text:
Submit VCell 7.4.0.31

id: vcell
version: 7.4.0.31
specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.4.0.31/biosimulators.json
specificationsPatch:
version: 7.4.0.31
image:
url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.31
digest: "sha256:9d7a5b57446b8fe371587fabd0d62919893c24640ad94c1aa580740e224e125c"
validateImage: true
commitSimulator: true

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!

Summary of tests

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 4 test cases:

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks

Skipped 40 test cases:

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

Failures
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (16.5 s)

Test that simulator logs the execution of COMBINE/OMEX archives
Exception:
The simulation log is invalid. Documentation about the log format is available at https://docs.biosimulations.org/concepts/conventions/simulation-run-logs/ and https://api.biosimulations.org.

Property or parameter 'exception' is invalid.

  Value:
    Exception { message: '', type: '' }

  Error(s):
    - Property or parameter 'type' is invalid.

        Value:
          ''

        Error(s):
          - isNotEmpty: type should not be empty
      Property 'message' is invalid.

        Value:
          ''

        Error(s):
          - isNotEmpty: message should not be empty

Property 'sedDocuments' is invalid.

  Value:
    [
      SedDocumentLog {
        exception: Exception { message: '', type: '' },
        skipReason: null,
        output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... Generating outputs... Done. Generating HDF5 file... Done. ',
        duration: null,
        tasks: [ [SedTaskLog] ],
        outputs: [ [SedReportLog] ],
        location: 'BIOMD0000000912_sim.sedml',
        status: 'QUEUED'
      }
    ]

  Error(s):
    - Property or parameter '0' is invalid.

        Value:
          SedDocumentLog {
            exception: Exception { message: '', type: '' },
            skipReason: null,
            output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... Generating outputs... Done. Generating HDF5 file... Done. ',
            duration: null,
            tasks: [
              SedTaskLog {
                exception: [Exception],
                skipReason: null,
                output: 'Initializing simulation... done. Starting simulation... done. ',
                duration: 1,
                algorithm: 'KISAO_0000019',
                simulatorDetails: null,
                id: 'BIOMD0000000912_task',
                status: 'SUCCEEDED'
              }
            ],
            outputs: [
              SedReportLog {
                exception: [Exception],
                skipReason: null,
                output: null,
                duration: null,
                dataSets: [Array],
                _type: 'SedReportLog',
                id: 'report',
                status: 'SUCCEEDED'
              }
            ],
            location: 'BIOMD0000000912_sim.sedml',
            status: 'QUEUED'
          }

        Error(s):
          - Property or parameter 'exception' is invalid.

              Value:
                Exception { message: '', type: '' }

              Error(s):
                - Property or parameter 'type' is invalid.

                    Value:
                      ''

                    Error(s):
                      - isNotEmpty: type should not be empty
                  Property 'message' is invalid.

                    Value:
                      ''

                    Error(s):
                      - isNotEmpty: message should not be empty
            Property 'tasks' is invalid.

              Value:
                [
                  SedTaskLog {
                    exception: Exception { message: '', type: '' },
                    skipReason: null,
                    output: 'Initializing simulation... done. Starting simulation... done. ',
                    duration: 1,
                    algorithm: 'KISAO_0000019',
                    simulatorDetails: null,
                    id: 'BIOMD0000000912_task',
                    status: 'SUCCEEDED'
                  }
                ]

              Error(s):
                - Property or parameter '0' is invalid.

                    Value:
                      SedTaskLog {
                        exception: Exception { message: '', type: '' },
                        skipReason: null,
                        output: 'Initializing simulation... done. Starting simulation... done. ',
                        duration: 1,
                        algorithm: 'KISAO_0000019',
                        simulatorDetails: null,
                        id: 'BIOMD0000000912_task',
                        status: 'SUCCEEDED'
                      }

                    Error(s):
                      - Property or parameter 'exception' is invalid.

                          Value:
                            Exception { message: '', type: '' }

                          Error(s):
                            - Property or parameter 'type' is invalid.

                                Value:
                                  ''

                                Error(s):
                                  - isNotEmpty: type should not be empty
                              Property 'message' is invalid.

                                Value:
                                  ''

                                Error(s):
                                  - isNotEmpty: message should not be empty
            Property 'outputs' is invalid.

