Submit VCell 7.4.0.68 #589

vcdaemon · 2022-10-09T01:49:21Z

id: vcell
version: 7.4.0.68
specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.4.0.68/biosimulators.json
specificationsPatch:
version: 7.4.0.68
image:
url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.68
digest: "sha256:190a1eed6736057a167ff60ea3698731b157626176b7a9e9e5784c9d032c35d7"
validateImage: true
commitSimulator: true

biosimulators-daemon · 2022-10-09T01:54:49Z

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

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

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

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

biosimulators-daemon · 2022-10-09T01:54:51Z

The specifications of your simulator is valid!

biosimulators-daemon · 2022-10-09T02:09:15Z

Summary of tests

Executed 74 test cases
Passed 38 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- 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.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 0 test cases
Skipped 36 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.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsComputeModelChanges
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- 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 · 2022-10-09T02:09:15Z

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (2.0 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 (3.9 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:

  /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found
  VCell shall execute <biosimulations >
   INFO (CLIStandalone:36) - Starting Vcell...
  ERROR (BiosimulationsCommand:122) - null
  java.lang.NullPointerException: null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:43) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:39) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:35) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:46) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [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`:

  /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found
  VCell shall execute <biosimulations -h>
   INFO (CLIStandalone:36) - 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`:

  /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found
  VCell shall execute <biosimulations --help>
   INFO (CLIStandalone:36) - 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 (3.1 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 (0.2 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 · 2022-10-09T02:09:16Z

Skips

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

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000263

Reason for skip:

Case requires model formats format_3972 and simulation algorithms KISAO_0000263

Log: None

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3972 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9012
Algorithm: KISAO_0000669

Reason for skip:

Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000088

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_000019

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_000019

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000496

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000496

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000029

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000029

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000437

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000437

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9001
Algorithm: KISAO_0000057

Reason for skip:

Case requires model formats format_9001 and simulation algorithms KISAO_0000057

Log: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.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.SimulatorSupportsComputeModelChanges (9.7 s)

Test that a simulator supports compute model changes

Reason for skip:

The execution of the COMBINE/OMEX archive did not fail as expected

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_e5165a8d-e74e-4f6e-b01d-74f24c0df0dd3376146329529883349

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - 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:191) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl:231) - 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:271) - 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:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

ERROR (SEDMLImporter:562) - couldn't find SBase with sid=null in SBMLSymbolMapping

 WARN (SEDMLImporter:787) - could not map changeAttribute for ID null to a VCell Constant

 INFO (XmlBase:4549) - RbmModelContainer is missing.

taskToSimulationMap: 1

taskToListOfSubTasksMap: 1

taskToVariableMap: 1

topTaskToBaseTask: 1

 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@3672276e

 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler:441) - Running simulation Caravagna2010, 75 ms

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

 INFO (SolverHandler:543) - Ran 1 simulation jobs for 1 biomodels.

 INFO (ExecuteImpl:308) - Generating outputs... 

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

 INFO (ExecuteImpl:327) - Generating HDF5 file... 

 INFO (ExecuteImpl:340) - Generating Plots... 

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

 INFO (ExecuteImpl:374) - Archiving result files

ERROR (RunUtils:529) - No PDF files found, skipping archiving `plots.zip` files

 INFO (RunUtils:533) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl:378) - SED-ML : BIOMD0000000912_sim.sedml successfully completed

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (6s)

sedml.SimulatorSupportsDataSetsWithDifferentShapes (7.5 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpacoklirv/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_c4ab5053-825a-457f-b278-1fccf7b7392f3709502103039362577

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - 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:191) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl:231) - 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:271) - 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:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (XmlBase:4549) - RbmModelContainer is missing.

taskToSimulationMap: 2

taskToListOfSubTasksMap: 2

taskToVariableMap: 2

topTaskToBaseTask: 2

 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@6ee8dcd3

 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler:441) - Running simulation Caravagna2010, 74 ms

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

 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@14379273

 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.

 INFO (SolverHandler:441) - Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 44 ms

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

 INFO (SolverHandler:543) - Ran 2 simulation jobs for 1 biomodels.

 INFO (ExecuteImpl:308) - Generating outputs... 

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

 INFO (ExecuteImpl:327) - Generating HDF5 file... 

