Submit VCell 7.5.0.76 #653

vcdaemon · 2023-10-31T15:24:28Z

id: vcell
version: 7.5.0.76
specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.5.0.76/biosimulators.json
specificationsPatch:
version: 7.5.0.76
image:
url: ghcr.io/virtualcell/biosimulators_vcell:7.5.0.76
digest: "sha256:892da548d62d6a47ceafcca888b577c37e9c02ed35dab45e88e4f40a4b664c1f"
validateImage: true
commitSimulator: true

biosimulators-daemon · 2023-10-31T15:31:44Z

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 · 2023-10-31T15:31:49Z

The specifications of your simulator is valid!

biosimulators-daemon · 2023-10-31T15:50:06Z

Summary of tests

Executed 74 test cases
Passed 37 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- 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.SimulatorSupportsDataSetsWithDifferentShapes
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 1 test cases:
- docker_image.SingularityImageExecutesSimulationsSuccessfully
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.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsRepeatedTasksWithChanges
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
- sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
- sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
- sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
- sedml.SimulatorSupportsSubstitutingAlgorithms
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

biosimulators-daemon · 2023-10-31T15:50:07Z

Failures

docker_image.SingularityImageExecutesSimulationsSuccessfully (12.7 s)

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

Exception:

The Docker image could not be successfully executed as a Singularity image:

Log: None

biosimulators-daemon · 2023-10-31T15:50:08Z

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (2.5 s)

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

Warnings:

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

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

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

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

Log: None

cli.CliDisplaysHelpInline (5.3 s)

Test that a command-line interface provides inline help.

Warnings:

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

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

  docker: Command recieved::<>
  <>
  Default case selected
  VCell shall execute <biosimulations >
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  ERROR (BiosimulationsCommand:112) - Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null []{}
  java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:51) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	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:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

  docker: Command recieved::<-h>
  <-h>
  Default case selected
  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`:

  docker: Command recieved::<--help>
  <--help>
  Default case selected
  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 (0.5 s)

Test that a Docker image has BioContainers labels with metadata about the image

Warnings:

Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

biosimulators-daemon · 2023-10-31T15:50:09Z

Skips

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