Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Submit VCell 7.4.0.60 #587

Closed
vcdaemon opened this issue Aug 29, 2022 · 8 comments
Closed

Submit VCell 7.4.0.60 #587

vcdaemon opened this issue Aug 29, 2022 · 8 comments
Labels
Invalid This doesn't seem right Validate/submit simulator Validate a simulation tool or request its submission to the BioSimulators registry

Comments

@vcdaemon
Copy link

id: vcell
version: 7.4.0.60
specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.4.0.60/biosimulators.json
specificationsPatch:
version: 7.4.0.60
image:
url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.60
digest: "sha256:9b8cff9c323695170fa05a46fd311b2e94d5cfd1d87a66ad0c3d6327323ea884"
validateImage: true
commitSimulator: false
@vcdaemon vcdaemon added the Validate/submit simulator Validate a simulation tool or request its submission to the BioSimulators registry label Aug 29, 2022
@biosimulators-daemon
Copy link

Thank you @vcdaemon for your submission to the BioSimulators simulator validation/submission system!

The BioSimulators validator bot is validating the specifications of your simulator, and validating your Docker image. You have chosen not to submit your simulator to the BioSimulators registry.

We will discuss any concerns with your submission in this issue.

A complete log of your simulator validation 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.

@biosimulators-daemon
Copy link

The specifications of your simulator is valid!

@biosimulators-daemon
Copy link

Summary of tests

  • Executed 74 test cases

  • Passed 17 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
    • log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
    • log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
    • log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
    • log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
    • sedml.SimulatorSupportsMultipleReportsPerSedDocument
    • sedml.SimulatorSupportsMultipleTasksPerSedDocument

  • Failed 16 test cases:

    • 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
    • published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength
    • results_report.SimulatorGeneratesReportsOfSimulationResults
    • sedml.SimulatorProducesLinear2DPlots
    • sedml.SimulatorProducesLogarithmic2DPlots
    • sedml.SimulatorProducesMultiplePlots
    • sedml.SimulatorSupportsAlgorithmParameters
    • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
    • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

  • Skipped 41 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.SimulatorSupportsDataGeneratorsWithDifferentShapes
    • sedml.SimulatorSupportsDataSetsWithDifferentShapes
    • sedml.SimulatorSupportsModelAttributeChanges
    • sedml.SimulatorSupportsRepeatedTasksWithChanges
    • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
    • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
    • sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
    • sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
    • sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
    • sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
    • sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
    • sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
    • sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
    • sedml.SimulatorSupportsSubstitutingAlgorithms
    • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

@biosimulators-daemon
Copy link

Failures

docker_image.SingularityImageExecutesSimulationsSuccessfully (12.6 s)

Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives

Exception:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (10.1 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

Report BIOMD0000000912_sim.sedml/report could not be read

Log:

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:53:52 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_64dfe4dc-03e9-42b5-81cd-310e4a7ec5cf2709631756120280104

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... 

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@65cc8228

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 170 ms

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

 INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels.

 INFO (ExecuteImpl.java:306) - Generating outputs... 

 INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_1_bottom_left` while CSV generation.

 INFO (RunUtils.java:233) - Generating report `report`.

 INFO (RunUtils.java:233) - Generating report `__plot__Figure_1_bottom_left`.

 INFO (ExecuteImpl.java:325) - Generating HDF5 file... 

 INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_1_bottom_left` while generating idNamePlotsMap.

 INFO (ExecuteImpl.java:338) - Generating Plots... 

 WARN (CLIPythonManager.java:65) - Using old style python invocation!

 INFO (ExecuteImpl.java:370) - Archiving result files

 INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`.

 INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl.java:374) - SED-ML : BIOMD0000000912_sim.sedml successfully completed

 INFO (ExecuteImpl.java:382) - Omex Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex processing completed (6s)
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (13.1 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

Report simulation_1.sedml/report could not be read

Log:

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:54:03 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_92b5bedf-70d3-4b89-9d55-3e295446ffae1233199362820172722

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:190) - Processing SED-ML: simulation_1.sedml

 INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : simulation_1.sedml

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

 INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... 

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SBMLImporter.java:3233) - model 'Ciliberto2003_Morphogenesis' doesn't have a spatial geometry

 INFO (SEDMLImporter.java:188) - Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000086' matched to RungeKuttaFehlberg