ERROR (ExecuteImpl:344) - 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:248) ~[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:330) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (4s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithChanges (9.2 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpacoklirv/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_49adceac-de84-4847-8475-21d519b1669e9008966330119623877

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_49adceac-de84-4847-8475-21d519b1669e9008966330119623877/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_28aff2b8-20e1-4f61-a09a-ee00f8c864e73116687205464130084

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_28aff2b8-20e1-4f61-a09a-ee00f8c864e73116687205464130084/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (9.2 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpacoklirv/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_862462c1-443f-4fe3-8977-9d6df6e434f91634616349953316522

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_862462c1-443f-4fe3-8977-9d6df6e434f91634616349953316522/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_2d835c0c-7bcd-4589-aab1-81ef01bb0e717179776378766722314

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_2d835c0c-7bcd-4589-aab1-81ef01bb0e717179776378766722314/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (4.5 s)

Test that a simulator supports repeated tasks over functional ranges

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpacoklirv/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_6f12f2de-fe2c-457b-8c70-a21f99d2a0194412360308735883165

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_6f12f2de-fe2c-457b-8c70-a21f99d2a0194412360308735883165/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (4.5 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpacoklirv/sedml/sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_73a270c5-c837-49b7-8b11-3255bde6fbab8814453993034965728

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_73a270c5-c837-49b7-8b11-3255bde6fbab8814453993034965728/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (4.8 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpacoklirv/sedml/sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_c91735ed-93a9-46e3-8419-2522801719532874953373254182668

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_c91735ed-93a9-46e3-8419-2522801719532874953373254182668/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (4.5 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpacoklirv/sedml/sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_f6b91b3f-fe49-42a2-a75b-f2c8993d588d1743777807174033376

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_f6b91b3f-fe49-42a2-a75b-f2c8993d588d1743777807174033376/ ...

biosimulators-daemon · 2022-10-09T02:09:17Z

The image for your simulator is valid!

biosimulators-daemon · 2022-10-09T02:10:34Z

The validation/submission of your simulator failed.

- 504 Server Error: Gateway Time-out for url: https://api.biosimulations.org/images/refresh

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

biosimulators-daemon · 2022-10-09T02:23:58Z

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

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

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

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

biosimulators-daemon · 2022-10-09T02:24:01Z

The specifications of your simulator is valid!

biosimulators-daemon · 2022-10-09T02:38:24Z

Summary of tests

Executed 74 test cases
Passed 38 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- 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.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 0 test cases
Skipped 36 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.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsComputeModelChanges
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- 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 · 2022-10-09T02:38:25Z

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.9 s)

Test that the inline help for a command-line interface describes the environment variables that the simulator supports.

Warnings:

The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'
  - '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 (3.6 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:

  /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found
  VCell shall execute <biosimulations >
   INFO (CLIStandalone:36) - Starting Vcell...
  ERROR (BiosimulationsCommand:122) - null
  java.lang.NullPointerException: null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:43) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:39) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:35) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:46) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [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`:

  /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found
  VCell shall execute <biosimulations -h>
   INFO (CLIStandalone:36) - 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`:

  /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found
  VCell shall execute <biosimulations --help>
   INFO (CLIStandalone:36) - 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 (1.6 s)

Test if a Docker image declares the environment variables that is supports

Warnings:

Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log: None

docker_image.HasBioContainersLabels (0.3 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 · 2022-10-09T02:38:26Z

Skips

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

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000263

Reason for skip:

Case requires model formats format_3972 and simulation algorithms KISAO_0000263

Log: None

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3972 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9012
Algorithm: KISAO_0000669

Reason for skip:

Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000088

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_000019

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_000019

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000496

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000496

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000029

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000029

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000437

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000437

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9001
Algorithm: KISAO_0000057

Reason for skip:

Case requires model formats format_9001 and simulation algorithms KISAO_0000057

Log: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.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.SimulatorSupportsComputeModelChanges (9.2 s)

Test that a simulator supports compute model changes

Reason for skip:

The execution of the COMBINE/OMEX archive did not fail as expected

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_a4c7d1e7-7b58-41b9-bb0b-e3ad108204a8445871879407616502

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - 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:191) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl:231) - 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:271) - 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:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

ERROR (SEDMLImporter:562) - couldn't find SBase with sid=null in SBMLSymbolMapping

 WARN (SEDMLImporter:787) - could not map changeAttribute for ID null to a VCell Constant

 INFO (XmlBase:4549) - RbmModelContainer is missing.

taskToSimulationMap: 1

taskToListOfSubTasksMap: 1

taskToVariableMap: 1

topTaskToBaseTask: 1

 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@3672276e

 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler:441) - Running simulation Caravagna2010, 68 ms

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

 INFO (SolverHandler:543) - Ran 1 simulation jobs for 1 biomodels.

 INFO (ExecuteImpl:308) - Generating outputs... 

