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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 #640

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/b1fa07bbbb18b985fe509a867f8e88e3ccce8e76/biosimulators.json specificationsPatch: version: 2.2.8 image: url: ghcr.io/biosimulators/biosimulators_tellurium/tellurium:2.2.8 digest: "sha256:05c1251633c999f6585c0790268cf3ed13c30b0dfc883905d0134b1fbd7b0ec7" 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 (0.8 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - '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.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (5.7 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``) and inherit the changes of the model. 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. - This tool validates XPaths for model changes and variables against their unmodified target models. As a result, this tool does not fully validate these XPaths. These XPaths could be invalidated by changes to their target models. - Model `__source__` 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. - Data generator `data_gen_T` has warnings. - Variable `var_T` has warnings. - XPath could not be validated. - Data generator `data_gen_E` has warnings. - Variable `var_E` has warnings. - XPath could not be validated. - Data generator `data_gen_I` has warnings. - Variable `var_I` has warnings. - XPath could not be validated. /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. - This tool validates XPaths for model changes and variables against their unmodified target models. As a result, this tool does not fully validate these XPaths. These XPaths could be invalidated by changes to their target models. - Model `__source__` 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. - Data generator `data_gen_T` has warnings. - Variable `var_T` has warnings. - XPath could not be validated. - Data generator `data_gen_E` has warnings. - Variable `var_E` has warnings. - XPath could not be validated. - Data generator `data_gen_I` has warnings. - Variable `var_I` has warnings. - XPath could not be validated. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - This tool validates XPaths for model changes and variables against their unmodified target models. As a result, this tool does not fully validate these XPaths. These XPaths could be invalidated by changes to their target models. - Data generator `data_gen_T` has warnings. - Variable `var_T` has warnings. - XPath could not be validated. - Data generator `data_gen_E` has warnings. - Variable `var_E` has warnings. - XPath could not be validated. - Data generator `data_gen_I` has warnings. - Variable `var_I` has warnings. - XPath could not be validated. Archive contains 1 SED-ML documents with 2 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: BIOMD0000000912_sim.sedml: Tasks (1): BIOMD0000000912_task Reports (1): report: 4 data sets /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - This tool validates XPaths for model changes and variables against their unmodified target models. As a result, this tool does not fully validate these XPaths. These XPaths could be invalidated by changes to their target models. 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 (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: can only concatenate str (not "NoneType") to str ```
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 (0.3 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.SimulatorSupportsAddReplaceRemoveModelElementChanges (10.8 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. 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. - This tool validates XPaths for model changes and variables against their unmodified target models. As a result, this tool does not fully validate these XPaths. These XPaths could be invalidated by changes to their target models. - 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. /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. - This tool validates XPaths for model changes and variables against their unmodified target models. As a result, this tool does not fully validate these XPaths. These XPaths could be invalidated by changes to their target models. - 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. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - This tool validates XPaths for model changes and variables against their unmodified target models. As a result, this tool does not fully validate these XPaths. These XPaths could be invalidated by changes to their target models. Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: BIOMD0000000912_sim.sedml: Tasks (1): BIOMD0000000912_task Reports (1): 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 (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: Changes for model `BIOMD0000000912` are not supported. - Model change 1 of type `RemoveElementModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange /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. - This tool validates XPaths for model changes and variables against their unmodified target models. As a result, this tool does not fully validate these XPaths. These XPaths could be invalidated by changes to their target models. - 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. /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. - This tool validates XPaths for model changes and variables against their unmodified target models. As a result, this tool does not fully validate these XPaths. These XPaths could be invalidated by changes to their target models. - 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. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - This tool validates XPaths for model changes and variables against their unmodified target models. As a result, this tool does not fully validate these XPaths. These XPaths could be invalidated by changes to their target models. Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: BIOMD0000000912_sim.sedml: Tasks (1): BIOMD0000000912_task Reports (1): 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 (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: Changes for model `BIOMD0000000912` are not supported. - Model change 1 of type `RemoveElementModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 2 of type `AddElementModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange ```
sedml.SimulatorSupportsComputeModelChanges (11.0 s)
