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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 tellurium 2.2.0 #124

Closed biosimulators-daemon closed 3 years ago

biosimulators-daemon commented 3 years ago

id: tellurium version: 2.2.0 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_tellurium/fda7b6b59de84ba54e07676531de0a554bcef50b/biosimulators.json specificationsPatch: version: 2.2.0 image: url: ghcr.io/biosimulators/biosimulators_tellurium/tellurium:2.2.0 validateImage: true commitSimulator: true

Unclear why tellurium failed in the previous run. Trying running again. again.

The appeared to be due to an issue with libSED-ML

Debugged workflow.

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

Failures

combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (4.0 s)

Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files.

Exception:

  Simulator did not generate the following expected reports
    - `Parmar2017_Deficient_Rich_tracer__copy.sedml/simulation_1`

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
    Parmar2017_Deficient_Rich_tracer.sedml:
      Tasks (1):
        simulation_1
      Reports (1):
        simulation_1: 2 data sets

  Executing SED-ML file 0: Parmar2017_Deficient_Rich_tracer.sedml ...

  Bundling outputs ...
  Cleaning up ...

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

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (13.0 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'

  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 (2.7 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:
    - '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 (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:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (4.4 s)

Required model formats and simulation algorithms for SED tasks:

biosimulators-daemon commented 3 years ago 
- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
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

Failures

combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (3.8 s)

Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files.

Exception:

  Simulator did not generate the following expected reports
    - `Parmar2017_Deficient_Rich_tracer__copy.sedml/simulation_1`

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
    Parmar2017_Deficient_Rich_tracer.sedml:
      Tasks (1):
        simulation_1
      Reports (1):
        simulation_1: 2 data sets

  Executing SED-ML file 0: Parmar2017_Deficient_Rich_tracer.sedml ...

  Bundling outputs ...
  Cleaning up ...

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

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (13.0 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'

  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 (3.3 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 (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:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (4.1 s)

Required model formats and simulation algorithms for SED tasks:

biosimulators-daemon commented 3 years ago 
- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
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

Failures

combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (3.7 s)

Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files.

Exception:

  Simulator did not generate the following expected reports
    - `Parmar2017_Deficient_Rich_tracer__copy.sedml/simulation_1`

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
    Parmar2017_Deficient_Rich_tracer.sedml:
      Tasks (1):
        simulation_1
      Reports (1):
        simulation_1: 2 data sets

  Executing SED-ML file 0: Parmar2017_Deficient_Rich_tracer.sedml ...

  Bundling outputs ...
  Cleaning up ...

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

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (12.7 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'

  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 (2.7 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:
    - '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 (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:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (3.9 s)

Required model formats and simulation algorithms for SED tasks:

biosimulators-daemon commented 3 years ago 
- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
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

Failures

combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (3.7 s)

Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files.

Exception:

  Simulator did not generate the following expected reports
    - `Parmar2017_Deficient_Rich_tracer__copy.sedml/simulation_1`

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
    Parmar2017_Deficient_Rich_tracer.sedml:
      Tasks (1):
        simulation_1
      Reports (1):
        simulation_1: 2 data sets

  Executing SED-ML file 0: Parmar2017_Deficient_Rich_tracer.sedml ...

  Bundling outputs ...
  Cleaning up ...

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

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (12.8 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 (3.0 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 (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:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (4.1 s)

Required model formats and simulation algorithms for SED tasks:

biosimulators-daemon commented 3 years ago 
- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
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 (13.7 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'

  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 (3.8 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 (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:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (4.7 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 tellurium to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.