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

 INFO (ExecuteImpl:327) - Generating HDF5 file... 

 INFO (ExecuteImpl:340) - Generating Plots... 

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

 INFO (ExecuteImpl:374) - Archiving result files

ERROR (RunUtils:529) - No PDF files found, skipping archiving `plots.zip` files

 INFO (RunUtils:533) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl:378) - SED-ML : BIOMD0000000912_sim.sedml successfully completed

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (6s)

sedml.SimulatorSupportsDataSetsWithDifferentShapes (7.3 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpaz0q4gha/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_45212c5c-0069-469d-932c-1178aae5251f131172385569003968

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - 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:191) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl:231) - 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:271) - 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:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (XmlBase:4549) - RbmModelContainer is missing.

taskToSimulationMap: 2

taskToListOfSubTasksMap: 2

taskToVariableMap: 2

topTaskToBaseTask: 2

 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@6ee8dcd3

 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler:441) - Running simulation Caravagna2010, 76 ms

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

 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@14379273

 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.

 INFO (SolverHandler:441) - Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 49 ms

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

 INFO (SolverHandler:543) - Ran 2 simulation jobs for 1 biomodels.

 INFO (ExecuteImpl:308) - Generating outputs... 

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

 INFO (ExecuteImpl:327) - Generating HDF5 file... 

ERROR (ExecuteImpl:344) - 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:248) ~[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:330) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (4s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithChanges (8.6 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpaz0q4gha/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_0d3f9c4a-0c49-42de-9805-cb7431ce5aff6132386816852463863

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_0d3f9c4a-0c49-42de-9805-cb7431ce5aff6132386816852463863/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_9274921d-d784-45b0-827c-0a696f5b605a8483171700412345202

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_9274921d-d784-45b0-827c-0a696f5b605a8483171700412345202/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (8.7 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpaz0q4gha/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_041c57f8-a1c6-4f2c-a7fa-3b4c46baae946654979560468393045

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_041c57f8-a1c6-4f2c-a7fa-3b4c46baae946654979560468393045/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_c5c94058-d724-4801-8d28-a4e69e6caf2a7341707128173641923

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_c5c94058-d724-4801-8d28-a4e69e6caf2a7341707128173641923/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (4.2 s)

Test that a simulator supports repeated tasks over functional ranges

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpaz0q4gha/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_5b0eb889-9bea-441d-abc5-4156c68aa6e87065346231788222029

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_5b0eb889-9bea-441d-abc5-4156c68aa6e87065346231788222029/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (4.2 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpaz0q4gha/sedml/sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_c6719480-f0a0-499a-b1e9-99a525c8c06b1012858991880157713

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_c6719480-f0a0-499a-b1e9-99a525c8c06b1012858991880157713/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (4.3 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpaz0q4gha/sedml/sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_4f9a2a10-9504-4a8b-8c7a-bc366f845e664869877278072008004

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_4f9a2a10-9504-4a8b-8c7a-bc366f845e664869877278072008004/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (4.3 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpaz0q4gha/sedml/sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_fc8cca1a-d05f-4148-b091-d557d497c11a2284377142081920051

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_fc8cca1a-d05f-4148-b091-d557d497c11a2284377142081920051/BI ...

biosimulators-daemon · 2022-10-09T02:38:27Z

The image for your simulator is valid!

biosimulators-daemon · 2022-10-09T02:39:38Z

The validation/submission of your simulator failed.

- 504 Server Error: Gateway Time-out for url: https://api.biosimulations.org/images/refresh

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

biosimulators-daemon · 2022-10-09T03:43:43Z

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

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

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

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

biosimulators-daemon · 2022-10-09T03:43:46Z

The specifications of your simulator is valid!

biosimulators-daemon · 2022-10-09T04:00:26Z

Summary of tests

Executed 74 test cases
Passed 38 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- 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.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 0 test cases
Skipped 36 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.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsComputeModelChanges
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- 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 · 2022-10-09T04:00:27Z

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (3.0 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 (4.7 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:

  /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found
  VCell shall execute <biosimulations >
   INFO (CLIStandalone:36) - Starting Vcell...
  ERROR (BiosimulationsCommand:122) - null
  java.lang.NullPointerException: null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:43) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:39) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:35) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:46) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [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`:

  /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found
  VCell shall execute <biosimulations -h>
   INFO (CLIStandalone:36) - 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`:

  /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found
  VCell shall execute <biosimulations --help>
   INFO (CLIStandalone:36) - 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 (0.3 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 · 2022-10-09T04:00:28Z

Skips

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

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000263

Reason for skip:

Case requires model formats format_3972 and simulation algorithms KISAO_0000263

Log: None

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3972 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9012
Algorithm: KISAO_0000669

Reason for skip:

Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000088

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_000019

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_000019

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000496

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000496

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000029

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000029

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000437

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000437

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9001
Algorithm: KISAO_0000057

Reason for skip:

Case requires model formats format_9001 and simulation algorithms KISAO_0000057

Log: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorProducesLinear3DPlots (0.4 s)

Test that a simulator produces linear 3D plots

Reason for skip:

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

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.4 s)

Test that a simulator produces logarithmic 3D plots

Reason for skip:

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

Log: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.4 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions

Reason for skip:

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

Log: None

sedml.SimulatorSupportsComputeModelChanges (11.1 s)

Test that a simulator supports compute model changes

Reason for skip:

The execution of the COMBINE/OMEX archive did not fail as expected

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_0843ab31-0269-4175-ae79-7827a4740d302989734413456027785

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - 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:191) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl:231) - 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:271) - 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:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

ERROR (SEDMLImporter:562) - couldn't find SBase with sid=null in SBMLSymbolMapping

 WARN (SEDMLImporter:787) - could not map changeAttribute for ID null to a VCell Constant

 INFO (XmlBase:4549) - RbmModelContainer is missing.

taskToSimulationMap: 1

taskToListOfSubTasksMap: 1

taskToVariableMap: 1

topTaskToBaseTask: 1

 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@3672276e

 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler:441) - Running simulation Caravagna2010, 87 ms

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

 INFO (SolverHandler:543) - Ran 1 simulation jobs for 1 biomodels.

 INFO (ExecuteImpl:308) - Generating outputs... 

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

 INFO (ExecuteImpl:327) - Generating HDF5 file... 

 INFO (ExecuteImpl:340) - Generating Plots... 

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

 INFO (ExecuteImpl:374) - Archiving result files

ERROR (RunUtils:529) - No PDF files found, skipping archiving `plots.zip` files

 INFO (RunUtils:533) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl:378) - SED-ML : BIOMD0000000912_sim.sedml successfully completed

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (7s)

sedml.SimulatorSupportsDataSetsWithDifferentShapes (8.6 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpk2i_ewl8/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_44b94efe-bcd2-430c-b1a3-ed6dc93932fd8820308804588177947

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - 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:191) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl:231) - 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:271) - 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:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (XmlBase:4549) - RbmModelContainer is missing.

taskToSimulationMap: 2

taskToListOfSubTasksMap: 2

taskToVariableMap: 2

topTaskToBaseTask: 2

 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@6ee8dcd3

 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler:441) - Running simulation Caravagna2010, 86 ms

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

 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@14379273

 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.

 INFO (SolverHandler:441) - Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 46 ms

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

 INFO (SolverHandler:543) - Ran 2 simulation jobs for 1 biomodels.

 INFO (ExecuteImpl:308) - Generating outputs... 

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

 INFO (ExecuteImpl:327) - Generating HDF5 file... 

ERROR (ExecuteImpl:344) - 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:248) ~[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:330) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (4s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithChanges (10.7 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpk2i_ewl8/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_0265f2d2-ac6e-4cb9-bab7-688a4bb698553723921088454895573

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_0265f2d2-ac6e-4cb9-bab7-688a4bb698553723921088454895573/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_b1eb0a57-df96-46f3-af86-6914ef24dc677669351892785627859

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_b1eb0a57-df96-46f3-af86-6914ef24dc677669351892785627859/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (10.6 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpk2i_ewl8/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_14e821ae-7d40-4f65-bdf1-77c2cf3c9d6f7540915807035546290

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_14e821ae-7d40-4f65-bdf1-77c2cf3c9d6f7540915807035546290/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_5dabfd89-6b32-4c26-9754-9a886dab7e401443125080653310309

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_5dabfd89-6b32-4c26-9754-9a886dab7e401443125080653310309/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (5.2 s)

Test that a simulator supports repeated tasks over functional ranges

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpk2i_ewl8/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_6fbdeb08-74ae-4dbf-8ea8-8403c0f2c63d4597071961875400927

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_6fbdeb08-74ae-4dbf-8ea8-8403c0f2c63d4597071961875400927/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (5.2 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpk2i_ewl8/sedml/sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_f2150a39-fd6f-492e-9384-cdcfe273d8cf2797432126703485690

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_f2150a39-fd6f-492e-9384-cdcfe273d8cf2797432126703485690/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (5.2 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpk2i_ewl8/sedml/sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_65354b22-30db-4c88-9592-96293df621a1605108360163553706

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_65354b22-30db-4c88-9592-96293df621a1605108360163553706/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (5.2 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpk2i_ewl8/sedml/sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_90d7f53f-02c3-428b-89a6-5b5cef9845446880560548946803025

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_90d7f53f-02c3-428b-89a6-5b5cef9845446880560548946803025 ...

biosimulators-daemon · 2022-10-09T04:00:29Z

The image for your simulator is valid!

biosimulators-daemon · 2022-10-09T04:01:41Z

The validation/submission of your simulator failed.