              Value:
                [
                  SedReportLog {
                    exception: Exception { message: '', type: '' },
                    skipReason: null,
                    output: null,
                    duration: null,
                    dataSets: [
                      [SedOutputElementLog],
                      [SedOutputElementLog],
                      [SedOutputElementLog],
                      [SedOutputElementLog]
                    ],
                    _type: 'SedReportLog',
                    id: 'report',
                    status: 'SUCCEEDED'
                  }
                ]

              Error(s):
                - Property or parameter '0' is invalid.

                    Value:
                      SedReportLog {
                        exception: Exception { message: '', type: '' },
                        skipReason: null,
                        output: null,
                        duration: null,
                        dataSets: [
                          SedOutputElementLog {
                            id: '__single_var_output_el__1',
                            status: 'SUCCEEDED'
                          },
                          SedOutputElementLog {
                            id: '__single_var_output_el__2',
                            status: 'SUCCEEDED'
                          },
                          SedOutputElementLog {
                            id: '__single_var_output_el__3',
                            status: 'SUCCEEDED'
                          },
                          SedOutputElementLog {
                            id: '__single_var_output_el__4',
                            status: 'SUCCEEDED'
                          }
                        ],
                        _type: 'SedReportLog',
                        id: 'report',
                        status: 'SUCCEEDED'
                      }

                    Error(s):
                      - Property or parameter 'exception' is invalid.

                          Value:
                            Exception { message: '', type: '' }

                          Error(s):
                            - Property or parameter 'type' is invalid.

                                Value:
                                  ''

                                Error(s):
                                  - isNotEmpty: type should not be empty
                              Property 'message' is invalid.

                                Value:
                                  ''

                                Error(s):
                                  - isNotEmpty: message should not be empty

Log:
Jan 21, 2022 11:11:16 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_a0234487-2130-4efb-bf1c-9e25a3b0e4b88043980124988786541

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 of 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

Starting simulate all tasks...

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@4b14918a, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@6d1ef78d, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@1a6c1270, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@18a136ac, 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/temp1055845868187231083.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@4a60ee36

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 112 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 (16.2 s)

Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives
Exception:
The simulation log is invalid. Documentation about the log format is available at https://docs.biosimulations.org/concepts/conventions/simulation-run-logs/ and https://api.biosimulations.org.

Property or parameter 'exception' is invalid.

  Value:
    Exception { message: '', type: '' }

  Error(s):
    - Property or parameter 'type' is invalid.

        Value:
          ''

        Error(s):
          - isNotEmpty: type should not be empty
      Property 'message' is invalid.

        Value:
          ''

        Error(s):
          - isNotEmpty: message should not be empty

Property 'sedDocuments' is invalid.

  Value:
    [
      SedDocumentLog {
        exception: Exception { message: '', type: '' },
        skipReason: null,
        output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... Generating outputs... Done. Generating HDF5 file... Done. ',
        duration: null,
        tasks: [ [SedTaskLog] ],
        outputs: [ [SedReportLog] ],
        location: 'BIOMD0000000912_sim.sedml',
        status: 'QUEUED'
      }
    ]

  Error(s):
    - Property or parameter '0' is invalid.

        Value:
          SedDocumentLog {
            exception: Exception { message: '', type: '' },
            skipReason: null,
            output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... Generating outputs... Done. Generating HDF5 file... Done. ',
            duration: null,
            tasks: [
              SedTaskLog {
                exception: [Exception],
                skipReason: null,
                output: 'Initializing simulation... done. Starting simulation... done. ',
                duration: 1,
                algorithm: 'KISAO_0000019',
                simulatorDetails: null,
                id: 'BIOMD0000000912_task',
                status: 'SUCCEEDED'
              }
            ],
            outputs: [
              SedReportLog {
                exception: [Exception],
                skipReason: null,
                output: null,
                duration: null,
                dataSets: [Array],
                _type: 'SedReportLog',
                id: 'report',
                status: 'SUCCEEDED'
              }
            ],
            location: 'BIOMD0000000912_sim.sedml',
            status: 'QUEUED'
          }

        Error(s):
          - Property or parameter 'exception' is invalid.

              Value:
                Exception { message: '', type: '' }

              Error(s):
                - Property or parameter 'type' is invalid.

                    Value:
                      ''

                    Error(s):
                      - isNotEmpty: type should not be empty
                  Property 'message' is invalid.

                    Value:
                      ''

                    Error(s):
                      - isNotEmpty: message should not be empty
            Property 'tasks' is invalid.