Test that a simulator supports compute model changes 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. /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. Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: BIOMD0000000912_sim.sedml: Tasks (1): BIOMD0000000912_task Reports (1): 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 (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: Changes for model `BIOMD0000000912` are not supported. - Model change 1 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 2 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 3 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 4 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 5 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 6 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 7 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 8 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 9 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 10 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 11 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 12 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 13 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 14 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 15 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 16 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 17 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 18 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 19 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 20 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 21 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 22 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 23 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 24 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 25 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 26 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 27 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 28 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 29 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 30 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 31 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 32 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 33 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 34 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 35 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 36 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange /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. - This tool validates XPaths for model changes and variables against their unmodified target models. As a result, this tool does not fully validate these XPaths. These XPaths could be invalidated by changes to their target models. - 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. /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. - This tool validates XPaths for model changes and variables against their unmodified target models. As a result, this tool does not fully validate these XPaths. These XPaths could be invalidated by changes to their target models. - 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. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - This tool validates XPaths for model changes and variables against their unmodified target models. As a result, this tool does not fully validate these XPaths. These XPaths could be invalidated by changes to their target models. Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: BIOMD0000000912_sim.sedml: Tasks (1): BIOMD0000000912_task Reports (1): 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 (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: Changes for model `BIOMD0000000912` are not supported. - Model change 1 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 3 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 5 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 7 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 9 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 11 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 13 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 15 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 17 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 19 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 21 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 23 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 25 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 27 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 29 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 31 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 33 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 35 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 37 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 39 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 41 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 43 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 45 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 47 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 49 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 51 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 53 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 55 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 57 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 59 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 61 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 63 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 65 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 67 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 69 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange - Model change 71 of type `ComputeModelChange` is not supported. Model changes must be instances of one of the following types: - ModelAttributeChange ```
sedml.SimulatorSupportsModelAttributeChanges (12.6 s)
