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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 Neuron 8.0.2 #547

Closed biosimulators-daemon closed 2 years ago

biosimulators-daemon commented 2 years ago

id: neuron version: 8.0.2 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_pyNeuroML/49a209029c515b25dc7350fce1396098f0fa817f/biosimulators-neuron.json specificationsPatch: version: 8.0.2 image: url: ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.2 digest: "sha256:0b7f8ddd450d0cb22e915704247eb20bb24889ec6120f0d6b0ec3f1a6e6193e0" validateImage: true commitSimulator: true

Changelog

biosimulators-daemon commented 2 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 2 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 years ago

Summary of tests

biosimulators-daemon commented 2 years ago

Warnings

docker_image.DeclaresSupportedEnvironmentVariables (0.7 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' - '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_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - '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: None
docker_image.HasBioContainersLabels (0.6 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 2 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: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000030 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9012`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9012) Algorithm: [`KISAO_0000669`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000669) Reason for skip: ``` Case requires model formats format_9012 and simulation algorithms KISAO_0000669 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000086`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000086) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000086 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000088`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000088 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000027 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) Reason for skip: ``` Case requires model formats format_9001 and simulation algorithms KISAO_0000057 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9010 and simulation algorithms KISAO_0000019 ``` Log: None
sedml.SimulatorProducesLinear3DPlots (0.8 s)
Test that a simulator produces linear 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (0.9 s)
Test that a simulator produces logarithmic 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.8 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.9 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsAlgorithmParameters (0.8 s)
Test that a simulator supports setting the values of parameters of algorithms Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsComputeModelChanges (0.9 s)
Test that a simulator supports compute model changes Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsModelAttributeChanges (1.0 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithChanges (0.7 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.9 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (23.8 s)
Test that a simulator supports nested repeated tasks Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.2' could not execute the archive: Unknown error ``` Log: ``` /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: COMBINE/OMEX archive may be invalid. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (3): __repeated_task_0 __repeated_task_1 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (3): Succeeded: 2 Skipped: 0 Failed: 1 Outputs (2): Succeeded: 2 Skipped: 0 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: '__output_file__' ```
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (31.0 s)
Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their ``order`` attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes. Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.2' could not execute the archive: Unknown error ``` Log: ``` /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: COMBINE/OMEX archive may be invalid. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Task `__repeated_task_1` may be invalid. - The outputs of the sub-tasks have different shapes. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Task `__repeated_task_1` may be invalid. - The outputs of the sub-tasks have different shapes. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (3): __repeated_task_0 __repeated_task_1 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (3): Succeeded: 2 Skipped: 0 Failed: 1 Outputs (2): Succeeded: 2 Skipped: 0 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: '__output_file__' ```
sedml.SimulatorSupportsSubstitutingAlgorithms (25.6 s)
Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.SAME_METHOD`. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.NONE`. Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.2' could not execute the archive: Unknown error ``` Log: ``` /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: COMBINE/OMEX archive may be invalid. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 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 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (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: Algorithms cannot be substituted at policy 'NONE'. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: COMBINE/OMEX archive may be invalid. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 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 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 1 Skipped: 0 Failed: 0 Tasks (1): Succeeded: 1 Skipped: 0 Failed: 0 Outputs (1): Succeeded: 1 Skipped: 0 Failed: 0 /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: COMBINE/OMEX archive may be invalid. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 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 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (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: Algorithm parameters are not supported. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: COMBINE/OMEX archive may be invalid. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 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 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (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: Algorithm parameters are not supported. ```
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (6.6 s)
Test that a simulator supports multiple time courses with non-zero initial times Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.2' could not execute the archive: Unknown error ``` Log: ``` /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: COMBINE/OMEX archive may be invalid. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 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 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (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, not 5e-05 ```
biosimulators-daemon commented 2 years ago

The image for your simulator is valid!

biosimulators-daemon commented 2 years ago

The validation/submission of your simulator failed.