              Value:
                [
                  SedTaskLog {
                    exception: Exception { message: '', type: '' },
                    skipReason: null,
                    output: 'Initializing simulation... done. Starting simulation... done. ',
                    duration: 1,
                    algorithm: 'KISAO_0000019',
                    simulatorDetails: null,
                    id: 'BIOMD0000000912_task',
                    status: 'SUCCEEDED'
                  }
                ]

              Error(s):
                - Property or parameter '0' is invalid.

                    Value:
                      SedTaskLog {
                        exception: Exception { message: '', type: '' },
                        skipReason: null,
                        output: 'Initializing simulation... done. Starting simulation... done. ',
                        duration: 1,
                        algorithm: 'KISAO_0000019',
                        simulatorDetails: null,
                        id: 'BIOMD0000000912_task',
                        status: 'SUCCEEDED'
                      }

                    Error(s):
                      - Property or parameter 'exception' is invalid.

                          Value:
                            Exception { message: '', type: '' }

                          Error(s):
                            - Property or parameter 'type' is invalid.

                                Value:
                                  ''

                                Error(s):
                                  - isNotEmpty: type should not be empty
                              Property 'message' is invalid.

                                Value:
                                  ''

                                Error(s):
                                  - isNotEmpty: message should not be empty
            Property 'outputs' is invalid.

              Value:
                [
                  SedReportLog {
                    exception: Exception { message: '', type: '' },
                    skipReason: null,
                    output: null,
                    duration: null,
                    dataSets: [
                      [SedOutputElementLog],
                      [SedOutputElementLog],
                      [SedOutputElementLog],
                      [SedOutputElementLog]
                    ],
                    _type: 'SedReportLog',
                    id: 'report',
                    status: 'SUCCEEDED'
                  }
                ]

              Error(s):
                - Property or parameter '0' is invalid.

                    Value:
                      SedReportLog {
                        exception: Exception { message: '', type: '' },
                        skipReason: null,
                        output: null,
                        duration: null,
                        dataSets: [
                          SedOutputElementLog {
                            id: '__single_var_output_el__1',
                            status: 'SUCCEEDED'
                          },
                          SedOutputElementLog {
                            id: '__single_var_output_el__2',
                            status: 'SUCCEEDED'
                          },
                          SedOutputElementLog {
                            id: '__single_var_output_el__3',
                            status: 'SUCCEEDED'
                          },
                          SedOutputElementLog {
                            id: '__single_var_output_el__4',
                            status: 'SUCCEEDED'
                          }
                        ],
                        _type: 'SedReportLog',
                        id: 'report',
                        status: 'SUCCEEDED'
                      }

                    Error(s):
                      - Property or parameter 'exception' is invalid.

                          Value:
                            Exception { message: '', type: '' }

                          Error(s):
                            - Property or parameter 'type' is invalid.

                                Value:
                                  ''

                                Error(s):
                                  - isNotEmpty: type should not be empty
                              Property 'message' is invalid.

                                Value:
                                  ''

                                Error(s):
                                  - isNotEmpty: message should not be empty

Log:
Jan 21, 2022 11:11:32 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_f2554001-a082-45de-a54a-f9647afb024b6164921814544283389

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 of 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

Starting simulate all tasks...

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@4b14918a, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@6d1ef78d, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@1a6c1270, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@18a136ac, 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/temp466668490922453811.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@4a60ee36

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 140 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 (16.2 s)

Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives
Exception:
The simulation log is invalid. Documentation about the log format is available at https://docs.biosimulations.org/concepts/conventions/simulation-run-logs/ and https://api.biosimulations.org.

Property or parameter 'exception' is invalid.

  Value:
    Exception { message: '', type: '' }

  Error(s):
    - Property or parameter 'type' is invalid.

        Value:
          ''

        Error(s):
          - isNotEmpty: type should not be empty
      Property 'message' is invalid.

        Value:
          ''

        Error(s):
          - isNotEmpty: message should not be empty

Property 'sedDocuments' is invalid.

  Value:
    [
      SedDocumentLog {
        exception: Exception { message: '', type: '' },
        skipReason: null,
        output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... Generating outputs... Done. Generating HDF5 file... Done. ',
        duration: null,
        tasks: [ [SedTaskLog] ],
        outputs: [ [SedReportLog] ],
        location: 'BIOMD0000000912_sim.sedml',
        status: 'QUEUED'
      }
    ]

  Error(s):
    - Property or parameter '0' is invalid.