 INFO (RowColumnResultSet.java:544) - rowCount=13762

 INFO (RowColumnResultSet.java:572) - scale[0] = 139.9749483060956

 INFO (RowColumnResultSet.java:572) - scale[1] = 0.10337204038188977

 INFO (RowColumnResultSet.java:572) - scale[2] = 0.18451723700540568

 INFO (RowColumnResultSet.java:572) - scale[3] = 1.248823182479924

 INFO (RowColumnResultSet.java:572) - scale[4] = 0.0866281958361408

 INFO (RowColumnResultSet.java:572) - scale[5] = 0.2487316750047834

 INFO (RowColumnResultSet.java:572) - scale[6] = 0.957165622333867

 INFO (RowColumnResultSet.java:572) - scale[7] = 0.5222071967202937

 INFO (RowColumnResultSet.java:572) - scale[8] = 1.6250612922233858

 INFO (RowColumnResultSet.java:572) - scale[9] = 1.163399212713716

 INFO (RowColumnResultSet.java:572) - scale[10] = 0.9944445913091504

 INFO (RowColumnResultSet.java:572) - scale[11] = 0.1689497310030451

 INFO (RowColumnResultSet.java:572) - scale[12] = 0.02826956834397453

 INFO (RowColumnResultSet.java:572) - scale[13] = 0.0032627104470246394

 INFO (RowColumnResultSet.java:572) - scale[14] = 0.013335866633246523

 INFO (RowColumnResultSet.java:572) - scale[15] = 0.8080848330089925

 INFO (RowColumnResultSet.java:572) - scale[16] = 0.932880719855319

 INFO (RowColumnResultSet.java:572) - scale[17] = 0.9725777981904435

 INFO (RowColumnResultSet.java:572) - scale[18] = 0.9307398276790282

 INFO (RowColumnResultSet.java:572) - scale[19] = 0.813079283325805

 INFO (RowColumnResultSet.java:572) - scale[20] = 1.0

 INFO (RowColumnResultSet.java:572) - scale[21] = 1.0

 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.01, size=8424

 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.02, size=4232

 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.03, size=2129

 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.04, size=1074

 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.05, size=552

final tolerance=0.1 final threshold=0.060000000000000005, 552 remaining (keepAtMost=1000)

 INFO (SolverHandler.java:200) - Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg_simulation_1.sedml_Ciliberto2003_Morphogenesis' Task 'simulation 1'.

 INFO (SolverHandler.java:207) - Running simulation task_1, 990 ms

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

 INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels.

 INFO (ExecuteImpl.java:306) - Generating outputs... 

 INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_3a` while CSV generation.

 INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_3b` while CSV generation.

 INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_3c` while CSV generation.

 INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_3d` while CSV generation.

 INFO (RunUtils.java:233) - Generating report `report`.

 INFO (RunUtils.java:233) - Generating report `__plot__Figure_3a`.

 INFO (RunUtils.java:233) - Generating report `__plot__Figure_3b`.

 INFO (RunUtils.java:233) - Generating report `__plot__Figure_3c`.

 INFO (RunUtils.java:233) - Generating report `__plot__Figure_3d`.

 INFO (ExecuteImpl.java:325) - Generating HDF5 file... 

 INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_3a` while generating idNamePlotsMap.

 INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_3b` while generating idNamePlotsMap.

 INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_3c` while generating idNamePlotsMap.

 INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_3d` while generating idNamePlotsMap.

 INFO (ExecuteImpl.java:338) - Generating Plots... 

 WARN (CLIPythonManager.java:65) - Using old style python invocation!

 INFO (ExecuteImpl.java:370) - Archiving result files

 INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`.

 INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl.java:374) - SED-ML : simulation_1.sedml successfully completed

 INFO (ExecuteImpl.java:382) - Omex Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex processing completed (9s)
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (12.3 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

Report simulation_1.sedml/report could not be read

Log:

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:54:16 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_6f51806e-d6e6-4a65-9f01-5c45bf80cf128031127589343496412

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:190) - Processing SED-ML: simulation_1.sedml

 INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : simulation_1.sedml

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

 INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... 

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SBMLImporter.java:3233) - model 'Ciliberto2003_Morphogenesis' doesn't have a spatial geometry

 INFO (SEDMLImporter.java:188) - Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@5eb2172

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous_simulation_1.sedml_Ciliberto2003_Morphogenesis' Task 'simulation 1'.

 INFO (SolverHandler.java:207) - Running simulation task_1, 180 ms

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

 INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels.

 INFO (ExecuteImpl.java:306) - Generating outputs... 

 INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_3a` while CSV generation.

 INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_3b` while CSV generation.

 INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_3c` while CSV generation.

 INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_3d` while CSV generation.

 INFO (RunUtils.java:233) - Generating report `report`.

 INFO (RunUtils.java:233) - Generating report `__plot__Figure_3a`.

 INFO (RunUtils.java:233) - Generating report `__plot__Figure_3b`.

 INFO (RunUtils.java:233) - Generating report `__plot__Figure_3c`.

 INFO (RunUtils.java:233) - Generating report `__plot__Figure_3d`.

 INFO (ExecuteImpl.java:325) - Generating HDF5 file... 

 INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_3a` while generating idNamePlotsMap.

 INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_3b` while generating idNamePlotsMap.

 INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_3c` while generating idNamePlotsMap.

 INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_3d` while generating idNamePlotsMap.

 INFO (ExecuteImpl.java:338) - Generating Plots... 

 WARN (CLIPythonManager.java:65) - Using old style python invocation!

 INFO (ExecuteImpl.java:370) - Archiving result files

 INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`.

 INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl.java:374) - SED-ML : simulation_1.sedml successfully completed

 INFO (ExecuteImpl.java:382) - Omex Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex processing completed (8s)
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (9.7 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

Report simulation.sedml/report could not be read

Log:

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:54:28 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/Elowitz-Nature-2000-Repressilator.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_265a2283-00ca-464f-9143-6392e2d1d46f2924184681532741438

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:190) - Processing SED-ML: simulation.sedml

 INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : simulation.sedml

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

 INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... 

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SBMLImporter.java:3233) - model 'BIOMD0000000012' doesn't have a spatial geometry

 INFO (SEDMLImporter.java:188) - Task (id='task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@6124287a

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'Elowitz-Nature-2000-Repressilator_simulation.sedml_model' Task 'task'.

 INFO (SolverHandler.java:207) - Running simulation task, 131 ms

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

 INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels.

