator [math=org.jmathml.ASTRootNode@2c78d320, name=time, getId()=data_gen_time]
DataGenerator [math=org.jmathml.ASTRootNode@132e0cc, name=T, getId()=data_gen_T]
DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=E, getId()=data_gen_E]
DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=I, getId()=data_gen_I]
org.jlibsedml.Report@c84c5553
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:704)
at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:71)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:248)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:85)
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.
No PDF files found, skipping archiving `plots.zip` files
No CSV files found, skipping archiving `reports.zip` files
One or more errors encountered while executing archive /tmp/in/archive.omex
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
(6.9 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:
Simulator did not produce the following reports:
- `BIOMD0000000912_sim.sedml/report`
Log:
Oct 14, 2021 3:28:54 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/archive.omex
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_12e517a0-d77e-40aa-b1fe-99eb43a2bdbc6894484501142993369
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
-----------------------------------------------------------------------------------------------------
name: BIOMD0000000912_sim
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=#__source__]
Model [id=__source__, name=null, language=urn:sedml:language:sbml, src=Caravagna2010.xml]
UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]
Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]
DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=time, getId()=data_gen_time]
DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=T, getId()=data_gen_T]
DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=E, getId()=data_gen_E]
DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=I, getId()=data_gen_I]
org.jlibsedml.Report@c84c5553
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:704)
at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:71)
at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:248)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:85)
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.
No PDF files found, skipping archiving `plots.zip` files
No CSV files found, skipping archiving `reports.zip` files
One or more errors encountered while executing archive /tmp/in/archive.omex
sedml.SimulatorProducesLinear3DPlots
(0.5 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
(0.5 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.SimulatorProducesReportsWithCuratedNumberOfDimensions
(0.5 s)Test that that the curated number of output dimensions matches the actual number of output dimensions
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing
Log:
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
(14.3 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:
Oct 14, 2021 3:30:37 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/archive.omex
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_5efd2fe7-7884-4ae1-ab11-8f574ebb23f92412648800226016130
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
-----------------------------------------------------------------------------------------------------
name: BIOMD0000000912_sim
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]
UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]
Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]
DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=time, getId()=data_gen_time]
DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=T, getId()=data_gen_T]
DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=E, getId()=data_gen_E]
DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=I, getId()=data_gen_I]
org.jlibsedml.Report@c84c5553
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/temp1451065028021494999.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@325f7fa9
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
Running simulation BIOMD0000000912_task_Caravagna2010, 103 ms
Ran 1 simulations for 1 biomodels.
Generating report report
.
report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv
HDF conversion successful
No PDF files found, skipping archiving plots.zip
files
Archiving resultant CSV files to reports.zip
.
### `sedml.SimulatorSupportsComputeModelChanges` (15.7 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:
Oct 14, 2021 3:31:06 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/archive.omex
TempPath Created: /tmp/vcell_temp_131aa28e-5a23-4ffc-9c42-4f32fd9ce46f1713633910265998299
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
name: BIOMD0000000912_sim
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]
UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]
Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]
DataGenerator [math=org.jmathml.ASTRootNode@59f63e24, name=time, getId()=data_gen_time]
DataGenerator [math=org.jmathml.ASTRootNode@61f05988, name=T, getId()=data_gen_T]
DataGenerator [math=org.jmathml.ASTRootNode@7ca33c24, name=E, getId()=data_gen_E]
DataGenerator [math=org.jmathml.ASTRootNode@fade1fc, name=I, getId()=data_gen_I]
org.jlibsedml.Report@c84c5553
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/temp5929185429568213331.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@3a91d146
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
Running simulation BIOMD0000000912_task_Caravagna2010, 97 ms
Ran 1 simulations for 1 biomodels.
Generating report report
.
report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv
HDF conversion successful
No PDF files found, skipping archiving plots.zip
files
Archiving resultant CSV files to reports.zip
.
### `sedml.SimulatorSupportsDataSetsWithDifferentShapes` (17.7 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/tmpjlyycvnc/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
Oct 14, 2021 3:31:40 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/archive.omex
TempPath Created: /tmp/vcell_temp_f1789939-51f9-4222-ac60-2757c18a94375344946191441881397
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
name: BIOMD0000000912_sim
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]
UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]
UniformTimeCourse [initialTime=0.0, numberOfPoints=20, outputEndTime=4.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim__copy_2]
Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]
Task [modelReference=BIOMD0000000912, name=null, simulationReference=BIOMD0000000912_simcopy_2, getId()=BIOMD0000000912_taskcopy_2]
DataGenerator [math=org.jmathml.ASTRootNode@6cce16f4, name=time, getId()=data_gen_time]
DataGenerator [math=org.jmathml.ASTRootNode@7efaad5a, name=T, getId()=data_gen_T]
DataGenerator [math=org.jmathml.ASTRootNode@291a7e3c, name=E, getId()=data_gen_E]
DataGenerator [math=org.jmathml.ASTRootNode@ca30bc1, name=I, getId()=data_gen_I]
DataGenerator [math=org.jmathml.ASTRootNode@1046d517, name=null, getId()=data_gen_time__copy_2]
DataGenerator [math=org.jmathml.ASTRootNode@3b7d3a38, name=null, getId()=data_gen_T__copy_2]
DataGenerator [math=org.jmathml.ASTRootNode@416c58f5, name=null, getId()=data_gen_E__copy_2]
DataGenerator [math=org.jmathml.ASTRootNode@5505ae1a, name=null, getId()=data_gen_I__copy_2]
org.jlibsedml.Report@c84c5553
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/temp2584846918752888852.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@1da6ee17
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
Running simulation BIOMD0000000912_task_Caravagna2010, 113 ms
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@2d140a7
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.
Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 49 ms
Ran 2 simulations for 1 biomodels.
Generating report report
.
report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv
Traceback (most recent call last):
File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 422, 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 155, in exec_plot_output_sed_doc
data_set_df = pd.read_csv(report_filename, header=None).T
File "/usr/local/lib/python3.8/dist-packages/pandas/util/_decorators.py", line 311, in wrapper
return func(*args, **kwargs)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 586, in read_csv
return _read(filepath_or_buffer, kwds)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 488, in _read
return parser.read(nrows)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 1047, in read
index, columns, col_dict = self._engine.read(nrows)
File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/c_parser_wrapper.py", line 223, in read
chunks = self._reader.read_low_memory(nrows)
File "pandas/_libs/parsers.pyx", line 801, in pandas._libs.parsers.TextReader.read_low_memory
File "pandas/_libs/parsers.pyx", line 857, in pandas._libs.parsers.TextReader._read_rows
File "pandas/_libs/parsers.pyx", line 843, in pandas._libs.parsers.TextReader._tokenize_rows
File "pandas/_libs/parsers.pyx", line 1925, in pandas._libs.parsers.raise_parser_error
pandas.errors.ParserError: Error tokenizing data. C error: Expected 14 fields in line 5, saw 24
HDF conversion failed
No PDF files found, skipping archiving plots.zip
files
Archiving resultant CSV files to reports.zip
.
### `sedml.SimulatorSupportsModelAttributeChanges` (15.7 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:
Oct 14, 2021 3:31:58 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/archive.omex
TempPath Created: /tmp/vcell_temp_8c0d1129-db76-4c11-8b65-550e61a92e78356324290094845823
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
name: BIOMD0000000912_sim
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]
UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]
Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]
DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=time, getId()=data_gen_time]
DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=T, getId()=data_gen_T]
DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=E, getId()=data_gen_E]
DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=I, getId()=data_gen_I]
org.jlibsedml.Report@c84c5553
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/temp4393410194198647383.xml
/tmp/out/BIOMD0000000912_sim.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@41aaedaa
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.
Running simulation BIOMD0000000912_task_Caravagna2010, 116 ms
Ran 1 simulations for 1 biomodels.
Generating report report
.
report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv
HDF conversion successful
No PDF files found, skipping archiving plots.zip
files
Archiving resultant CSV files to reports.zip
.
### `sedml.SimulatorSupportsRepeatedTasksWithChanges` (9.7 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/tmpjlyycvnc/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
Oct 14, 2021 3:33:01 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/archive.omex
TempPath Created: /tmp/vcell_temp_abb08274-9865-4157-9e90-e738faecf47e4791968440916073779
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:183)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:85)
SED-ML processing for /tmp/vcell_temp_abb08274-9865-4157-9e90-e738faecf47e4791968440916073779/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:183)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:85)
One or more errors encountered while executing archive /tmp/in/archive.omex
Oct 14, 2021 3:33:06 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/archive.omex
TempPath Created: /tmp/vcell_temp_99ec059a-0386-4dfe-8dda-55ff3cb4dd613188467349812228107
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:183)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:85)
SED-ML processing for /tmp/vcell_temp_99ec059a-0386-4dfe-8dda-55ff3cb4dd613188467349812228107/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:183)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:85)
One or more errors encountered while executing archive /tmp/in/archive.omex
### `sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables` (9.7 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/tmpjlyycvnc/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
Oct 14, 2021 3:33:11 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/archive.omex
TempPath Created: /tmp/vcell_temp_a78ab3c3-1aaf-46c6-93bd-0d06b1d72c9c2460464595509854125
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:183)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:85)
SED-ML processing for /tmp/vcell_temp_a78ab3c3-1aaf-46c6-93bd-0d06b1d72c9c2460464595509854125/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:183)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:85)
One or more errors encountered while executing archive /tmp/in/archive.omex
Oct 14, 2021 3:33:16 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/archive.omex
TempPath Created: /tmp/vcell_temp_32fb40e8-8429-4a5e-92c7-24bd4fbbdfa7526665689368640141
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:183)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:85)
SED-ML processing for /tmp/vcell_temp_32fb40e8-8429-4a5e-92c7-24bd4fbbdfa7526665689368640141/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:183)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:85)
One or more errors encountered while executing archive /tmp/in/archive.omex
### `sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges` (4.9 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/tmpjlyycvnc/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Log:
Oct 14, 2021 3:33:21 AM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
VCell CLI input archive /tmp/in/archive.omex
TempPath Created: /tmp/vcell_temp_8be924f0-b1ff-4148-8d62-c3097ddad8fd8557662267852176231
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:183)
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:85)
SED-ML processing for /tmp/vcell_temp_8be924f0-b1ff-4148-8d62-c30 ...
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.
id: vcell version: 7.4.0.23 specificationsUrl: https://raw.githubusercontent.com/virtualcell/vcell/7.4.0.23/biosimulators.json specificationsPatch: version: 7.4.0.23 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.23 validateImage: true commitSimulator: true