        Value:
          SedDocumentLog {
            exception: Exception { message: '', type: '' },
            skipReason: null,
            output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... Generating outputs... Done. Generating HDF5 file... Done. ',
            duration: null,
            tasks: [
              SedTaskLog {
                exception: [Exception],
                skipReason: null,
                output: 'Initializing simulation... done. Starting simulation... done. ',
                duration: 1,
                algorithm: 'KISAO_0000019',
                simulatorDetails: null,
                id: 'BIOMD0000000912_task',
                status: 'SUCCEEDED'
              }
            ],
            outputs: [
              SedReportLog {
                exception: [Exception],
                skipReason: null,
                output: null,
                duration: null,
                dataSets: [Array],
                _type: 'SedReportLog',
                id: 'report',
                status: 'SUCCEEDED'
              }
            ],
            location: 'BIOMD0000000912_sim.sedml',
            status: 'QUEUED'
          }

        Error(s):
          - Property or parameter 'exception' is invalid.

              Value:
                Exception { message: '', type: '' }

              Error(s):
                - Property or parameter 'type' is invalid.

                    Value:
                      ''

                    Error(s):
                      - isNotEmpty: type should not be empty
                  Property 'message' is invalid.

                    Value:
                      ''

                    Error(s):
                      - isNotEmpty: message should not be empty
            Property 'tasks' is invalid.

              Value:
                [
                  SedTaskLog {
                    exception: Exception { message: '', type: '' },
                    skipReason: null,
                    output: 'Initializing simulation... done. Starting simulation... done. ',
                    duration: 1,
                    algorithm: 'KISAO_0000019',
                    simulatorDetails: null,
                    id: 'BIOMD0000000912_task',
                    status: 'SUCCEEDED'
                  }
                ]

              Error(s):
                - Property or parameter '0' is invalid.

                    Value:
                      SedTaskLog {
                        exception: Exception { message: '', type: '' },
                        skipReason: null,
                        output: 'Initializing simulation... done. Starting simulation... done. ',
                        duration: 1,
                        algorithm: 'KISAO_0000019',
                        simulatorDetails: null,
                        id: 'BIOMD0000000912_task',
                        status: 'SUCCEEDED'
                      }

                    Error(s):
                      - Property or parameter 'exception' is invalid.

                          Value:
                            Exception { message: '', type: '' }

                          Error(s):
                            - Property or parameter 'type' is invalid.

                                Value:
                                  ''

                                Error(s):
                                  - isNotEmpty: type should not be empty
                              Property 'message' is invalid.

                                Value:
                                  ''

                                Error(s):
                                  - isNotEmpty: message should not be empty
            Property 'outputs' is invalid.

              Value:
                [
                  SedReportLog {
                    exception: Exception { message: '', type: '' },
                    skipReason: null,
                    output: null,
                    duration: null,
                    dataSets: [
                      [SedOutputElementLog],
                      [SedOutputElementLog],
                      [SedOutputElementLog],
                      [SedOutputElementLog]
                    ],
                    _type: 'SedReportLog',
                    id: 'report',
                    status: 'SUCCEEDED'
                  }
                ]

              Error(s):
                - Property or parameter '0' is invalid.

                    Value:
                      SedReportLog {
                        exception: Exception { message: '', type: '' },
                        skipReason: null,
                        output: null,
                        duration: null,
                        dataSets: [
                          SedOutputElementLog {
                            id: '__single_var_output_el__1',
                            status: 'SUCCEEDED'
                          },
                          SedOutputElementLog {
                            id: '__single_var_output_el__2',
                            status: 'SUCCEEDED'
                          },
                          SedOutputElementLog {
                            id: '__single_var_output_el__3',
                            status: 'SUCCEEDED'
                          },
                          SedOutputElementLog {
                            id: '__single_var_output_el__4',
                            status: 'SUCCEEDED'
                          }
                        ],
                        _type: 'SedReportLog',
                        id: 'report',
                        status: 'SUCCEEDED'
                      }

                    Error(s):
                      - Property or parameter 'exception' is invalid.

                          Value:
                            Exception { message: '', type: '' }

                          Error(s):
                            - Property or parameter 'type' is invalid.

                                Value:
                                  ''

                                Error(s):
                                  - isNotEmpty: type should not be empty
                              Property 'message' is invalid.