Test that a simulator supports changes to the attributes of model elements 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. - This tool validates XPaths for model changes and variables against their unmodified target models. As a result, this tool does not fully validate these XPaths. These XPaths could be invalidated by changes to their target models. - 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. /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. - This tool validates XPaths for model changes and variables against their unmodified target models. As a result, this tool does not fully validate these XPaths. These XPaths could be invalidated by changes to their target models. - 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. /usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect. - This tool validates XPaths for model changes and variables against their unmodified target models. As a result, this tool does not fully validate these XPaths. These XPaths could be invalidated by changes to their target models. Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots: BIOMD0000000912_sim.sedml: Tasks (1): BIOMD0000000912_task Reports (1): 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 (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: The targets for the following changes are not valid: - 10: /sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[6]/sbml:listOfReactants[1]/sbml:speciesReference[1]/@species: None - 11: /sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[6]/sbml:listOfReactants[1]/sbml:speciesReference[1]/@stoichiometry: None - 12: /sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[6]/sbml:annotation[1]/COPASI:COPASI[1]/rdf:RDF[1]/rdf:Description[1]/@rdf:about: None - 134: /sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[3]/sbml:annotation[1]/COPASI:COPASI[1]/rdf:RDF[1]/rdf:Description[1]/@rdf:about: None - 135: /sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[3]/sbml:annotation[1]/COPASI:COPASI[1]/rdf:RDF[1]/rdf:Description[1]/bqbiol:hasProperty[1]/@rdf:resource: None - 136: /sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[3]/sbml:annotation[1]/rdf:RDF[1]/rdf:Description[1]/@rdf:about: None - 137: /sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[3]/sbml:annotation[1]/rdf:RDF[1]/rdf:Description[1]/bqbiol:hasProperty[1]/rdf:Bag[1]/rdf:li[1]/@rdf:resource: None - 13: /sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[6]/sbml:annotation[1]/COPASI:COPASI[1]/rdf:RDF[1]/rdf:Description[1]/CopasiMT:isVersionOf[1]/@rdf:resource: None - 145: /sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[2]/sbml:annotation[1]/COPASI:COPASI[1]/rdf:RDF[1]/rdf:Description[1]/@rdf:about: None - 146: /sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[2]/sbml:annotation[1]/COPASI:COPASI[1]/rdf:RDF[1]/rdf:Description[1]/bqbiol:hasProperty[1]/@rdf:resource: None - 147: /sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[2]/sbml:annotation[1]/rdf:RDF[1]/rdf:Description[1]/@rdf:about: None - 148: /sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[2]/sbml:annotation[1]/rdf:RDF[1]/rdf:Description[1]/bqbiol:hasProperty[1]/rdf:Bag[1]/rdf:li[1]/@rdf:resource: None - 14: /sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[6]/sbml:annotation[1]/rdf:RDF[1]/rdf:Description[1]/@rdf:about: None - 156: /sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[1]/sbml:annotation[1]/COPASI:COPASI[1]/rdf:RDF[1]/rdf:Description[1]/@rdf:about: None - 157: /sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[1]/sbml:annotation[1]/COPASI:COPASI[1]/rdf:RDF[1]/rdf:Description[1]/CopasiMT:isVersionOf[1]/@rdf:resource: None - 158: /sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[1]/sbml:annotation[1]/rdf:RDF[1]/rdf:Description[1]/@rdf:about: None - 159: /sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[1]/sbml:annotation[1]/rdf:RDF[1]/rdf:Description[1]/bqbiol:isVersionOf[1]/rdf:Bag[1]/rdf:li[1]/@rdf:resource: None - 15: /sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[6]/sbml:annotation[1]/rdf:RDF[1]/rdf:Description[1]/bqbiol:isVersionOf[1]/rdf:Bag[1]/rdf:li[1]/@rdf:resource: None - 165: /sbml:sbml[1]/sbml:model[1]/sbml:listOfUnitDefinitions[1]/sbml:unitDefinition[3]/@id: substance - 166: /sbml:sbml[1]/sbml:model[1]/sbml:listOfUnitDefinitions[1]/sbml:unitDefinition[3]/@name: substance - 167: /sbml:sbml[1]/sbml:model[1]/sbml:listOfUnitDefinitions[1]/sbml:unitDefinition[3]/sbml:listOfUnits[1]/sbml:unit[1]/@exponent: None - 168: /sbml:sbml[1]/sbml:model[1]/sbml:listOfUnitDefinitions[1]/sbml:unitDefinition[3]/sbml:listOfUnits[1]/sbml:unit[1]/@kind: None - 169: /sbml:sbml[1]/sbml:model[1]/sbml:listOfUnitDefinitions[1]/sbml:unitDefinition[3]/sbml:listOfUnits[1]/sbml:unit[1]/@multiplier: None - 16: /sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[5]/@id: Activation_of_interleukin_2 - 170: /sbml:sbml[1]/sbml:model[1]/sbml:listOfUnitDefinitions[1]/sbml:unitDefinition[3]/sbml:listOfUnits[1]/sbml:unit[1]/@scale: None - 171: /sbml:sbml[1]/sbml:model[1]/sbml:listOfUnitDefinitions[1]/sbml:unitDefinition[2]/@id: time - 172: /sbml:sbml[1]/sbml:model[1]/sbml:listOfUnitDefinitions[1]/sbml:unitDefinition[2]/@name: time - 173: /sbml:sbml[1]/sbml:model[1]/sbml:listOfUnitDefinitions[1]/sbml:unitDefinition[2]/sbml:listOfUnits[1]/sbml:unit[1]/@exponent: None - 174: /sbml:sbml[1]/sbml:model[1]/sbml:listOfUnitDefinitions[1]/sbml:unitDefinition[2]/sbml:listOfUnits[1]/sbml:unit[1]/@kind: None - 175: /sbml:sbml[1]/sbml:model[1]/sbml:listOfUnitDefinitions[1]/sbml:unitDefinition[2]/sbml:listOfUnits[1]/sbml:unit[1]/@multiplier: None - 176: /sbml:sbml[1]/sbml:model[1]/sbml:listOfUnitDefinitions[1]/sbml:unitDefinition[2]/sbml:listOfUnits[1]/sbml:unit[1]/@scale: None - 177: /sbml:sbml[1]/sbml:model[1]/sbml:listOfUnitDefinitions[1]/sbml:unitDefinition[1]/@id: volume - 178: /sbml:sbml[1]/sbml:model[1]/sbml:listOfUnitDefinitions[1]/sbml:unitDefinition[1]/@name: volume - 179: /sbml:sbml[1]/sbml:model[1]/sbml:listOfUnitDefinitions[1]/sbml:unitDefinition[1]/sbml:listOfUnits[1]/sbml:unit[1]/@exponent: None - 17: /sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[5]/@metaid: Activation_of_interleukin_2 - 180: /sbml:sbml[1]/sbml:model[1]/sbml:listOfUnitDefinitions[1]/sbml:unitDefinition[1]/sbml:listOfUnits[1]/sbml:unit[1]/@kind: None - 181: /sbml:sbml[1]/sbml:model[1]/sbml:listOfUnitDefinitions[1]/sbml:unitDefinition[1]/sbml:listOfUnits[1]/sbml:unit[1]/@multiplier: None - 182: /sbml:sbml[1]/sbml:model[1]/sbml:listOfUnitDefinitions[1]/sbml:unitDefinition[1]/sbml:listOfUnits[1]/sbml:unit[1]/@scale: None - 183: /sbml:sbml[1]/sbml:model[1]/sbml:listOfFunctionDefinitions[1]/sbml:functionDefinition[6]/@id: Function_for_deactivation_and_removal_of_ ...
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.

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).