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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 VCell 7.4.0.48 #581

Closed vcdaemon closed 2 years ago

vcdaemon commented 2 years ago

id: vcell version: 7.4.0.48 specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.4.0.48/biosimulators.json specificationsPatch: version: 7.4.0.48 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.48 digest: "sha256:03f0e622174dfaf313a40e45be7c839aecfca252b4ddefc66dff49838b2ec23e" validateImage: true commitSimulator: true

biosimulators-daemon commented 2 years ago

Thank you @vcdaemon for your submission to the BioSimulators simulator validation/submission system!

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

We will discuss any concerns with your submission in this issue.

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

biosimulators-daemon commented 2 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 years ago

Summary of tests

biosimulators-daemon commented 2 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.3 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports. Warnings: ``` The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports. The command-line interface does not describe the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - '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' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be described in the inline help for its command-line interface. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
cli.CliDisplaysHelpInline (2.0 s)
Test that a command-line interface provides inline help. Warnings: ``` Command-line interface should support the `-h` option for displaying help inline. The command-line interface displayed the following when executed with `-h`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` ``` Command-line interface should support the `--help` option for displaying help inline. The command-line interface displayed the following when executed with `--help`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` Log: None
cli.CliDisplaysVersionInformationInline (1.6 s)
Test that a command-line interface provides version information inline. Warnings: ``` Command-line interface should support the `-v` option for displaying version information inline. The command-line interface displayed the following when executed with `-v`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` ``` Command-line interface should support the `--version` option for displaying version information inline. The command-line interface displayed the following when executed with `--version`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` Log: None
docker_image.DeclaresSupportedEnvironmentVariables (0.7 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - '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' - 'VERBOSE' - '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 2 years ago