                                Value:
                                  ''

                                Error(s):
                                  - isNotEmpty: message should not be empty

Log:
Jan 21, 2022 11:11:48 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_e9557814-96b1-44f2-9816-0777e9bc4e452174516412460589159

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 of 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

Starting simulate all tasks...

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@4b14918a, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@6d1ef78d, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@1a6c1270, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@18a136ac, 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/temp5802407724495980956.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@4a60ee36

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 121 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 (16.0 s)

Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives
Exception:
The simulation log is invalid. Documentation about the log format is available at https://docs.biosimulations.org/concepts/conventions/simulation-run-logs/ and https://api.biosimulations.org.

Property or parameter 'exception' is invalid.

  Value:
    Exception { message: '', type: '' }

  Error(s):
    - Property or parameter 'type' is invalid.

        Value:
          ''

        Error(s):
          - isNotEmpty: type should not be empty
      Property 'message' is invalid.

        Value:
          ''

        Error(s):
          - isNotEmpty: message should not be empty

Property 'sedDocuments' is invalid.

  Value:
    [
      SedDocumentLog {
        exception: Exception { message: '', type: '' },
        skipReason: null,
        output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... Generating outputs... Done. Generating HDF5 file... Done. ',
        duration: null,
        tasks: [ [SedTaskLog] ],
        outputs: [ [SedReportLog] ],
        location: 'BIOMD0000000912_sim.sedml',
        status: 'QUEUED'
      }
    ]

  Error(s):
    - Property or parameter '0' is invalid.

        Value:
          SedDocumentLog {
            exception: Exception { message: '', type: '' },
            skipReason: null,
            output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... Generating outputs... Done. Generating HDF5 file... Done. ',
            duration: null,
            tasks: [
              SedTaskLog {
                exception: [Exception],
                skipReason: null,
                output: 'Initializing simulation... done. Starting simulation... done. ',
                duration: 1,
                algorithm: 'KISAO_0000019',
                simulatorDetails: null,
                id: 'BIOMD0000000912_task',
                status: 'SUCCEEDED'
              }
            ],
            outputs: [
              SedReportLog {
                exception: [Exception],
                skipReason: null,
                output: null,
                duration: null,
                dataSets: [Array],
                _type: 'SedReportLog',
                id: 'report',
                status: 'SUCCEEDED'
              }
            ],
            location: 'BIOMD0000000912_sim.sedml',
            status: 'QUEUED'
          }

        Error(s):
          - Property or parameter 'exception' is invalid.

              Value:
                Exception { message: '', type: '' }

              Error(s):
                - Property or parameter 'type' is invalid.

                    Value:
                      ''

                    Error(s):
                      - isNotEmpty: type should not be empty
                  Property 'message' is invalid.

                    Value:
                      ''

                    Error(s):
                      - isNotEmpty: message should not be empty
            Property 'tasks' is invalid.

              Value:
                [
                  SedTaskLog {
                    exception: Exception { message: '', type: '' },
                    skipReason: null,
                    output: 'Initializing simulation... done. Starting simulation... done. ',
                    duration: 1,
                    algorithm: 'KISAO_0000019',
                    simulatorDetails: null,
                    id: 'BIOMD0000000912_task',
                    status: 'SUCCEEDED'
                  }
                ]

              Error(s):
                - Property or parameter '0' is invalid.

                    Value:
                      SedTaskLog {
                        exception: Exception { message: '', type: '' },
                        skipReason: null,
                        output: 'Initializing simulation... done. Starting simulation... done. ',
                        duration: 1,
                        algorithm: 'KISAO_0000019',
                        simulatorDetails: null,
                        id: 'BIOMD0000000912_task',
                        status: 'SUCCEEDED'
                      }

                    Error(s):
                      - Property or parameter 'exception' is invalid.

                          Value:
                            Exception { message: '', type: '' }

                          Error(s):
                            - Property or parameter 'type' is invalid.

                                Value:
                                  ''

                                Error(s):
                                  - isNotEmpty: type should not be empty
                              Property 'message' is invalid.

                                Value:
                                  ''

                                Error(s):
                                  - isNotEmpty: message should not be empty
            Property 'outputs' is invalid.

              Value:
                [
                  SedReportLog {
                    exception: Exception { message: '', type: '' },
                    skipReason: null,
                    output: null,
                    duration: null,
                    dataSets: [
                      [SedOutputElementLog],
                      [SedOutputElementLog],
                      [SedOutputElementLog],
                      [SedOutputElementLog]
                    ],
                    _type: 'SedReportLog',
                    id: 'report',
                    status: 'SUCCEEDED'
                  }
                ]

              Error(s):
                - Property or parameter '0' is invalid.

