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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 pyNeuroML 0.5.11 #299

Closed biosimulators-daemon closed 3 years ago

biosimulators-daemon commented 3 years ago

id: pyneuroml version: 0.5.11 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_pyNeuroML/65a64d0aab2b40e11d218aede041e0e4b0776fe0/biosimulators-pyneuroml.json specificationsPatch: version: 0.5.11 image: url: ghcr.io/biosimulators/biosimulators_pyneuroml/pyneuroml:0.5.11 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 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

Failures

docker_image.SingularityImageExecutesSimulationsSuccessfully (10.3 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:
    INFO:    Convert SIF file to sandbox...
    The COMBINE/OMEX archive is invalid.
      - The SED-ML file at location `simulation.sedml` is invalid.
        - Model `net1` is invalid.
          - The model file `model.xml` is invalid.
            - `/tmp/tmph_jum27z/model.xml` is not valid LEMS file.
              - pyNeuroML >>> *** Problem running command: 
                pyNeuroML >>>        Command 'java -Xmx400M  -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmph_jum27z/model.xml" -norun' returned non-zero exit status 1.
                pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3
                pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmph_jum27z/model.xml with jLEMS, NO RUN mode...
                pyNeuroML >>>  jNeuroML >>  Exception in thread "main" java.lang.UnsatisfiedLinkError: Can't load library: /usr/lib/jvm/java-11-openjdk-amd64/lib/libawt_xawt.so
                pyNeuroML >>>  jNeuroML >>      at java.base/java.lang.ClassLoader.loadLibrary(ClassLoader.java:2630)
                pyNeuroML >>>  jNeuroML >>      at java.base/java.lang.Runtime.load0(Runtime.java:768)
                pyNeuroML >>>  jNeuroML >>      at java.base/java.lang.System.load(System.java:1837)
                pyNeuroML >>>  jNeuroML >>      at java.base/java.lang.ClassLoader$NativeLibrary.load0(Native Method)
                pyNeuroML >>>  jNeuroML >>      at java.base/java.lang.ClassLoader$NativeLibrary.load(ClassLoader.java:2442)
                pyNeuroML >>>  jNeuroML >>      at java.base/java.lang.ClassLoader$NativeLibrary.loadLibrary(ClassLoader.java:2498)
                pyNeuroML >>>  jNeuroML >>      at java.base/java.lang.ClassLoader.loadLibrary0(ClassLoader.java:2694)
                pyNeuroML >>>  jNeuroML >>      at java.base/java.lang.ClassLoader.loadLibrary(ClassLoader.java:2648)
                pyNeuroML >>>  jNeuroML >>      at java.base/java.lang.Runtime.loadLibrary0(Runtime.java:830)
                pyNeuroML >>>  jNeuroML >>      at java.base/java.lang.System.loadLibrary(System.java:1873)
                pyNeuroML >>>  jNeuroML >>      at java.desktop/java.awt.Toolkit$3.run(Toolkit.java:1399)
                pyNeuroML >>>  jNeuroML >>      at java.desktop/java.awt.Toolkit$3.run(Toolkit.java:1397)
                pyNeuroML >>>  jNeuroML >>      at java.base/java.security.AccessController.doPrivileged(Native Method)
                pyNeuroML >>>  jNeuroML >>      at java.desktop/java.awt.Toolkit.loadLibraries(Toolkit.java:1396)
                pyNeuroML >>>  jNeuroML >>      at java.desktop/java.awt.Toolkit.<clinit>(Toolkit.java:1429)
                pyNeuroML >>>  jNeuroML >>      at java.desktop/java.awt.Component.<clinit>(Component.java:621)
                pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.<init>(ControlPanel.java:47)
                pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.<init>(Utils.java:498)
                pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:498)
                pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:610)
                pyNeuroML >>>  jNeuroML >>  
                pyNeuroML >>> Error: execute_command_in_dir returned with output: None
                
    INFO:    Cleaning up image...

Log:

biosimulators-daemon commented 3 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (2.8 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 (1.0 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:neuroml-lems/Hodgkin-Huxley-cell-Euler (13.0 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 
- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/1122770461). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/1122770461).
jonrkarr commented 3 years ago

Fixed by switching default-jre-headless to default-jre. This appears to stem from a release change in the headless package.