- A Singularity image could not be generated for the Docker image
- 
-   - Internal Server Error (500):
-     
-       An unexpected error occurred

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly 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.

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 2 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 2 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 years ago

Summary of tests

biosimulators-daemon commented 2 years ago

Warnings

docker_image.DeclaresSupportedEnvironmentVariables (0.3 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' - '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_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - '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: None
docker_image.HasBioContainersLabels (0.2 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 2 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: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000030 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9012`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9012) Algorithm: [`KISAO_0000669`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000669) Reason for skip: ``` Case requires model formats format_9012 and simulation algorithms KISAO_0000669 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000086`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000086) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000086 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000088`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000088 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000027 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) Reason for skip: ``` Case requires model formats format_9001 and simulation algorithms KISAO_0000057 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9010 and simulation algorithms KISAO_0000019 ``` Log: None
sedml.SimulatorProducesLinear3DPlots (0.8 s)
Test that a simulator produces linear 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (0.9 s)
Test that a simulator produces logarithmic 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.8 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.9 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsAlgorithmParameters (0.8 s)
Test that a simulator supports setting the values of parameters of algorithms Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsComputeModelChanges (0.9 s)
Test that a simulator supports compute model changes Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsModelAttributeChanges (0.8 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithChanges (0.8 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.9 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` 'cython_function_or_method' object has no attribute 'rpartition' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (23.2 s)
Test that a simulator supports nested repeated tasks Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.2' could not execute the archive: Unknown error ``` Log: ``` /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: COMBINE/OMEX archive may be invalid. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (3): __repeated_task_0 __repeated_task_1 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (3): Succeeded: 2 Skipped: 0 Failed: 1 Outputs (2): Succeeded: 2 Skipped: 0 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: '__output_file__' ```
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (30.7 s)
Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their ``order`` attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes. Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.2' could not execute the archive: Unknown error ``` Log: ``` /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: COMBINE/OMEX archive may be invalid. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Task `__repeated_task_1` may be invalid. - The outputs of the sub-tasks have different shapes. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid. - The SED-ML file at location `simulation.sedml` may be invalid. - Task `__repeated_task_1` may be invalid. - The outputs of the sub-tasks have different shapes. - Output `__repeated_task_report` may be invalid. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots: simulation.sedml: Tasks (3): __repeated_task_0 __repeated_task_1 task Reports (2): __repeated_task_report: 5 data sets task_report: 5 data sets Executing SED-ML file 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (3): Succeeded: 2 Skipped: 0 Failed: 1 Outputs (2): Succeeded: 2 Skipped: 0 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: '__output_file__' ```
sedml.SimulatorSupportsSubstitutingAlgorithms (24.5 s)
Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.SAME_METHOD`. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.NONE`. Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.2' could not execute the archive: Unknown error ``` Log: ``` /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: COMBINE/OMEX archive may be invalid. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 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 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (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: Algorithms cannot be substituted at policy 'NONE'. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: COMBINE/OMEX archive may be invalid. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 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 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 1 Skipped: 0 Failed: 0 Tasks (1): Succeeded: 1 Skipped: 0 Failed: 0 Outputs (1): Succeeded: 1 Skipped: 0 Failed: 0 /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: COMBINE/OMEX archive may be invalid. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 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 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (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: Algorithm parameters are not supported. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: COMBINE/OMEX archive may be invalid. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 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 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (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: Algorithm parameters are not supported. ```
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (6.2 s)
Test that a simulator supports multiple time courses with non-zero initial times Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.2' could not execute the archive: Unknown error ``` Log: ``` /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: COMBINE/OMEX archive may be invalid. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. warnings.warn(termcolor.colored(message, Colors.warning.value), category) Archive contains 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 1: simulation.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (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, not 5e-05 ```
biosimulators-daemon commented 2 years ago

The image for your simulator is valid!

biosimulators-daemon commented 2 years ago

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

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