                    Value:
                      SedReportLog {
                        exception: Exception { message: '', type: '' },
                        skipReason: null,
                        output: null,
                        duration: null,
                        dataSets: [
                          SedOutputElementLog {
                            id: '__single_var_output_el__1',
                            status: 'SUCCEEDED'
                          },
                          SedOutputElementLog {
                            id: '__single_var_output_el__2',
                            status: 'SUCCEEDED'
                          },
                          SedOutputElementLog {
                            id: '__single_var_output_el__3',
                            status: 'SUCCEEDED'
                          },
                          SedOutputElementLog {
                            id: '__single_var_output_el__4',
                            status: 'SUCCEEDED'
                          }
                        ],
                        _type: 'SedReportLog',
                        id: 'report',
                        status: 'SUCCEEDED'
                      }

                    Error(s):
                      - Property or parameter 'exception' is invalid.

                          Value:
                            Exception { message: '', type: '' }

                          Error(s):
                            - Property or parameter 'type' is invalid.

                                Value:
                                  ''

                                Error(s):
                                  - isNotEmpty: type should not be empty
                              Property 'message' is invalid.

                                Value:
                                  ''

                                Error(s):
                                  - isNotEmpty: message should not be empty

Log:
Jan 21, 2022 11:12:05 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_db1058bb-6001-402a-918a-a6dd014ecf832472478984792967426

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 of 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

Starting simulate all tasks...

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@4b14918a, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@6d1ef78d, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@1a6c1270, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@18a136ac, 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/temp3338061188507020038.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@4a60ee36

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 104 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`.

Warnings
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_IMPORTED_MODEL_FILES'
  - '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: None

cli.CliDisplaysHelpInline (2.2 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: None

cli.CliDisplaysVersionInformationInline (1.7 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: None

docker_image.DeclaresSupportedEnvironmentVariables (0.6 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_IMPORTED_MODEL_FILES'
  - '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: None

docker_image.HasBioContainersLabels (0.5 s)

Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

Skips
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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (9.8 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:
Jan 21, 2022 11:04:47 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_3926ddfd-4720-42ae-80c5-6647aae84efe9159668708341237457

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 of 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

Starting simulate all tasks...

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@4b14918a, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@6d1ef78d, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@1a6c1270, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@18a136ac, 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:74)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:375)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

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.

Generating report `report`.

java.lang.NullPointerException

	at org.vcell.cli.CLIUtils.generateReportsAsCSV(CLIUtils.java:530)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:404)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

HDF conversion successful

 All sedml documents in this archive failed to execute

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (10.1 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:
Jan 21, 2022 11:04:57 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_42e1a5b6-afe0-43bd-9b55-b9abf200681b1600366122550531886

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 of 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

Starting simulate all tasks...

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@1a6c1270, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@18a136ac, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@77d67cf3, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@6dee4f1b, 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:74)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:375)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

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.

Generating report `report`.

java.lang.NullPointerException

	at org.vcell.cli.CLIUtils.generateReportsAsCSV(CLIUtils.java:530)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:404)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

HDF conversion successful

 All sedml documents in this archive failed to execute

sedml.SimulatorProducesLinear3DPlots (0.4 s)

Test that a simulator produces linear 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.4 s)

Test that a simulator produces logarithmic 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.4 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: None

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (15.2 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:
Jan 21, 2022 11:06:50 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_cce602ea-aa51-4b8c-9613-6ec8ce6fe0397467982871056591194

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 of 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

Starting simulate all tasks...

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@1a6c1270, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@18a136ac, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@77d67cf3, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@6dee4f1b, 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/temp4486890221821698106.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@65f00478

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 94 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 (16.5 s)

Test that a simulator supports compute model changes
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

Log:
Jan 21, 2022 11:07:20 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_5e8c401f-102e-4147-8728-b02bde9e640b8267504984779667244

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 of 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

Starting simulate all tasks...

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@1d0d6318, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@4bc28c33, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@4409e975, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@5c153b9e, 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/temp6102787769443452010.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@178270b2

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 127 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 (16.3 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/tmp3r2ko95j/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
Jan 21, 2022 11:07:53 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_f2fd6a01-7a66-45f6-b8f0-1185b04d0a8c4622506339754861793

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 of 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

Starting simulate all tasks...