- 504 Server Error: Gateway Time-out for url: https://api.biosimulations.org/images/refresh

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

biosimulators-daemon · 2022-10-09T04:11:48Z

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

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

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

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

biosimulators-daemon · 2022-10-09T04:11:52Z

The specifications of your simulator is valid!

biosimulators-daemon · 2022-10-09T04:26:25Z

Summary of tests

Executed 74 test cases
Passed 38 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- 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.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 0 test cases
Skipped 36 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.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsComputeModelChanges
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- 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 · 2022-10-09T04:26:25Z

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (2.7 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 (4.0 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:

  /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found
  VCell shall execute <biosimulations >
   INFO (CLIStandalone:36) - Starting Vcell...
  ERROR (BiosimulationsCommand:122) - null
  java.lang.NullPointerException: null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:43) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:39) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:35) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:46) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [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`:

  /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found
  VCell shall execute <biosimulations -h>
   INFO (CLIStandalone:36) - 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`:

  /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found
  VCell shall execute <biosimulations --help>
   INFO (CLIStandalone:36) - 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 (0.4 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 (0.3 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 · 2022-10-09T04:26:26Z

Skips

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

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000263

Reason for skip:

Case requires model formats format_3972 and simulation algorithms KISAO_0000263

Log: None

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3972 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9012
Algorithm: KISAO_0000669

Reason for skip:

Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000088

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_000019

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_000019

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000496

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000496

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000029

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000029

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000437

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000437

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9001
Algorithm: KISAO_0000057

Reason for skip:

Case requires model formats format_9001 and simulation algorithms KISAO_0000057

Log: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorProducesLinear3DPlots (0.4 s)

Test that a simulator produces linear 3D plots

Reason for skip:

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

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.3 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.SimulatorSupportsComputeModelChanges (10.1 s)

Test that a simulator supports compute model changes

Reason for skip:

The execution of the COMBINE/OMEX archive did not fail as expected

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_f61b6612-ddee-4e86-9068-bdc78f70459c3893215672602225377

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - 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:191) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl:231) - 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:271) - 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:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

ERROR (SEDMLImporter:562) - couldn't find SBase with sid=null in SBMLSymbolMapping

 WARN (SEDMLImporter:787) - could not map changeAttribute for ID null to a VCell Constant

 INFO (XmlBase:4549) - RbmModelContainer is missing.

taskToSimulationMap: 1

taskToListOfSubTasksMap: 1

taskToVariableMap: 1

topTaskToBaseTask: 1

 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@3672276e

 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler:441) - Running simulation Caravagna2010, 85 ms

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

 INFO (SolverHandler:543) - Ran 1 simulation jobs for 1 biomodels.

 INFO (ExecuteImpl:308) - Generating outputs... 

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

 INFO (ExecuteImpl:327) - Generating HDF5 file... 

 INFO (ExecuteImpl:340) - Generating Plots... 

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

 INFO (ExecuteImpl:374) - Archiving result files

ERROR (RunUtils:529) - No PDF files found, skipping archiving `plots.zip` files

 INFO (RunUtils:533) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl:378) - SED-ML : BIOMD0000000912_sim.sedml successfully completed

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (6s)

sedml.SimulatorSupportsDataSetsWithDifferentShapes (7.5 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmppe5vlr10/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_56ae9be6-73b5-4197-bedf-13acc69ece7b784267666532515222

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - 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:191) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl:231) - 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:271) - 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:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (XmlBase:4549) - RbmModelContainer is missing.

taskToSimulationMap: 2

taskToListOfSubTasksMap: 2

taskToVariableMap: 2

topTaskToBaseTask: 2

 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@6ee8dcd3

 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler:441) - Running simulation Caravagna2010, 71 ms

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

 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@14379273

 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.

 INFO (SolverHandler:441) - Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 37 ms

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

 INFO (SolverHandler:543) - Ran 2 simulation jobs for 1 biomodels.

 INFO (ExecuteImpl:308) - Generating outputs... 

