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biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
MIT License
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Submit VCell 7.4.0.23 #441

Closed jonrkarr closed 3 years ago

jonrkarr commented 3 years ago

id: vcell version: 7.4.0.23 specificationsUrl: https://raw.githubusercontent.com/virtualcell/vcell/7.4.0.23/biosimulators.json specificationsPatch: version: 7.4.0.23 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.23 validateImage: true commitSimulator: true

@moraru Rerun of #440 with test suite corrected from pyyaml 6.0

biosimulators-daemon commented 3 years ago

Thank you @jonrkarr 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 commented 3 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 3 years ago

Summary of tests

biosimulators-daemon commented 3 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.6 s)

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

Warnings:

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

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

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

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

Log:

cli.CliDisplaysHelpInline (3.2 s)

Test that a command-line interface provides inline help.

Warnings:

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

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

    usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]

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

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

    usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]

Log:

cli.CliDisplaysVersionInformationInline (2.4 s)

Test that a command-line interface provides version information inline.

Warnings:

  Command-line interface should support the `-v` option for displaying version information inline.

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

    usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]

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

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

    usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]

Log:

docker_image.DeclaresSupportedEnvironmentVariables (0.6 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_OMEX_MANIFESTS'
    - 'VALIDATE_OMEX_METADATA'
    - 'VALIDATE_RESULTS'
    - 'VALIDATE_SEDML'
    - 'VALIDATE_SEDML_MODELS'
    - 'VERBOSE'
    - 'VIZ_FORMATS'

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

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

Log:

docker_image.HasBioContainersLabels (0.6 s)

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

Warnings:

  The Docker image should have the following BioContainers labels:
    extra.identifiers.biotools

Log:

docker_image.HasOciLabels (0.5 s)

Test that a Docker image has Open Container Initiative (OCI) labels with metadata about the image

Warnings:

  The Docker image should have the following Open Container Initiative (OCI) labels:
    org.opencontainers.image.created
    org.opencontainers.image.revision

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (18.6 s)

Required model formats and simulation algorithms for SED tasks:

biosimulators-daemon commented 3 years ago

Skips

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

Required model formats and simulation algorithms for SED tasks:

biosimulators-daemon commented 3 years ago

The image for your simulator is valid!

biosimulators-daemon commented 3 years ago

A member of the BioSimulators team will review your submission and publish your image before final committment to the registry.

biosimulators-daemon commented 3 years ago

Thank you @jonrkarr 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 commented 3 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 3 years ago

Summary of tests

biosimulators-daemon commented 3 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.7 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_OMEX_MANIFESTS'
    - 'VALIDATE_OMEX_METADATA'
    - 'VALIDATE_RESULTS'
    - 'VALIDATE_SEDML'
    - 'VALIDATE_SEDML_MODELS'
    - 'VERBOSE'
    - 'VIZ_FORMATS'

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

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

Log:

cli.CliDisplaysHelpInline (2.9 s)

Test that a command-line interface provides inline help.

Warnings:

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

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

    usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]

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

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

    usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]

Log:

cli.CliDisplaysVersionInformationInline (2.4 s)

Test that a command-line interface provides version information inline.

Warnings:

  Command-line interface should support the `-v` option for displaying version information inline.

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

    usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]

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

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

    usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]

Log:

docker_image.DeclaresSupportedEnvironmentVariables (0.4 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_OMEX_MANIFESTS'
    - 'VALIDATE_OMEX_METADATA'
    - 'VALIDATE_RESULTS'
    - 'VALIDATE_SEDML'
    - 'VALIDATE_SEDML_MODELS'
    - 'VERBOSE'
    - 'VIZ_FORMATS'

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

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

Log:

docker_image.HasBioContainersLabels (0.3 s)

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

Warnings:

  The Docker image should have the following BioContainers labels:
    extra.identifiers.biotools

Log:

docker_image.HasOciLabels (0.3 s)

Test that a Docker image has Open Container Initiative (OCI) labels with metadata about the image

Warnings:

  The Docker image should have the following Open Container Initiative (OCI) labels:
    org.opencontainers.image.created
    org.opencontainers.image.revision

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (17.5 s)

Required model formats and simulation algorithms for SED tasks:

biosimulators-daemon commented 3 years ago

Skips

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

Required model formats and simulation algorithms for SED tasks:

biosimulators-daemon commented 3 years ago

The image for your simulator is valid!

biosimulators-daemon commented 3 years ago

Your submission was committed to the BioSimulators registry. Thank you!

Future submissions of subsequent versions of VCell to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.