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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 BoolNet 2.1.5 #111

Closed biosimulators-daemon closed 3 years ago

biosimulators-daemon commented 3 years ago

id: boolnet version: 2.1.5 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_BoolNet/0857716a68ad19571781bf43c52819eedb18aaa8/biosimulators.json specificationsPatch: version: 2.1.5 image: url: ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5 validateImage: true commitSimulator: true

Fixed permissions for actions

biosimulators-daemon commented 3 years ago

Thank you @biosimulators-daemon 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 is available here.

biosimulators-daemon commented 3 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 3 years ago

Summary of tests

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (12.4 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'

  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:

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:
    - 'ALGORITHM_SUBSTITUTION_POLICY'

  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 (1.0 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:

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (4.8 s)

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

Warnings:

  The execution status report produced by the simulator is not valid:

    could not determine a constructor for the tag 'tag:yaml.org,2002:python/object/new:rpy2.robjects.vectors.StrVector'
      in "/tmp/tmpg6jjvtxx/outputs/log.yml", line 51, column 15

Log:

  Matplotlib created a temporary config/cache directory at /tmp/matplotlib-lea54vgx because the default path (/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
    simulation.sedml:
      Tasks (1):
        task
      Reports (1):
        report: 5 data sets

  Executing SED-ML file 0: simulation.sedml ...

  Bundling outputs ...
  Cleaning up ...

  ============= SUMMARY =============
  Executed 1 COMBINE/OMEX archives:
    Archives (1):
      Succeeded: 1
      Skipped: 0
      Failed: 0
    Tasks (1):
      Succeeded: 1
      Skipped: 0
      Failed: 0
    Outputs (1):
      Succeeded: 1
      Skipped: 0
      Failed: 0

  R[write to console]: Warning messages:

  R[write to console]: 1: 
  R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :
  R[write to console]: 

  R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

  R[write to console]: 2: 
  R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :
  R[write to console]: 

  R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

  R[write to console]: 3: There is no transition and no initial level for gene "egf"! Assuming an input! 

  R[write to console]: 4: There is no transition and no initial level for gene "tnfa"! Assuming an input!

sedml.SimulatorProducesLinear2DPlots (0.0 s)

Test that a simulator produces linear 2D plots

Warnings:

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

Log:

sedml.SimulatorProducesLinear3DPlots (0.0 s)

Test that a simulator produces linear 3D plots

Warnings:

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

Log:

sedml.SimulatorProducesLogarithmic2DPlots (0.0 s)

Test that a simulator produces logarithmic 2D plots

Warnings:

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

Log:

sedml.SimulatorProducesLogarithmic3DPlots (0.0 s)

Test that a simulator produces logarithmic 3D plots

Warnings:

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

Log:

sedml.SimulatorProducesMultiplePlots (0.0 s)

Test that a simulator produces multiple plots

Warnings:

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

Log:

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (4.0 s)

Test that a simulator supports multiple time courses with non-zero initial times

Warnings:

  The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

    Unknown error

Log:

  Matplotlib created a temporary config/cache directory at /tmp/matplotlib-rdndbv3u because the default path (/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
    simulation.sedml:
      Tasks (1):
        task
      Reports (1):
        report: 5 data sets

  Executing SED-ML file 0: simulation.sedml ...

  Bundling outputs ...
  Cleaning up ...

  ============= SUMMARY =============
  Executed 1 COMBINE/OMEX archives:
    Archives (1):
      Succeeded: 0
      Skipped: 0
      Failed: 1
    Tasks (1):
      Succeeded: 0
      Skipped: 0
      Failed: 1
    Outputs (1):
      Succeeded: 0
      Skipped: 1
      Failed: 0

  The COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

      Initial time must be 0.
  R[write to console]: Warning message:

  R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :
  R[write to console]: 

  R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages
biosimulators-daemon commented 3 years ago

The image for your simulator is valid!

biosimulators-daemon commented 3 years ago

The validation/submission of your simulator failed.

- 403 Client Error: Forbidden for url: https://auth.biosimulations.org/oauth/token

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

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 commented 3 years ago

Thank you @biosimulators-daemon 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 is available here.

biosimulators-daemon commented 3 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 3 years ago

Summary of tests

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (11.6 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'

  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:

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:
    - 'ALGORITHM_SUBSTITUTION_POLICY'

  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 (1.1 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:

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (4.5 s)

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

Warnings:

  The execution status report produced by the simulator is not valid:

    could not determine a constructor for the tag 'tag:yaml.org,2002:python/object/new:rpy2.robjects.vectors.StrVector'
      in "/tmp/tmpteimxnud/outputs/log.yml", line 51, column 15

Log:

  Matplotlib created a temporary config/cache directory at /tmp/matplotlib-7nha024z because the default path (/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
    simulation.sedml:
      Tasks (1):
        task
      Reports (1):
        report: 5 data sets

  Executing SED-ML file 0: simulation.sedml ...

  Bundling outputs ...
  Cleaning up ...

  ============= SUMMARY =============
  Executed 1 COMBINE/OMEX archives:
    Archives (1):
      Succeeded: 1
      Skipped: 0
      Failed: 0
    Tasks (1):
      Succeeded: 1
      Skipped: 0
      Failed: 0
    Outputs (1):
      Succeeded: 1
      Skipped: 0
      Failed: 0

  R[write to console]: Warning messages:

  R[write to console]: 1: 
  R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :
  R[write to console]: 

  R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

  R[write to console]: 2: 
  R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :
  R[write to console]: 

  R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

  R[write to console]: 3: There is no transition and no initial level for gene "egf"! Assuming an input! 

  R[write to console]: 4: There is no transition and no initial level for gene "tnfa"! Assuming an input!

sedml.SimulatorProducesLinear2DPlots (0.0 s)

Test that a simulator produces linear 2D plots

Warnings:

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

Log:

sedml.SimulatorProducesLinear3DPlots (0.0 s)

Test that a simulator produces linear 3D plots

Warnings:

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

Log:

sedml.SimulatorProducesLogarithmic2DPlots (0.0 s)

Test that a simulator produces logarithmic 2D plots

Warnings:

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

Log:

sedml.SimulatorProducesLogarithmic3DPlots (0.0 s)

Test that a simulator produces logarithmic 3D plots

Warnings:

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

Log:

sedml.SimulatorProducesMultiplePlots (0.0 s)

Test that a simulator produces multiple plots

Warnings:

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

Log:

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (4.0 s)

Test that a simulator supports multiple time courses with non-zero initial times

Warnings:

  The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

    Unknown error

Log:

  Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2rbz4e6c because the default path (/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
    simulation.sedml:
      Tasks (1):
        task
      Reports (1):
        report: 5 data sets

  Executing SED-ML file 0: simulation.sedml ...

  Bundling outputs ...
  Cleaning up ...

  ============= SUMMARY =============
  Executed 1 COMBINE/OMEX archives:
    Archives (1):
      Succeeded: 0
      Skipped: 0
      Failed: 1
    Tasks (1):
      Succeeded: 0
      Skipped: 0
      Failed: 1
    Outputs (1):
      Succeeded: 0
      Skipped: 1
      Failed: 0

  The COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

      Initial time must be 0.
  R[write to console]: Warning message:

  R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :
  R[write to console]: 

  R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages
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 boolnet to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.