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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 COmplex PAthway SImulator 4.29.227 #74

Closed biosimulators-daemon closed 3 years ago

biosimulators-daemon commented 3 years ago

id: copasi version: 4.29.227 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_COPASI/73f1d983333e2196f981075fad37e4c064eafc3d/biosimulators.json specificationsPatch: version: 4.29.227 validateImage: true commitSimulator: true

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.CliDisplaysVersionInformationInline (3.1 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`:

    COPASI: 4.30.233, CLI: 0.1.12, Python: 3.7.9, OS: Linux debian 10.7 5.4.0-1032-azure, Machine: x86_64

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

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

    COPASI: 4.30.233, CLI: 0.1.12, Python: 3.7.9, OS: Linux debian 10.7 5.4.0-1032-azure, Machine: x86_64

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:

sedml.SimulatorProducesLinear2DPlots (2.0 s)

Test that a simulator produces linear 2D plots

Warnings:

  Simulator did not produce plots

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
    simulation_1.sedml:
      Tasks (1):
        simulation_1
      Plots (1):
        plot_0: 20 curves

  Executing SED-ML file 0: simulation_1.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLinear3DPlots (2.0 s)

Test that a simulator produces linear 3D plots

Warnings:

  Simulator did not produce plots

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
    simulation_1.sedml:
      Tasks (1):
        simulation_1
      Plots (1):
        plot_0: 20 surfaces

  Executing SED-ML file 0: simulation_1.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:226: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic2DPlots (2.0 s)

Test that a simulator produces logarithmic 2D plots

Warnings:

  Simulator did not produce plots

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
    simulation_1.sedml:
      Tasks (1):
        simulation_1
      Plots (1):
        plot_0: 20 curves

  Executing SED-ML file 0: simulation_1.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic3DPlots (2.1 s)

Test that a simulator produces logarithmic 3D plots

Warnings:

  Simulator did not produce plots

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
    simulation_1.sedml:
      Tasks (1):
        simulation_1
      Plots (1):
        plot_0: 20 surfaces

  Executing SED-ML file 0: simulation_1.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:226: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesMultiplePlots (2.0 s)

Test that a simulator produces multiple plots

Warnings:

  Simulator did not produce plots

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 2 plots:
    simulation_1.sedml:
      Tasks (1):
        simulation_1
      Plots (2):
        plot_0: 10 curves
        plot_1: 10 curves

  Executing SED-ML file 0: simulation_1.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_1 skipped because outputs of type Plot2D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)
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 copasi to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.