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

 INFO (ExecuteImpl:327) - Generating HDF5 file... 

ERROR (ExecuteImpl:344) - 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:248) ~[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:330) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (4s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithChanges (9.1 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmppe5vlr10/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_bdda6aae-0d71-42a2-ab9e-27a24da556389153883222339185404

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_bdda6aae-0d71-42a2-ab9e-27a24da556389153883222339185404/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_34843931-7a19-4714-b764-b75856272cec1450867022620374607

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_34843931-7a19-4714-b764-b75856272cec1450867022620374607/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (9.1 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmppe5vlr10/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_4078346b-4151-4099-94dc-cdd6e13688811644388099436354718

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_4078346b-4151-4099-94dc-cdd6e13688811644388099436354718/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_6ece7b69-0972-444b-93f6-b1c4de79c3e65806050898441496224

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_6ece7b69-0972-444b-93f6-b1c4de79c3e65806050898441496224/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (4.4 s)

Test that a simulator supports repeated tasks over functional ranges

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmppe5vlr10/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_085a5286-b0db-43e2-8ffa-ed399b7e199b5095312702794570051

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_085a5286-b0db-43e2-8ffa-ed399b7e199b5095312702794570051/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (4.5 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmppe5vlr10/sedml/sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_0343b0d0-1eb3-416b-875a-5ad82f5a58264787156128399698810

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_0343b0d0-1eb3-416b-875a-5ad82f5a58264787156128399698810/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (4.5 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmppe5vlr10/sedml/sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_eea969db-e67b-4aac-9526-ed25df4b34d01571752082043874215

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_eea969db-e67b-4aac-9526-ed25df4b34d01571752082043874215/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (4.4 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmppe5vlr10/sedml/sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_dd552dd6-70b9-459c-b23e-2ea001c461846446898103524571826

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_dd552dd6-70b9-459c-b23e-2ea001c461846446898103524571826/ ...

biosimulators-daemon · 2022-10-09T04:26:27Z

The image for your simulator is valid!

biosimulators-daemon · 2022-10-09T04:27:37Z

The validation/submission of your simulator failed.

- 504 Server Error: Gateway Time-out for url: https://api.biosimulations.org/images/refresh

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

moraru · 2022-10-09T11:26:44Z

After passing validation final step of building and uploading the singularity image fails due to biosimulators/Biosimulators_test_suite#64

should be re-run after fixing above

biosimulators-daemon · 2022-10-09T15:07:11Z

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

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

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

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

biosimulators-daemon · 2022-10-09T15:07:15Z

The specifications of your simulator is valid!

biosimulators-daemon · 2022-10-09T15:25:30Z

Summary of tests

Executed 74 test cases
Passed 38 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- 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.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 0 test cases
Skipped 36 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.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsComputeModelChanges
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- 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 · 2022-10-09T15:25:31Z

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (4.0 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 (5.8 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:

  /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found
  VCell shall execute <biosimulations >
   INFO (CLIStandalone:36) - Starting Vcell...
  ERROR (BiosimulationsCommand:122) - null
  java.lang.NullPointerException: null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:43) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:39) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:35) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:46) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [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`:

  /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found
  VCell shall execute <biosimulations -h>
   INFO (CLIStandalone:36) - 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`:

  /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found
  VCell shall execute <biosimulations --help>
   INFO (CLIStandalone:36) - 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 (1.4 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 (1.1 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 · 2022-10-09T15:25:32Z

Skips

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

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000263

Reason for skip:

Case requires model formats format_3972 and simulation algorithms KISAO_0000263

Log: None

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3972 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9012
Algorithm: KISAO_0000669

Reason for skip:

Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000088

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_000019

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_000019

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000496

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000496

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000029

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000029

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000437

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000437

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9001
Algorithm: KISAO_0000057

Reason for skip:

Case requires model formats format_9001 and simulation algorithms KISAO_0000057

Log: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorProducesLinear3DPlots (0.5 s)

Test that a simulator produces linear 3D plots

Reason for skip:

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

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.4 s)

Test that a simulator produces logarithmic 3D plots

Reason for skip:

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

Log: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.4 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions

Reason for skip:

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

Log: None

sedml.SimulatorSupportsComputeModelChanges (13.0 s)

Test that a simulator supports compute model changes

Reason for skip:

The execution of the COMBINE/OMEX archive did not fail as expected

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_5fb88cec-31e1-46de-80c5-cbb43ceca4525735342145614217077

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - 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:191) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl:231) - 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:271) - 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:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

ERROR (SEDMLImporter:562) - couldn't find SBase with sid=null in SBMLSymbolMapping

 WARN (SEDMLImporter:787) - could not map changeAttribute for ID null to a VCell Constant

 INFO (XmlBase:4549) - RbmModelContainer is missing.

taskToSimulationMap: 1

taskToListOfSubTasksMap: 1

taskToVariableMap: 1

topTaskToBaseTask: 1

 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@3672276e

 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler:441) - Running simulation Caravagna2010, 103 ms

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

 INFO (SolverHandler:543) - Ran 1 simulation jobs for 1 biomodels.