 INFO (ExecuteImpl.java:306) - Generating outputs... 

 INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_1c` while CSV generation.

 INFO (RunUtils.java:233) - Generating report `report`.

 INFO (RunUtils.java:233) - Generating report `__plot__Figure_1c`.

 INFO (ExecuteImpl.java:325) - Generating HDF5 file... 

 INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_1c` while generating idNamePlotsMap.

 INFO (ExecuteImpl.java:338) - Generating Plots... 

 WARN (CLIPythonManager.java:65) - Using old style python invocation!

 INFO (ExecuteImpl.java:370) - Archiving result files

 INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`.

 INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl.java:374) - SED-ML : simulation.sedml successfully completed

 INFO (ExecuteImpl.java:382) - Omex Elowitz-Nature-2000-Repressilator.omex processing completed (6s)
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (24.0 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

Report simulation.sedml/report_Fig_1a could not be read

Report simulation.sedml/report_low_delta_R_det could not be read

Report simulation.sedml/report_Euler_small_step_size could not be read

Report simulation.sedml/report_Fig_1_c could not be read

Report simulation.sedml/report_low_delta_R_stoch could not be read

Log:

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:55:05 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_85842ed6-7aa3-4dd7-a74e-7b9461afa96f3293380909276017486

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:190) - Processing SED-ML: simulation.sedml

 INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : simulation.sedml

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

 INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... 

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SBMLImporter.java:3233) - model '__example_biosim_vilar_ODE_deterministic' doesn't have a spatial geometry

 WARN (AbstractNameScope.java:276) - AbstractNameScope.getRelativeScopePrefix() scopes 'cell_mapping' and 'PrmA_scs' are unrelated

ERROR (SBMLImporter.java:2740) - failed to set expression for SBML object species [ id="PrmA" boundaryCondition="false" compartment="cell" constant="false" hasOnlySubstanceUnits="true" substanceUnits="molecules"] on vcell object cbit.vcell.mapping.SpeciesContextSpec$SpeciesContextSpecParameter@773bd77b: <initConc> = 'Expression@b9f2 '0.0'' [molecules.um-3], "initial concentration for PrmA"

 WARN (AbstractNameScope.java:276) - AbstractNameScope.getRelativeScopePrefix() scopes 'cell_mapping' and 'PrmR_scs' are unrelated

ERROR (SBMLImporter.java:2740) - failed to set expression for SBML object species [ id="PrmR" boundaryCondition="false" compartment="cell" constant="false" hasOnlySubstanceUnits="true" substanceUnits="molecules"] on vcell object cbit.vcell.mapping.SpeciesContextSpec$SpeciesContextSpecParameter@6b580b88: <initConc> = 'Expression@b9f2 '0.0'' [molecules.um-3], "initial concentration for PrmR"

ERROR (SBMLImporter.java:1756) - SKIPPING translation back to vcell unit system ... testing only

 WARN (DiffEquMathMapping.java:1483) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique

 INFO (SBMLImporter.java:3233) - model '__example_biosim_vilar_ODE_stochastic' doesn't have a spatial geometry

ERROR (SBMLImporter.java:1756) - SKIPPING translation back to vcell unit system ... testing only

 WARN (DiffEquMathMapping.java:1483) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique

 INFO (SEDMLImporter.java:188) - Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (SEDMLImporter.java:188) - Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (SEDMLImporter.java:188) - Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler

 INFO (SEDMLImporter.java:188) - Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson

 INFO (SEDMLImporter.java:188) - Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@2a03d65c

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_deterministic' Task 'tsk_0_0'.

 INFO (SolverHandler.java:207) - Running simulation tsk_0_0, 169 ms

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

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@588307f7

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_deterministic' Task 'tsk_0_1'.

 INFO (SolverHandler.java:207) - Running simulation tsk_0_1, 45 ms

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

 INFO (RowColumnResultSet.java:544) - rowCount=200001

 INFO (RowColumnResultSet.java:572) - scale[0] = 199.998

 INFO (RowColumnResultSet.java:572) - scale[1] = 1.0

 INFO (RowColumnResultSet.java:572) - scale[2] = 1.0

 INFO (RowColumnResultSet.java:572) - scale[3] = 1.0

 INFO (RowColumnResultSet.java:572) - scale[4] = 1.0

 INFO (RowColumnResultSet.java:572) - scale[5] = 1.0

 INFO (RowColumnResultSet.java:572) - scale[6] = 1.0

 INFO (RowColumnResultSet.java:572) - scale[7] = 1.0

 INFO (RowColumnResultSet.java:572) - scale[8] = 1.0

 INFO (RowColumnResultSet.java:572) - scale[9] = 1.0

 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.01, size=100001

 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.02, size=50001

 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.03, size=25001

 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.04, size=12501

 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.05, size=6251

 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.060000000000000005, size=3126

 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.07, size=1564

 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.08, size=783

final tolerance=0.1 final threshold=0.09, 783 remaining (keepAtMost=1000)

 INFO (SolverHandler.java:200) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_deterministic' Task 'tsk_0_3'.

 INFO (SolverHandler.java:207) - Running simulation tsk_0_3, 697 ms

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

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.stoch.GibsonSolver@763cf5b9

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_stochastic' Task 'tsk_1_0'.

 INFO (SolverHandler.java:207) - Running simulation tsk_1_0, 234 ms

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

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.stoch.GibsonSolver@2f508f3c

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_stochastic' Task 'tsk_1_1'.