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-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-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) Reason for skip: ``` Case requires model formats format_9001 and simulation algorithms KISAO_0000057 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9010 and simulation algorithms KISAO_0000019 ``` Log: None
sedml.SimulatorProducesLinear3DPlots (0.3 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 (13.1 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` Jun 02, 2022 11:41:37 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_8268815b-a859-4e94-927a-da3eb793b0fd1080688282818758707 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim sedml_name: BIOMD0000000912_sim content.location: ./BIOMD0000000912_sim.sedml content_filename: /tmp/out/temp/./BIOMD0000000912_sim.sedml SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] There are 1 changes. UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@421bba99, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@5d12a356, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@134d26af, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@66ac5762, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp9191749700160968696.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@497570fb Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 103 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv report HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsComputeModelChanges (14.2 s)
Test that a simulator supports compute model changes Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` Jun 02, 2022 11:42:03 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_ddb64fef-d4c7-43bd-9fc6-1cac9312eced5020222761724151398 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim sedml_name: BIOMD0000000912_sim content.location: ./BIOMD0000000912_sim.sedml content_filename: /tmp/out/temp/./BIOMD0000000912_sim.sedml SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] There are 36 changes. UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@7ec3394b, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@bff34c6, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@1522d8a0, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@312ab28e, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp3731895463746355484.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@26e412ef Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 79 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv report HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (14.1 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpx3lj2vh_/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 02, 2022 11:42:32 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_5cba7ade-892c-4729-ac88-2dcd29be72de8228783126240719426 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim sedml_name: BIOMD0000000912_sim content.location: ./BIOMD0000000912_sim.sedml content_filename: /tmp/out/temp/./BIOMD0000000912_sim.sedml SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] There are 0 changes. UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] UniformTimeCourse [initialTime=0.0, numberOfPoints=20, outputEndTime=4.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim__copy_2] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] Task [modelReference=BIOMD0000000912, name=null, simulationReference=BIOMD0000000912_sim__copy_2, getId()=BIOMD0000000912_task__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@2250b9f2, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@7e3181aa, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@253d9f73, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@142269f2, name=I, getId()=data_gen_I] DataGenerator [math=org.jmathml.ASTRootNode@331acdad, name=null, getId()=data_gen_time__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@41d426b5, name=null, getId()=data_gen_T__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@8dbfffb, name=null, getId()=data_gen_E__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@f316aeb, name=null, getId()=data_gen_I__copy_2] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp8801405342986754140.xml Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@40620d8e Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 89 ms ----------------------------------------------------------------------------------------------------- /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@3b8ee898 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'. Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 43 ms ----------------------------------------------------------------------------------------------------- Ran 2 simulations for 1 biomodels. Generating report `report`. {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv Traceback (most recent call last): File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 433, in fire.Fire({ File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire component_trace = _Fire(component, args, parsed_flag_args, context, name) File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire component, remaining_args = _CallAndUpdateTrace( File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace component = fn(*varargs, **kwargs) File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 166, in exec_plot_output_sed_doc data_set_df = pd.read_csv(report_filename, header=None).T File "/usr/local/lib/python3.8/dist-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 581, in _read return parser.read(nrows) File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 1254, in read index, columns, col_dict = self._engine.read(nrows) File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/c_parser_wrapper.py", line 225, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 805, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1960, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 14 fields in line 5, saw 24 HDF conversion failed All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsModelAttributeChanges (14.2 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` Jun 02, 2022 11:42:46 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_60dd41d2-ad26-4377-ad83-77e2175a41d2241868047917730911 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim sedml_name: BIOMD0000000912_sim content.location: ./BIOMD0000000912_sim.sedml content_filename: /tmp/out/temp/./BIOMD0000000912_sim.sedml SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] There are 226 changes. UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@421bba99, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@5d12a356, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@134d26af, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@66ac5762, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp8381400470437993042.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@3b6c624 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 82 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv report HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsRepeatedTasksWithChanges (8.4 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpx3lj2vh_/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 02, 2022 11:43:42 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_e00529f8-a58b-45b1-9e30-97299b6f140d413326970047748409 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_e00529f8-a58b-45b1-9e30-97299b6f140d413326970047748409/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute Jun 02, 2022 11:43:46 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_09220453-d6e4-4776-80d9-5a5b324eef442236824924895554659 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_09220453-d6e4-4776-80d9-5a5b324eef442236824924895554659/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (8.3 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpx3lj2vh_/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 02, 2022 11:43:50 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_8ac0ab2c-9acf-44c3-ba97-747de43c03ff8628953786207610297 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_8ac0ab2c-9acf-44c3-ba97-747de43c03ff8628953786207610297/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute Jun 02, 2022 11:43:54 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_7854975e-b4d8-4b88-bc3c-75f53b57c79f3280104715571050388 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_7854975e-b4d8-4b88-bc3c-75f53b57c79f3280104715571050388/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (4.1 s)
Test that a simulator supports repeated tasks over functional ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpx3lj2vh_/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 02, 2022 11:43:58 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_d16a9136-03c1-408d-976e-be23727fc32e8733140152066576916 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_d16a9136-03c1-408d-976e-be23727fc32e8733140152066576916/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (4.1 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpx3lj2vh_/sedml/sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 02, 2022 11:44:03 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_c12b336f-24f4-4227-be2a-fc2aec9946269182739470084109286 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_c12b336f-24f4-4227-be2a-fc2aec9946269182739470084109286/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (4.2 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpx3lj2vh_/sedml/sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 02, 2022 11:44:07 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_23421096-3b11-414b-a049-44067f5e0ac57710086992914520690 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_23421096-3b11-414b-a049-44067f5e0ac57710086992914520690/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (4.1 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpx3lj2vh_/sedml/sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 02, 2022 11:44:11 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_ed908a97-c206-4ffe-9401-50d18e409783810910397206050437 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_ed908a97-c206-4ffe-9401-50d18e409783810910397206050437/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (4.1 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpx3lj2vh_/sedml/sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 02, 2022 11:44:15 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_224cb093-8ec8-4223-bed8-8f9afcb4fe976446696437510518858 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_224cb093-8ec8-4223-bed8-8f9afcb4fe976446696437510518858/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (4.2 s)
Test that a simulator supports nested repeated tasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpx3lj2vh_/sedml/sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 02, 2022 11:44:19 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_bdb5b3e7-8e0e-42e9-8929-9acf7682af787342467718691943635 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_bdb5b3e7-8e0e-42e9-8929-9acf7682af787342467718691943635/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (4.1 s)
Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their ``order`` attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes. Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpx3lj2vh_/sedml/sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 02, 2022 11:44:23 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_9603dccc-efe7-4fb2-a8db-75cf7a095be98375875965068201585 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_9603dccc-efe7-4fb2-a8db-75cf7a095be98375875965068201585/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (4.1 s)
Test that a simulator supports repeated tasks over vector ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpx3lj2vh_/sedml/sedml.SimulatorSupportsRepeatedTasksWithVectorRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 02, 2022 11:44:28 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_33288f56-e89d-40fc-a2af-3ae6db2fae982881380621536562912 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_33288f56-e89d-40fc-a2af-3ae6db2fae982881380621536562912/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsSubstitutingAlgorithms (12.9 s)
Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.SAME_METHOD`. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.NONE`. Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` Jun 02, 2022 11:44:32 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_7d8050c1-81cf-454d-b672-7329b8d195a64746647242964854792 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim sedml_name: BIOMD0000000912_sim content.location: ./BIOMD0000000912_sim.sedml content_filename: /tmp/out/temp/./BIOMD0000000912_sim.sedml SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Sta ...
biosimulators-daemon commented 2 years ago

The image for your simulator is valid!

biosimulators-daemon commented 2 years ago

The validation/submission of your simulator failed.