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_sim__copy_2, getId()=BIOMD0000000912_task__copy_2]

DataGenerator [math=org.jmathml.ASTRootNode@3f270e0a, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@1a760689, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@7241a47d, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@70f59913, name=I, getId()=data_gen_I]

DataGenerator [math=org.jmathml.ASTRootNode@77258e59, name=null, getId()=data_gen_time__copy_2]

DataGenerator [math=org.jmathml.ASTRootNode@5dcd8c7a, name=null, getId()=data_gen_T__copy_2]

DataGenerator [math=org.jmathml.ASTRootNode@2250b9f2, name=null, getId()=data_gen_E__copy_2]

DataGenerator [math=org.jmathml.ASTRootNode@7e3181aa, 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/temp589039487101363903.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@4564e94b

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 101 ms

-----------------------------------------------------------------------------------------------------

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@7af1cd63

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.

Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 54 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 421, in <module>

    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 224, 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

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsModelAttributeChanges (16.1 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:
Jan 21, 2022 11:08:10 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_c4c2042e-6858-4f1a-a3eb-3ea46f838de23119811047489215701

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 of 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

Starting simulate all tasks...

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@1a6c1270, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@18a136ac, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@77d67cf3, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@6dee4f1b, 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/temp7347680517917060723.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@3c017078

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 93 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 (9.9 s)

Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp3r2ko95j/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
Jan 21, 2022 11:09:15 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_a04801e0-a6ec-4622-b52f-81b9391e75fb851724628405302025

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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_a04801e0-a6ec-4622-b52f-81b9391e75fb851724628405302025/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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

Jan 21, 2022 11:09:20 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_57323e4a-0a89-4acb-bb32-38ac8e1ffb7c4596784387697925675

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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_57323e4a-0a89-4acb-bb32-38ac8e1ffb7c4596784387697925675/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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (9.9 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp3r2ko95j/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
Jan 21, 2022 11:09:25 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_f66adae7-14f4-46d6-b60e-c023ab1fac558230961805744365802

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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_f66adae7-14f4-46d6-b60e-c023ab1fac558230961805744365802/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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

Jan 21, 2022 11:09:30 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_fbaa895b-b40c-4111-92e5-b3ca647061831542067461384170240

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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_fbaa895b-b40c-4111-92e5-b3ca647061831542067461384170240/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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (4.8 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/tmp3r2ko95j/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
Jan 21, 2022 11:09:35 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_69722960-aefa-479e-ac16-6b119af991533650661552472393090

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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_69722960-aefa-479e-ac16-6b119af991533650661552472393090/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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (5.0 s)

Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp3r2ko95j/sedml/sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
Jan 21, 2022 11:09:40 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_a31aae44-e734-4f75-977c-668efa1b0f4a5055989968209988014

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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_a31aae44-e734-4f75-977c-668efa1b0f4a5055989968209988014/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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (4.8 s)

Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp3r2ko95j/sedml/sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
Jan 21, 2022 11:09:45 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_cc8dfe08-b37a-4b38-9a52-e3b8fc0f1358623458518456606973

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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_cc8dfe08-b37a-4b38-9a52-e3b8fc0f1358623458518456606973/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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (4.9 s)

Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp3r2ko95j/sedml/sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
Jan 21, 2022 11:09:50 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_03da7795-4c96-4ed0-b853-aba2f7b9867a1699891608195886498

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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_03da7795-4c96-4ed0-b853-aba2f7b9867a1699891608195886498/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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (4.7 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp3r2ko95j/sedml/sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
Jan 21, 2022 11:09:55 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_df013f62-955f-4c3b-966b-5c197bcb97b47188729570485793459

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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_df013f62-955f-4c3b-966b-5c197bcb97b47188729570485793459/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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (4.9 s)

Test that a simulator supports nested repeated tasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp3r2ko95j/sedml/sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
Jan 21, 2022 11:10:00 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_551fecdb-8a14-4538-a60b-46ceddab5cdc6031422973769591672

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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

SED-ML processing for /tmp/vcell_temp_551fecdb-8a14-4538-a60b-46ceddab5cdc6031422973769591672/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:298)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148)

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRe ...

- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
-
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/1731158085). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/1731158085).

authors: biosimulators-daemon vcdaemon

repo: biosimulators/Biosimulators