 INFO (ExecuteImpl:308) - Generating outputs... 

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

 INFO (ExecuteImpl:327) - Generating HDF5 file... 

 INFO (ExecuteImpl:340) - Generating Plots... 

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

 INFO (ExecuteImpl:374) - Archiving result files

ERROR (RunUtils:529) - No PDF files found, skipping archiving `plots.zip` files

 INFO (RunUtils:533) - Archiving resultant CSV files to `reports.zip`.

 INFO (ExecuteImpl:378) - SED-ML : BIOMD0000000912_sim.sedml successfully completed

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (7s)

sedml.SimulatorSupportsDataSetsWithDifferentShapes (9.7 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/tmphmfmjwn8/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_bc866238-0aeb-44e4-9be9-4d177926938a7516058548143991960

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - 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:191) - Processing SED-ML: BIOMD0000000912_sim.sedml

 INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

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

 INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion...

 INFO (ExecuteImpl:231) - 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:271) - 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:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 WARN (SolverUtilities:168) - KISAO - bad format, skipping

 INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

 INFO (XmlBase:4549) - RbmModelContainer is missing.

taskToSimulationMap: 2

taskToListOfSubTasksMap: 2

taskToVariableMap: 2

topTaskToBaseTask: 2

 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@6ee8dcd3

 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'.

 INFO (SolverHandler:441) - Running simulation Caravagna2010, 93 ms

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

 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@14379273

 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed

 INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.

 INFO (SolverHandler:441) - Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 47 ms

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

 INFO (SolverHandler:543) - Ran 2 simulation jobs for 1 biomodels.

 INFO (ExecuteImpl:308) - Generating outputs... 

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

 INFO (ExecuteImpl:327) - Generating HDF5 file... 

ERROR (ExecuteImpl:344) - 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:248) ~[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:330) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (4s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithChanges (12.3 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmphmfmjwn8/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_eb9f8d49-1e24-4a27-81e8-e3e7a9b75a1e3639528374154117278

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_eb9f8d49-1e24-4a27-81e8-e3e7a9b75a1e3639528374154117278/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_10866051-6675-4899-ad26-3db8a0618b9b1372628713589121055

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_10866051-6675-4899-ad26-3db8a0618b9b1372628713589121055/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (14.1 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmphmfmjwn8/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_7bb3d18f-8972-440a-8794-4c45950987134803198280904479394

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_7bb3d18f-8972-440a-8794-4c45950987134803198280904479394/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_aa1d4c8c-0289-462a-ae02-8501522a16522016147036215399891

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_aa1d4c8c-0289-462a-ae02-8501522a16522016147036215399891/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (6.4 s)

Test that a simulator supports repeated tasks over functional ranges

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmphmfmjwn8/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_2ff4998e-8360-4434-b722-ef2b327a366e2487726734354716853

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_2ff4998e-8360-4434-b722-ef2b327a366e2487726734354716853/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (6.7 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmphmfmjwn8/sedml/sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_8f5b2746-197e-4163-a8ad-9739d84a9f391277534808561115017

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_8f5b2746-197e-4163-a8ad-9739d84a9f391277534808561115017/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (6.5 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmphmfmjwn8/sedml/sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_7d7b8fbf-2ad6-4bad-9f6b-11b515fa5c531670896892910677298

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_7d7b8fbf-2ad6-4bad-9f6b-11b515fa5c531670896892910677298/BIOMD0000000912_sim.sedml failed with error: 

org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s)

ERROR (ExecuteImpl:396) -  All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (6.5 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmphmfmjwn8/sedml/sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

/usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:36) - Starting Vcell...

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

 INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68

 INFO (BiosimulationsCommand:109) - Beginning execution

 INFO (CLIPythonManager:129) - Initializing Python...



 INFO (CLIPythonManager:149) - Python initalization success!



 INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex

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

 INFO (NativeLib:29) - Loading combinej

 INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_d3abeae1-6c9a-4f30-80d2-cc0bd3c673de594302512492200082

 INFO (ExecuteImpl:164) - Preparing output directory...