 INFO (SolverHandler.java:207) - Running simulation tsk_1_1, 164 ms

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

 INFO (SolverHandler.java:282) - Ran 5 simulations for 2 biomodels.

 INFO (ExecuteImpl.java:306) - Generating outputs... 

 INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_Fig_1a` while CSV generation.

 INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation.

 INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation.

 INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation.

 INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation.

 INFO (RunUtils.java:233) - Generating report `report_Fig_1a`.

 INFO (RunUtils.java:233) - Generating report `report_low_delta_R_det`.

 INFO (RunUtils.java:233) - Generating report `report_Euler_small_step_size`.

 INFO (RunUtils.java:233) - Generating report `report_Fig_1_c`.

 INFO (RunUtils.java:233) - Generating report `report_low_delta_R_stoch`.

 INFO (RunUtils.java:233) - Generating report `__plot__plot2d_Fig_1a`.

 INFO (RunUtils.java:233) - Generating report `__plot__plot2d_low_delta_R_det`.

 INFO (RunUtils.java:233) - Generating report `__plot__plot2d_Euler_small_step_size`.

 INFO (RunUtils.java:233) - Generating report `__plot__plot2d_Fig_1_c`.

 INFO (RunUtils.java:233) - Generating report `__plot__plot2d_low_delta_R_stoch`.

 INFO (ExecuteImpl.java:325) - Generating HDF5 file... 

 INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_Fig_1a` while generating idNamePlotsMap.

 INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_low_delta_R_det` while generating idNamePlotsMap.

 INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_Euler_small_step_size` while generating idNamePlotsMap.

 INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_Fig_1_c` while generating idNamePlotsMap.

 INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_low_delta_R_stoch` while generating idNamePlotsMap.

 INFO (ExecuteImpl.java:338) - Generating Plots... 

 WARN (CLIPythonManager.java:65) - Using old style python invocation!

 INFO (ExecuteImpl.java:370) - Archiving result files

 INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`.

 INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl.java:374) - SED-ML : simulation.sedml successfully completed

 INFO (ExecuteImpl.java:382) - Omex Vilar-PNAS-2002-minimal-circardian-clock.omex processing completed (20s)
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (12.9 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

Report simulation.sedml/report_Fig_1a could not be read

Report simulation.sedml/report_low_delta_R_det could not be read

Log:

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:54:38 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_5a210c3d-f54d-47c0-a3b5-9dd664b59f186370883313959451802

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:190) - Processing SED-ML: simulation.sedml

 INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : simulation.sedml

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

 INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... 

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SBMLImporter.java:3233) - model '__example_biosim_vilar_ODE_deterministic' doesn't have a spatial geometry

 WARN (AbstractNameScope.java:276) - AbstractNameScope.getRelativeScopePrefix() scopes 'cell_mapping' and 'PrmA_scs' are unrelated

ERROR (SBMLImporter.java:2740) - failed to set expression for SBML object species [ id="PrmA" boundaryCondition="false" compartment="cell" constant="false" hasOnlySubstanceUnits="true" substanceUnits="molecules"] on vcell object cbit.vcell.mapping.SpeciesContextSpec$SpeciesContextSpecParameter@7b22ec89: <initConc> = 'Expression@b9f2 '0.0'' [molecules.um-3], "initial concentration for PrmA"

 WARN (AbstractNameScope.java:276) - AbstractNameScope.getRelativeScopePrefix() scopes 'cell_mapping' and 'PrmR_scs' are unrelated

ERROR (SBMLImporter.java:2740) - failed to set expression for SBML object species [ id="PrmR" boundaryCondition="false" compartment="cell" constant="false" hasOnlySubstanceUnits="true" substanceUnits="molecules"] on vcell object cbit.vcell.mapping.SpeciesContextSpec$SpeciesContextSpecParameter@790132f7: <initConc> = 'Expression@b9f2 '0.0'' [molecules.um-3], "initial concentration for PrmR"

ERROR (SBMLImporter.java:1756) - SKIPPING translation back to vcell unit system ... testing only

 WARN (DiffEquMathMapping.java:1483) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique

 INFO (SEDMLImporter.java:188) - Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (SEDMLImporter.java:188) - Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@4c27d39d

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous_simulation.sedml_ODE_deterministic' Task 'tsk_0_0'.

 INFO (SolverHandler.java:207) - Running simulation tsk_0_0, 106 ms

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

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@3adbe50f

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous_simulation.sedml_ODE_deterministic' Task 'tsk_0_1'.

 INFO (SolverHandler.java:207) - Running simulation tsk_0_1, 45 ms

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

 INFO (SolverHandler.java:282) - Ran 2 simulations for 1 biomodels.

 INFO (ExecuteImpl.java:306) - Generating outputs... 

 INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_2ab` while CSV generation.

 INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_Fig_1a` while CSV generation.

 INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation.

 INFO (RunUtils.java:233) - Generating report `report_Fig_1a`.

 INFO (RunUtils.java:233) - Generating report `report_low_delta_R_det`.

 INFO (RunUtils.java:233) - Generating report `__plot__Figure_2ab`.

 INFO (RunUtils.java:233) - Generating report `__plot__plot2d_Fig_1a`.

 INFO (RunUtils.java:233) - Generating report `__plot__plot2d_low_delta_R_det`.

 INFO (ExecuteImpl.java:325) - Generating HDF5 file... 

 INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_2ab` while generating idNamePlotsMap.

 INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_Fig_1a` while generating idNamePlotsMap.

 INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_low_delta_R_det` while generating idNamePlotsMap.

 INFO (ExecuteImpl.java:338) - Generating Plots... 

 WARN (CLIPythonManager.java:65) - Using old style python invocation!

 INFO (ExecuteImpl.java:370) - Archiving result files

 INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`.

 INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl.java:374) - SED-ML : simulation.sedml successfully completed

 INFO (ExecuteImpl.java:382) - Omex Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex processing completed (9s)
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (13.7 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

Report simulation.sedml/report_Fig_1_c could not be read

Report simulation.sedml/report_low_delta_R_stoch could not be read

Log:

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:54:51 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_f0440068-78b9-4042-9ab0-2932eb5a9db83976787186033063842

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:190) - Processing SED-ML: simulation.sedml

 INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : simulation.sedml

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

 INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... 

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SBMLImporter.java:3233) - model '__example_biosim_vilar_ODE_stochastic' doesn't have a spatial geometry

ERROR (SBMLImporter.java:1756) - SKIPPING translation back to vcell unit system ... testing only

 WARN (DiffEquMathMapping.java:1483) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique

 INFO (SEDMLImporter.java:188) - Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson

 INFO (SEDMLImporter.java:188) - Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.stoch.GibsonSolver@14bf57b2

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM_simulation.sedml_ODE_stochastic' Task 'tsk_1_0'.

 INFO (SolverHandler.java:207) - Running simulation tsk_1_0, 379 ms

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

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.stoch.GibsonSolver@bc4d5e1

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM_simulation.sedml_ODE_stochastic' Task 'tsk_1_1'.

 INFO (SolverHandler.java:207) - Running simulation tsk_1_1, 159 ms

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

 INFO (SolverHandler.java:282) - Ran 2 simulations for 1 biomodels.

 INFO (ExecuteImpl.java:306) - Generating outputs... 

 INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation.

 INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation.

 INFO (RunUtils.java:233) - Generating report `report_Fig_1_c`.

 INFO (RunUtils.java:233) - Generating report `report_low_delta_R_stoch`.

 INFO (RunUtils.java:233) - Generating report `__plot__plot2d_Fig_1_c`.

 INFO (RunUtils.java:233) - Generating report `__plot__plot2d_low_delta_R_stoch`.

 INFO (ExecuteImpl.java:325) - Generating HDF5 file... 

 INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_Fig_1_c` while generating idNamePlotsMap.

 INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_low_delta_R_stoch` while generating idNamePlotsMap.

 INFO (ExecuteImpl.java:338) - Generating Plots... 

 WARN (CLIPythonManager.java:65) - Using old style python invocation!

 INFO (ExecuteImpl.java:370) - Archiving result files

 INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`.

 INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl.java:374) - SED-ML : simulation.sedml successfully completed

 INFO (ExecuteImpl.java:382) - Omex Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex processing completed (10s)
published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength (10.8 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

Report biomodel_100596964.sedml/report_Simulation1 could not be read

Log:

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:55:29 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_ee0a108f-636f-4015-bbce-26df76c0908c682944670831763597

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

 INFO (ExecuteImpl.java:190) - Processing SED-ML: biomodel_100596964.sedml

 INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : biomodel_100596964.sedml

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

 INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML

 INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... 

 INFO (XmlReader.java:4580) - RbmModelContainer is missing.

 INFO (SEDMLImporter.java:188) - Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solvers.CombinedSundialsSolver@5c84624f

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength_biomodel_100596964.sedml_minepsp' Task ''.

 INFO (SolverHandler.java:207) - Running simulation tsk_0_0, 165 ms

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

 INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels.

 INFO (ExecuteImpl.java:306) - Generating outputs... 

 INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_Simulation1` while CSV generation.

 INFO (RunUtils.java:233) - Generating report `report_Simulation1`.

 INFO (RunUtils.java:233) - Generating report `__plot__plot2d_Simulation1`.

 INFO (ExecuteImpl.java:325) - Generating HDF5 file... 

 INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_Simulation1` while generating idNamePlotsMap.

 INFO (ExecuteImpl.java:338) - Generating Plots... 

 WARN (CLIPythonManager.java:65) - Using old style python invocation!

 INFO (ExecuteImpl.java:370) - Archiving result files

 INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`.

 INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl.java:374) - SED-ML : biomodel_100596964.sedml successfully completed

 INFO (ExecuteImpl.java:382) - Omex Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength.omex processing completed (7s)
results_report.SimulatorGeneratesReportsOfSimulationResults (8.4 s)

Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.

Exception:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:53:08 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_7e41857e-7cf0-458a-965d-73a1a52660055392436976761597864

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... 

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@56de6d6b

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 78 ms

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

 INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels.

 INFO (ExecuteImpl.java:306) - Generating outputs... 

 INFO (RunUtils.java:233) - Generating report `report`.

 INFO (ExecuteImpl.java:325) - Generating HDF5 file... 

 INFO (ExecuteImpl.java:338) - Generating Plots... 

 WARN (CLIPythonManager.java:65) - Using old style python invocation!

 INFO (ExecuteImpl.java:370) - Archiving result files

ERROR (RunUtils.java:434) - No PDF files found, skipping archiving `plots.zip` files

 INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl.java:374) - SED-ML : BIOMD0000000912_sim.sedml successfully completed

 INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (5s)
sedml.SimulatorProducesLinear2DPlots (9.0 s)

Test that a simulator produces linear 2D plots

Exception:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:49:22 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_94b2cc5c-8fc6-47f5-8707-f54bc3d0ba815636475759970342312

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... 

