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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 2.2.8 #642

Closed biosimulators-daemon closed 1 year ago

biosimulators-daemon commented 1 year ago

id: tellurium version: 2.2.8 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_tellurium/f50ee4fa861652a681ce77c2f46126b6c9db1e16/biosimulators.json specificationsPatch: version: 2.2.8 image: url: ghcr.io/biosimulators/biosimulators_tellurium/tellurium:2.2.8 digest: "sha256:f3e495611017b1d77eb84e42da36ee260ba6b660a56ac964ff320ee5dd680a6b" validateImage: true commitSimulator: true

biosimulators-daemon commented 1 year 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 1 year ago

The specifications of your simulator is valid!

biosimulators-daemon commented 1 year ago

Summary of tests

biosimulators-daemon commented 1 year ago

Warnings

docker_image.DeclaresSupportedEnvironmentVariables (0.6 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - '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 (0.5 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 1 year 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-CVODE (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_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_9004 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/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/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-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-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:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9000`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9000) 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_9000 and simulation algorithms KISAO_0000019 ``` 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 (0.3 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 (0.4 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 (0.3 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.SimulatorSupportsRepeatedTasksWithChanges (12.5 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_tellurium/tellurium:2.2.8' could not execute the archive: Unknown error ``` Log: ``` /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Model `BIOMD0000000912` has warnings. - The model file `Caravagna2010.xml` has warnings. - 6 warnings of type SBML unit consistency (99505). The following is the first warning at line 570, column 8: - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 14 warnings of type Modeling practice (80701). The following is the first warning at line 525, column 6: - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'r2' does not have a 'units' attribute. - Output `__repeated_task_report` has warnings. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive has warnings. - The SED-ML file at location `./BIOMD0000000912_sim.sedml` has warnings. - Model `BIOMD0000000912` has warnings. - The model file `Caravagna2010.xml` has warnings. - 6 warnings of type SBML unit consistency (99505). The following is the first warning at line 570, column 8: - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 14 warnings of type Modeling practice (80701). The following is the first warning at line 525, column 6: - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'r2' does not have a 'units' attribute. - Output `__repeated_task_report` has warnings. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` has warnings. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute. Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots: BIOMD0000000912_sim.sedml: Tasks (2): BIOMD0000000912_task __repeated_task_0 Reports (2): __repeated_task_report: 4 data sets task_report: 4 data sets Executing SED-ML file 1: BIOMD0000000912_sim.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (2): Succeeded: 1 Skipped: 0 Failed: 1 Outputs (2): Succeeded: 1 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: can only concatenate str (not "NoneType") to str /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Model `BIOMD0000000912` has warnings. - The model file `Caravagna2010.xml` has warnings. - 6 warnings of type SBML unit consistency (99505). The following is the first warning at line 570, column 8: - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 14 warnings of type Modeling practice (80701). The following is the first warning at line 525, column 6: - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'r2' does not have a 'units' attribute. - Output `__repeated_task_report` has warnings. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive has warnings. - The SED-ML file at location `./BIOMD0000000912_sim.sedml` has warnings. - Model `BIOMD0000000912` has warnings. - The model file `Caravagna2010.xml` has warnings. - 6 warnings of type SBML unit consistency (99505). The following is the first warning at line 570, column 8: - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 14 warnings of type Modeling practice (80701). The following is the first warning at line 525, column 6: - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'r2' does not have a 'units' attribute. - Output `__repeated_task_report` has warnings. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` has warnings. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute. Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots: BIOMD0000000912_sim.sedml: Tasks (2): BIOMD0000000912_task __repeated_task_0 Reports (2): __repeated_task_report: 4 data sets task_report: 4 data sets Executing SED-ML file 1: BIOMD0000000912_sim.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (2): Succeeded: 1 Skipped: 0 Failed: 1 Outputs (2): Succeeded: 1 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: can only concatenate str (not "NoneType") to str ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (12.7 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` The image 'ghcr.io/biosimulators/biosimulators_tellurium/tellurium:2.2.8' could not execute the archive: Unknown error ``` Log: ``` /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Model `BIOMD0000000912` has warnings. - The model file `Caravagna2010.xml` has warnings. - 6 warnings of type SBML unit consistency (99505). The following is the first warning at line 570, column 8: - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 14 warnings of type Modeling practice (80701). The following is the first warning at line 525, column 6: - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'r2' does not have a 'units' attribute. - Output `__repeated_task_report` has warnings. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive has warnings. - The SED-ML file at location `./BIOMD0000000912_sim.sedml` has warnings. - Model `BIOMD0000000912` has warnings. - The model file `Caravagna2010.xml` has warnings. - 6 warnings of type SBML unit consistency (99505). The following is the first warning at line 570, column 8: - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 14 warnings of type Modeling practice (80701). The following is the first warning at line 525, column 6: - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'r2' does not have a 'units' attribute. - Output `__repeated_task_report` has warnings. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` has warnings. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute. Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots: BIOMD0000000912_sim.sedml: Tasks (2): BIOMD0000000912_task __repeated_task_0 Reports (2): __repeated_task_report: 4 data sets task_report: 4 data sets Executing SED-ML file 1: BIOMD0000000912_sim.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (2): Succeeded: 1 Skipped: 0 Failed: 1 Outputs (2): Succeeded: 1 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: can only concatenate str (not "NoneType") to str /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: COMBINE/OMEX archive has warnings. - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Model `BIOMD0000000912` has warnings. - The model file `Caravagna2010.xml` has warnings. - 6 warnings of type SBML unit consistency (99505). The following is the first warning at line 570, column 8: - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 14 warnings of type Modeling practice (80701). The following is the first warning at line 525, column 6: - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'r2' does not have a 'units' attribute. - Output `__repeated_task_report` has warnings. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive has warnings. - The SED-ML file at location `./BIOMD0000000912_sim.sedml` has warnings. - Model `BIOMD0000000912` has warnings. - The model file `Caravagna2010.xml` has warnings. - 6 warnings of type SBML unit consistency (99505). The following is the first warning at line 570, column 8: - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. The units of the expression 'compartment * Function_for_induction_of_tumor(r2, T, b, V)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate. - 14 warnings of type Modeling practice (80701). The following is the first warning at line 525, column 6: - As a principle of best modeling practice, the units of a should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models. The with the id 'r2' does not have a 'units' attribute. - Output `__repeated_task_report` has warnings. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - Output `__repeated_task_report` has warnings. - Some simulation tools will not be able to generate this output because it uses data from repeated tasks, which some simulation tools do not have the capability to execute. Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots: BIOMD0000000912_sim.sedml: Tasks (2): BIOMD0000000912_task __repeated_task_0 Reports (2): __repeated_task_report: 4 data sets task_report: 4 data sets Executing SED-ML file 1: BIOMD0000000912_sim.sedml ... Bundling outputs ... Cleaning up ... ============= SUMMARY ============= Executed 1 SED documents: SED documents (1): Succeeded: 0 Skipped: 0 Failed: 1 Tasks (2): Succeeded: 1 Skipped: 0 Failed: 1 Outputs (2): Succeeded: 1 Skipped: 1 Failed: 0 The COMBINE/OMEX did not execute successfully: The SED document did not execute successfully: can only concatenate str (not "NoneType") to str ```
biosimulators-daemon commented 1 year ago

The image for your simulator is valid!

biosimulators-daemon commented 1 year ago

The validation/submission of your simulator failed.

- 504 Server Error: Gateway Time-out for url: https://api.biosimulations.org/images/refresh

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

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Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

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