- 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).

biosimulators-daemon commented 2 years ago

Thank you @vcdaemon for your submission to the BioSimulators simulator validation/submission system!

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

We will discuss any concerns with your submission in this issue.

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

biosimulators-daemon commented 2 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 years ago

Summary of tests

biosimulators-daemon commented 2 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.1 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports. Warnings: ``` The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports. The command-line interface does not describe the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - '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' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be described in the inline help for its command-line interface. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
cli.CliDisplaysHelpInline (1.8 s)
Test that a command-line interface provides inline help. Warnings: ``` Command-line interface should support the `-h` option for displaying help inline. The command-line interface displayed the following when executed with `-h`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` ``` Command-line interface should support the `--help` option for displaying help inline. The command-line interface displayed the following when executed with `--help`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` Log: None
cli.CliDisplaysVersionInformationInline (1.4 s)
Test that a command-line interface provides version information inline. Warnings: ``` Command-line interface should support the `-v` option for displaying version information inline. The command-line interface displayed the following when executed with `-v`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` ``` Command-line interface should support the `--version` option for displaying version information inline. The command-line interface displayed the following when executed with `--version`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` Log: None
docker_image.DeclaresSupportedEnvironmentVariables (0.4 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: - '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' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.2 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 2 years ago

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-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-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) Reason for skip: ``` Case requires model formats format_9001 and simulation algorithms KISAO_0000057 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9010 and simulation algorithms KISAO_0000019 ``` Log: None
sedml.SimulatorProducesLinear3DPlots (0.3 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 (12.7 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` Jun 03, 2022 4:00:22 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_4c22e612-12d9-4462-b35b-696357d758d25836240016124528665 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim sedml_name: BIOMD0000000912_sim content.location: ./BIOMD0000000912_sim.sedml content_filename: /tmp/out/temp/./BIOMD0000000912_sim.sedml SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] There are 1 changes. UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@421bba99, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@5d12a356, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@134d26af, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@66ac5762, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp1065209523828098170.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@497570fb Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 83 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv report HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsComputeModelChanges (14.5 s)
Test that a simulator supports compute model changes Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` Jun 03, 2022 4:00:48 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_97e87f2c-7279-4be7-990b-61674d0565c32715419300015991023 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim sedml_name: BIOMD0000000912_sim content.location: ./BIOMD0000000912_sim.sedml content_filename: /tmp/out/temp/./BIOMD0000000912_sim.sedml SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] There are 36 changes. UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@7ec3394b, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@bff34c6, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@1522d8a0, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@312ab28e, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp3887610866129978838.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@26e412ef Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 79 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv report HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (14.6 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpl0iywszh/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 03, 2022 4:01:17 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_914e1f6b-9e68-4c08-a90a-3298c4d2f34a3083074142021840680 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim sedml_name: BIOMD0000000912_sim content.location: ./BIOMD0000000912_sim.sedml content_filename: /tmp/out/temp/./BIOMD0000000912_sim.sedml SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] There are 0 changes. UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] UniformTimeCourse [initialTime=0.0, numberOfPoints=20, outputEndTime=4.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim__copy_2] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] Task [modelReference=BIOMD0000000912, name=null, simulationReference=BIOMD0000000912_sim__copy_2, getId()=BIOMD0000000912_task__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@2250b9f2, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@7e3181aa, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@253d9f73, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@142269f2, name=I, getId()=data_gen_I] DataGenerator [math=org.jmathml.ASTRootNode@331acdad, name=null, getId()=data_gen_time__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@41d426b5, name=null, getId()=data_gen_T__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@8dbfffb, name=null, getId()=data_gen_E__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@f316aeb, name=null, getId()=data_gen_I__copy_2] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp1089684517178059088.xml Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@40620d8e Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 98 ms ----------------------------------------------------------------------------------------------------- /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@3b8ee898 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'. Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 43 ms ----------------------------------------------------------------------------------------------------- Ran 2 simulations for 1 biomodels. Generating report `report`. {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv Traceback (most recent call last): File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 433, in fire.Fire({ File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire component_trace = _Fire(component, args, parsed_flag_args, context, name) File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire component, remaining_args = _CallAndUpdateTrace( File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace component = fn(*varargs, **kwargs) File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 166, in exec_plot_output_sed_doc data_set_df = pd.read_csv(report_filename, header=None).T File "/usr/local/lib/python3.8/dist-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 581, in _read return parser.read(nrows) File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 1254, in read index, columns, col_dict = self._engine.read(nrows) File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/c_parser_wrapper.py", line 225, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 805, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1960, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 14 fields in line 5, saw 24 HDF conversion failed All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsModelAttributeChanges (14.1 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` Jun 03, 2022 4:01:31 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_8cc7454d-dfff-4ff3-a3b8-c3d8c41aa49b4547371532786963806 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim sedml_name: BIOMD0000000912_sim content.location: ./BIOMD0000000912_sim.sedml content_filename: /tmp/out/temp/./BIOMD0000000912_sim.sedml SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] There are 226 changes. UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@421bba99, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@5d12a356, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@134d26af, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@66ac5762, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp8624159534112454147.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@3b6c624 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 81 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv report HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsRepeatedTasksWithChanges (8.3 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpl0iywszh/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 03, 2022 4:02:29 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_5cd3b739-a204-4998-8813-ddfd6c12f5414785846418880667513 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_5cd3b739-a204-4998-8813-ddfd6c12f5414785846418880667513/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute Jun 03, 2022 4:02:33 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_97f7d79a-ab7f-48d9-af8a-3efab21124942497731238335551217 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_97f7d79a-ab7f-48d9-af8a-3efab21124942497731238335551217/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (8.1 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpl0iywszh/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 03, 2022 4:02:37 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_219d80bd-195c-4b0e-a6d8-d671e0ac43622627867989620979375 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_219d80bd-195c-4b0e-a6d8-d671e0ac43622627867989620979375/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute Jun 03, 2022 4:02:41 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_ba6e5e82-b36b-4928-ac8e-32bec856584f1670329248163556669 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_ba6e5e82-b36b-4928-ac8e-32bec856584f1670329248163556669/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (4.0 s)
Test that a simulator supports repeated tasks over functional ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpl0iywszh/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 03, 2022 4:02:45 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_4c1a4d27-904e-40af-b937-e84d8ea1de255995973141010454057 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_4c1a4d27-904e-40af-b937-e84d8ea1de255995973141010454057/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (4.0 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpl0iywszh/sedml/sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 03, 2022 4:02:49 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_50cf1aea-8cf1-4c0f-9898-8b6fae7106556963591629084790219 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_50cf1aea-8cf1-4c0f-9898-8b6fae7106556963591629084790219/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (4.0 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpl0iywszh/sedml/sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 03, 2022 4:02:53 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_45251d13-a830-4aa7-a76e-4ab57fddfa2b7528571032545514912 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_45251d13-a830-4aa7-a76e-4ab57fddfa2b7528571032545514912/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (4.1 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpl0iywszh/sedml/sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 03, 2022 4:02:57 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_2678bff8-5b03-466a-a361-0271d38e551c3198489488640266563 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_2678bff8-5b03-466a-a361-0271d38e551c3198489488640266563/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (4.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpl0iywszh/sedml/sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 03, 2022 4:03:01 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_1b6c54f0-8fcf-44c4-968f-533d21b22966763950904539683354 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_1b6c54f0-8fcf-44c4-968f-533d21b22966763950904539683354/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (3.7 s)
Test that a simulator supports nested repeated tasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpl0iywszh/sedml/sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 03, 2022 4:03:05 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_b173ba8f-20be-4d52-98cd-ca7b865729e83602687659212258990 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_b173ba8f-20be-4d52-98cd-ca7b865729e83602687659212258990/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (3.9 s)
Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their ``order`` attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes. Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpl0iywszh/sedml/sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 03, 2022 4:03:09 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_60de052c-160d-4b02-adc7-117a9285d7044781570872198302927 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_60de052c-160d-4b02-adc7-117a9285d7044781570872198302927/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (3.7 s)
Test that a simulator supports repeated tasks over vector ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpl0iywszh/sedml/sedml.SimulatorSupportsRepeatedTasksWithVectorRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jun 03, 2022 4:03:13 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_5a637760-43f5-4c6e-bfd7-333c3bd18cf75936608750642506239 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) SED-ML processing for /tmp/vcell_temp_5a637760-43f5-4c6e-bfd7-333c3bd18cf75936608750642506239/BIOMD0000000912_sim.sedml failed with error: null org.jlibsedml.XMLException at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsSubstitutingAlgorithms (13.6 s)
Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.SAME_METHOD`. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.NONE`. Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` Jun 03, 2022 4:03:17 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_2fe6df4a-7d20-4b69-9e7e-30fe553b30161793478717268909533 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim sedml_name: BIOMD0000000912_sim content.location: ./BIOMD0000000912_sim.sedml content_filename: /tmp/out/temp/./BIOMD0000000912_sim.sedml SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate ...
biosimulators-daemon commented 2 years ago

The image for your simulator is valid!

biosimulators-daemon commented 2 years ago

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

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