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@56de6d6b

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 79 ms

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

 INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels.

 INFO (ExecuteImpl.java:306) - Generating outputs... 

 INFO (RunUtils.java:231) - Ignoring unsupported output `plot_0` while CSV generation.

 INFO (RunUtils.java:233) - Generating report `__plot__plot_0`.

 INFO (ExecuteImpl.java:325) - Generating HDF5 file... 

 INFO (RunUtils.java:387) - Ignoring unsupported output `plot_0` while generating idNamePlotsMap.

 INFO (ExecuteImpl.java:338) - Generating Plots... 

 WARN (CLIPythonManager.java:65) - Using old style python invocation!

 INFO (ExecuteImpl.java:370) - Archiving result files

 INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`.

 INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl.java:374) - SED-ML : BIOMD0000000912_sim.sedml successfully completed

 INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (5s)
sedml.SimulatorProducesLogarithmic2DPlots (9.1 s)

Test that a simulator produces logarithmic 2D plots

Exception:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:49:31 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_90d6cca9-f272-4a6a-8470-77c18a200f195614387254456221131

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... 

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@56de6d6b

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 85 ms

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

 INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels.

 INFO (ExecuteImpl.java:306) - Generating outputs... 

 INFO (RunUtils.java:231) - Ignoring unsupported output `plot_0` while CSV generation.

 INFO (RunUtils.java:233) - Generating report `__plot__plot_0`.

 INFO (ExecuteImpl.java:325) - Generating HDF5 file... 

 INFO (RunUtils.java:387) - Ignoring unsupported output `plot_0` while generating idNamePlotsMap.

 INFO (ExecuteImpl.java:338) - Generating Plots... 

 WARN (CLIPythonManager.java:65) - Using old style python invocation!

 INFO (ExecuteImpl.java:370) - Archiving result files

 INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`.

 INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl.java:374) - SED-ML : BIOMD0000000912_sim.sedml successfully completed

 INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (5s)
sedml.SimulatorProducesMultiplePlots (9.1 s)

Test that a simulator produces multiple plots

Exception:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:49:40 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_538003e7-8a0a-4425-8689-7950eacb3ed36308411309292550586

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

SED-ML versio ...

@biosimulators-daemon
Copy link

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (2.5 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 (4.3 s)

Test that a command-line interface provides inline help.

Warnings:

Command-line interfaces should display basic help when no arguments are provided.

The command-line interface displayed the following when no argument was provided:

   INFO (CLIStandalone.java:29) - Starting Vcell...
  ERROR (BiosimulationsCommand.java:119) - null
  java.lang.NullPointerException: null
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:60) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:32) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  

Command-line interface should support the `-h` option for displaying help inline.

The command-line interface displayed the following when executed with `-h`:

   INFO (CLIStandalone.java:29) - Starting Vcell...
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit
  

Command-line interface should support the `--help` option for displaying help inline.

The command-line interface displayed the following when executed with `--help`:

   INFO (CLIStandalone.java:29) - Starting Vcell...
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit

Log: None

docker_image.DeclaresSupportedEnvironmentVariables (0.7 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

@biosimulators-daemon
Copy link

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

Required model formats and simulation algorithms for SED tasks:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (6.6 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:

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:49:08 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_a20baed6-9a8f-41b5-b755-272df97e3eb54691195488345918356

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... 

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

ERROR (SolverHandler.java:87) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

null

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

null

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:338) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:580) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:85) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:272) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:32) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.util.ConcurrentModificationException

	at java.util.ArrayList$Itr.checkForComodification(ArrayList.java:911) ~[?:1.8.0_342]

	at java.util.ArrayList$Itr.next(ArrayList.java:861) ~[?:1.8.0_342]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:331) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 14 more

ERROR (ExecuteImpl.java:279) - Unable to initialize bioModel for the given selection

null

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

null

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:338) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:580) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:85) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:272) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:32) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.util.ConcurrentModificationException

	at java.util.ArrayList$Itr.checkForComodification(ArrayList.java:911) ~[?:1.8.0_342]

	at java.util.ArrayList$Itr.next(ArrayList.java:861) ~[?:1.8.0_342]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:331) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 14 more

 INFO (ExecuteImpl.java:306) - Generating outputs... 

 INFO (RunUtils.java:233) - Generating report `report`.

ERROR (RunUtils.java:374) - Encountered exception: null

java.lang.NullPointerException: null

	at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:302) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:307) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:32) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl.java:325) - Generating HDF5 file... 

ERROR (ExecuteImpl.java:342) - Failed to generate the HDF5 output file. 

java.lang.RuntimeException: Failed to generate the HDF5 output file. 

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:333) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:32) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (3s)

ERROR (ExecuteImpl.java:392) -  All sedml documents in this archive failed to execute
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (6.6 s)

Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1) and inherit the changes of the model.

Reason for skip:

Simulator did not produce the following reports:
  - `BIOMD0000000912_sim.sedml/report`

Log:

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:49:15 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_575f1a5c-61e9-4469-b75c-f1142ec336c35112620803683021966

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... 