 INFO (ExecuteImpl:174) - Initializing SED-ML document...

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364)

	at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317)

	at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415)

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112)

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20)

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)

	at picocli.CommandLine.access$1300(CommandLine.java:145)

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)

	at picocli.CommandLine.execute(CommandLine.java:2078)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40)

ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_d3abeae1-6c9a-4f30-80d2-cc0bd3c673de59430251249220008 ...

biosimulators-daemon · 2022-10-09T15:25:33Z

The image for your simulator is valid!

biosimulators-daemon · 2022-10-09T15:26:52Z

The validation/submission of your simulator failed.

- 504 Server Error: Gateway Time-out for url: https://api.biosimulations.org/images/refresh

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

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vcdaemon added the Validate/submit simulator Validate a simulation tool or request its submission to the BioSimulators registry label Oct 9, 2022

biosimulators-daemon added Validated Approved labels Oct 9, 2022

biosimulators-daemon added the Invalid This doesn't seem right label Oct 9, 2022

biosimulators-daemon removed Validated Invalid This doesn't seem right labels Oct 9, 2022

biosimulators-daemon added Validated Invalid This doesn't seem right labels Oct 9, 2022

biosimulators-daemon removed Invalid This doesn't seem right Validated labels Oct 9, 2022

biosimulators-daemon added the Invalid This doesn't seem right label Oct 9, 2022

biosimulators-daemon removed Validated Invalid This doesn't seem right labels Oct 9, 2022

biosimulators-daemon added the Validated label Oct 9, 2022

biosimulators-daemon added the Invalid This doesn't seem right label Oct 9, 2022

This was referenced Oct 9, 2022

build large singularity images fails with default settings biosimulators/Biosimulators_test_suite#64

Open

Submit VCell 7.4.0.61 #588

Closed

moraru removed the Invalid This doesn't seem right label Oct 9, 2022

moraru assigned bilalshaikh42 and CodeByDrescher Oct 9, 2022

biosimulators-daemon removed the Validated label Oct 9, 2022

biosimulators-daemon added Validated Invalid This doesn't seem right labels Oct 9, 2022

luciansmith closed this as completed Jun 15, 2023

Submit VCell 7.4.0.68 #589

Submit VCell 7.4.0.68 #589

Comments

vcdaemon commented Oct 9, 2022 • edited by CodeByDrescher Loading

biosimulators-daemon commented Oct 9, 2022

biosimulators-daemon commented Oct 9, 2022

biosimulators-daemon commented Oct 9, 2022

Summary of tests

biosimulators-daemon commented Oct 9, 2022

Warnings

biosimulators-daemon commented Oct 9, 2022

Skips

biosimulators-daemon commented Oct 9, 2022

biosimulators-daemon commented Oct 9, 2022

biosimulators-daemon commented Oct 9, 2022

biosimulators-daemon commented Oct 9, 2022

biosimulators-daemon commented Oct 9, 2022

Summary of tests

biosimulators-daemon commented Oct 9, 2022

Warnings

biosimulators-daemon commented Oct 9, 2022

Skips

biosimulators-daemon commented Oct 9, 2022

biosimulators-daemon commented Oct 9, 2022

biosimulators-daemon commented Oct 9, 2022

biosimulators-daemon commented Oct 9, 2022

biosimulators-daemon commented Oct 9, 2022

Summary of tests

biosimulators-daemon commented Oct 9, 2022

Warnings

biosimulators-daemon commented Oct 9, 2022

Skips

biosimulators-daemon commented Oct 9, 2022

biosimulators-daemon commented Oct 9, 2022

biosimulators-daemon commented Oct 9, 2022

biosimulators-daemon commented Oct 9, 2022

biosimulators-daemon commented Oct 9, 2022

Summary of tests

biosimulators-daemon commented Oct 9, 2022

Warnings

biosimulators-daemon commented Oct 9, 2022

Skips

biosimulators-daemon commented Oct 9, 2022

biosimulators-daemon commented Oct 9, 2022

moraru commented Oct 9, 2022

biosimulators-daemon commented Oct 9, 2022

biosimulators-daemon commented Oct 9, 2022

biosimulators-daemon commented Oct 9, 2022

Summary of tests

biosimulators-daemon commented Oct 9, 2022

Warnings

biosimulators-daemon commented Oct 9, 2022

Skips

biosimulators-daemon commented Oct 9, 2022

biosimulators-daemon commented Oct 9, 2022

vcdaemon commented Oct 9, 2022 •

edited by CodeByDrescher

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