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

ERROR (SolverHandler.java:87) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

null

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

null

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:338) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:580) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:85) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:272) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:32) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.util.ConcurrentModificationException

	at java.util.ArrayList$Itr.checkForComodification(ArrayList.java:911) ~[?:1.8.0_342]

	at java.util.ArrayList$Itr.next(ArrayList.java:861) ~[?:1.8.0_342]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:331) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 14 more

ERROR (ExecuteImpl.java:279) - Unable to initialize bioModel for the given selection

null

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

null

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:338) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:580) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:85) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:272) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:32) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.util.ConcurrentModificationException

	at java.util.ArrayList$Itr.checkForComodification(ArrayList.java:911) ~[?:1.8.0_342]

	at java.util.ArrayList$Itr.next(ArrayList.java:861) ~[?:1.8.0_342]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:331) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 14 more

 INFO (ExecuteImpl.java:306) - Generating outputs... 

 INFO (RunUtils.java:233) - Generating report `report`.

ERROR (RunUtils.java:374) - Encountered exception: null

java.lang.NullPointerException: null

	at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:302) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:307) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:32) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl.java:325) - Generating HDF5 file... 

ERROR (ExecuteImpl.java:342) - Failed to generate the HDF5 output file. 

java.lang.RuntimeException: Failed to generate the HDF5 output file. 

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:333) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:32) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (3s)

ERROR (ExecuteImpl.java:392) -  All sedml documents in this archive failed to execute
sedml.SimulatorProducesLinear3DPlots (0.3 s)

Test that a simulator produces linear 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.3 s)

Test that a simulator produces logarithmic 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 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 (18.2 s)

Test that a simulator supports model changes that involve adding, replacing, and removing model elements.

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:49:50 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_01f5625d-7071-419c-bafb-2f12414608556488458953318021672

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... 

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@160396db

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 79 ms

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

 INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels.

 INFO (ExecuteImpl.java:306) - Generating outputs... 

 INFO (RunUtils.java:233) - Generating report `report`.

 INFO (ExecuteImpl.java:325) - Generating HDF5 file... 

 INFO (ExecuteImpl.java:338) - Generating Plots... 

 WARN (CLIPythonManager.java:65) - Using old style python invocation!

 INFO (ExecuteImpl.java:370) - Archiving result files

ERROR (RunUtils.java:434) - No PDF files found, skipping archiving `plots.zip` files

 INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl.java:374) - SED-ML : BIOMD0000000912_sim.sedml successfully completed

 INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (5s)

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:49:58 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_f09f067d-3478-426c-a6c7-4e7fb44324495315842626461988247

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... 

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@30d25c03

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 81 ms

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

 INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels.

 INFO (ExecuteImpl.java:306) - Generating outputs... 

 INFO (RunUtils.java:233) - Generating report `report`.

 INFO (ExecuteImpl.java:325) - Generating HDF5 file... 

 INFO (ExecuteImpl.java:338) - Generating Plots... 

 WARN (CLIPythonManager.java:65) - Using old style python invocation!

 INFO (ExecuteImpl.java:370) - Archiving result files

ERROR (RunUtils.java:434) - No PDF files found, skipping archiving `plots.zip` files

 INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl.java:374) - SED-ML : BIOMD0000000912_sim.sedml successfully completed

 INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (6s)
sedml.SimulatorSupportsComputeModelChanges (19.6 s)

Test that a simulator supports compute model changes

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:50:17 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_136a217e-9043-4284-b65f-11f4468287721289695864863136137

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... 

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

ERROR (SEDMLImporter.java:396) - couldn't find SBase with sid=null in SBMLSymbolMapping

 WARN (SEDMLImporter.java:526) - could not map changeAttribute for ID null to a VCell Constant

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@f4c0e4e

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 74 ms

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

 INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels.

 INFO (ExecuteImpl.java:306) - Generating outputs... 

 INFO (RunUtils.java:233) - Generating report `report`.

 INFO (ExecuteImpl.java:325) - Generating HDF5 file... 

 INFO (ExecuteImpl.java:338) - Generating Plots... 

 WARN (CLIPythonManager.java:65) - Using old style python invocation!

 INFO (ExecuteImpl.java:370) - Archiving result files

ERROR (RunUtils.java:434) - No PDF files found, skipping archiving `plots.zip` files

 INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl.java:374) - SED-ML : BIOMD0000000912_sim.sedml successfully completed

 INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (6s)

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:50:26 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_61068138-b6bf-4c73-aa11-d361bb7885da3187943323326337214

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... 

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

ERROR (SEDMLImporter.java:396) - couldn't find SBase with sid=null in SBMLSymbolMapping

 WARN (SEDMLImporter.java:526) - could not map changeAttribute for ID null to a VCell Constant

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@680d4a6a

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 81 ms

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

 INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels.

 INFO (ExecuteImpl.java:306) - Generating outputs... 

 INFO (RunUtils.java:233) - Generating report `report`.

 INFO (ExecuteImpl.java:325) - Generating HDF5 file... 

 INFO (ExecuteImpl.java:338) - Generating Plots... 

 WARN (CLIPythonManager.java:65) - Using old style python invocation!

 INFO (ExecuteImpl.java:370) - Archiving result files

ERROR (RunUtils.java:434) - No PDF files found, skipping archiving `plots.zip` files

 INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl.java:374) - SED-ML : BIOMD0000000912_sim.sedml successfully completed

 INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (6s)
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (8.8 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:50:36 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_5d1f353c-b4b1-4ad3-a1bc-89e3fe900cf930260853785705076

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... 

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@267517e4

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 81 ms

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

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@f14e5bf

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.

 INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task__copy_2, 46 ms

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

 INFO (SolverHandler.java:282) - Ran 2 simulations for 1 biomodels.

 INFO (ExecuteImpl.java:306) - Generating outputs... 

 INFO (RunUtils.java:233) - Generating report `report__copy_2`.

 INFO (ExecuteImpl.java:325) - Generating HDF5 file... 

 INFO (ExecuteImpl.java:338) - Generating Plots... 

 WARN (CLIPythonManager.java:65) - Using old style python invocation!

 INFO (ExecuteImpl.java:370) - Archiving result files

ERROR (RunUtils.java:434) - No PDF files found, skipping archiving `plots.zip` files

 INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl.java:374) - SED-ML : BIOMD0000000912_sim.sedml successfully completed

 INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (5s)
sedml.SimulatorSupportsDataSetsWithDifferentShapes (6.7 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpyja84g0j/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

 INFO (CLIStandalone.java:29) - Starting Vcell...

 INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory

 INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60

 INFO (BiosimulationsCommand.java:105) - Beginning execution

Aug 29, 2022 8:50:45 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

 INFO (CLIPythonManager.java:128) - Initializing Python...



 INFO (CLIPythonManager.java:148) - Python initalization success!



 INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_7298538f-b310-4fcf-9601-6f1b0dc8a24d8586339332424846862

 INFO (ExecuteImpl.java:162) - Preparing output directory...

 INFO (ExecuteImpl.java:172) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... 

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@7923f5b3

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 99 ms

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

 INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@11841b15

 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.

 INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task__copy_2, 43 ms

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

 INFO (SolverHandler.java:282) - Ran 2 simulations for 1 biomodels.

 INFO (ExecuteImpl.java:306) - Generating outputs... 

 INFO (RunUtils.java:233) - Generating report `report`.

 INFO (ExecuteImpl.java:325) - Generating HDF5 file... 

ERROR (ExecuteImpl.java:342) - Python error caught: <

Traceback (most recent call last):

  File "<stdin>", line 1, in <module>

  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/wrapper.py", line 15, in execPlotOutputSedDoc

    cli.exec_plot_output_sed_doc(omexFilePath, idNamePlotsMap, baseOutPath)

  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 167, in exec_plot_output_sed_doc

    data_set_df = pd.read_csv(report_filename, header=None).T

  File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper

    return func(*args, **kwargs)

  File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv

    return _read(filepath_or_buffer, kwds)

  File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 581, in _read

    return parser.read(nrows)

  File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1255, in read

    index, columns, col_dict = self._engine.read(nrows)

  File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 225, in read

    chunks = self._reader.read_low_memory(nrows)

  File "pandas/_libs/parsers.pyx", line 805, in pandas._libs.parsers.TextReader.read_low_memory

  File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._read_rows

  File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader._tokenize_rows

  File "pandas/_libs/parsers.pyx", line 1960, in pandas._libs.parsers.raise_parser_error

pandas.errors.ParserError: Error tokenizing data. C error: Expected 14 fields in line 5, saw 24



{'report': 'null'}

report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv



>

Result: HDF conversion failed







org.vcell.cli.PythonStreamException: Python error caught: <

Traceback (most recent call last):

  File "<stdin>", line 1, in <module>

  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/wrapper.py", line 15, in execPlotOutputSedDoc

    cli.exec_plot_output_sed_doc(omexFilePath, idNamePlotsMap, baseOutPath)

  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 167, in exec_plot_output_sed_doc

    data_set_df = pd.read_csv(report_filename, header=None).T

  File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper

    return func(*args, **kwargs)

  File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv

    return _read(filepath_or_buffer, kwds)

  File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 581, in _read

    return parser.read(nrows)

  File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1255, in read

    index, columns, col_dict = self._engine.read(nrows)

  File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 225, in read

    chunks = self._reader.read_low_memory(nrows)

  File "pandas/_libs/parsers.pyx", line 805, in pandas._libs.parsers.TextReader.read_low_memory

  File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._read_rows

  File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader._tokenize_rows

  File "pandas/_libs/parsers.pyx", line 1960, in pandas._libs.parsers.raise_parser_error

pandas.errors.ParserError: Error tokenizing data. C error: Expected 14 fields in line 5, saw 24



{'report': 'null'}

report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv



>

Result: HDF conversion failed







	at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:247) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.PythonCalls.execPlotOutputSedDoc(PythonCalls.java:29) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:328) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:32) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (3s)

ERROR (ExecuteImpl.java:392) -  All sedml documents in this archive failed to execute
sedml.SimulatorSupportsModelAttributeChanges (19.7 s)

Test that a simulator supports changes to the attributes of model elements

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

 INFO (CLISta ...

@biosimulators-daemon
Copy link 

- 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/2951586729). 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/2951586729).

@biosimulators-daemon biosimulators-daemon added the Invalid This doesn't seem right label Aug 29, 2022
@moraru moraru mentioned this issue Aug 29, 2022
Closed
@CodeByDrescher
Copy link
Contributor

this is a result of biosimulators/Biosimulators_test_suite#63

@moraru moraru closed this as completed Sep 2, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
Invalid This doesn't seem right Validate/submit simulator Validate a simulation tool or request its submission to the BioSimulators registry
Milestone
No milestone
Development

No branches or pull requests
4 participants
@moraru @biosimulators-daemon @vcdaemon @CodeByDrescher