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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 7.4.0.33 #536

Closed vcdaemon closed 2 years ago

vcdaemon commented 2 years ago

id: vcell version: 7.4.0.33 specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.4.0.33/biosimulators.json specificationsPatch: version: 7.4.0.33 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.33 digest: "sha256:60681afa6b8ed5728d0a450e04f770ce7d93ecf78548e262f60984fa924c8630" 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 (1.2 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 (1.5 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 (0.3 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - '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 (0.3 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.SimulatorCanResolveModelSourcesDefinedByUriFragments (10.3 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``). Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` Jan 25, 2022 12:10:52 AM 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_cc568828-fb23-487a-80e8-b2a98a384041980711803391908629 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 2 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 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=#__source__] Model [id=__source__, name=null, language=urn:sedml:language:sbml, src=Caravagna2010.xml] 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@4b14918a, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@6d1ef78d, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@1a6c1270, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@18a136ac, 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 [Fatal Error] :1:1: Content is not allowed in prolog. [Fatal Error] :1:1: Content is not allowed in prolog. java.lang.RuntimeException: Error importing from SBML : no SBML source. at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:449) at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:704) at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:74) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:375) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Error importing from SBML : no SBML source. Generating report `report`. java.lang.NullPointerException at org.vcell.cli.CLIUtils.generateReportsAsCSV(CLIUtils.java:530) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:404) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) HDF conversion successful All sedml documents in this archive failed to execute ```
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (10.1 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``) and inherit the changes of the model. Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` Jan 25, 2022 12:11:03 AM 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_d7f37057-435a-4490-8d3f-1a08b006970f6049431785916829019 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 2 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 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=#__source__] Model [id=__source__, name=null, language=urn:sedml:language:sbml, src=Caravagna2010.xml] 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@1a6c1270, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@18a136ac, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@77d67cf3, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@6dee4f1b, 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 [Fatal Error] :1:1: Content is not allowed in prolog. [Fatal Error] :1:1: Content is not allowed in prolog. java.lang.RuntimeException: Error importing from SBML : no SBML source. at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:449) at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:704) at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:74) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:375) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Error importing from SBML : no SBML source. Generating report `report`. java.lang.NullPointerException at org.vcell.cli.CLIUtils.generateReportsAsCSV(CLIUtils.java:530) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:404) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) HDF conversion successful All sedml documents in this archive failed to execute ```
sedml.SimulatorProducesLinear3DPlots (0.4 s)
Test that a simulator produces linear 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (0.4 s)
Test that a simulator produces logarithmic 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.4 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 (15.7 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: ``` Jan 25, 2022 12:12:57 AM 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_8f1b8419-22a0-4fd8-830c-f21bba7c17349055392770068085150 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 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] 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@1a6c1270, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@18a136ac, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@77d67cf3, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@6dee4f1b, 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/temp3860720267533920769.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@65f00478 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 135 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsComputeModelChanges (17.0 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: ``` Jan 25, 2022 12:13:29 AM 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_9c99b558-0693-4187-8027-48303971dada2309179405701450894 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 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] 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@1d0d6318, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@4bc28c33, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@4409e975, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@5c153b9e, 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/temp7549256483732527792.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@178270b2 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 137 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (16.7 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/tmpq4t9fqmw/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 25, 2022 12:14:02 AM 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_0d749342-2eda-4c34-a9fd-09e18c4908c65926854592617295586 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 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] 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@3f270e0a, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@1a760689, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@7241a47d, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@70f59913, name=I, getId()=data_gen_I] DataGenerator [math=org.jmathml.ASTRootNode@77258e59, name=null, getId()=data_gen_time__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@5dcd8c7a, name=null, getId()=data_gen_T__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@2250b9f2, name=null, getId()=data_gen_E__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@7e3181aa, 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/temp4677243234950730145.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@4564e94b Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 95 ms ----------------------------------------------------------------------------------------------------- /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@7af1cd63 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 : /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 421, 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 155, 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 1250, 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 (17.0 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: ``` Jan 25, 2022 12:14:19 AM 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_134381d6-19f4-4c08-8ff3-95933ea60cfc3525965145674135592 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 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] 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@1a6c1270, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@18a136ac, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@77d67cf3, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@6dee4f1b, 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/temp8740969631835738906.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@3c017078 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 96 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsRepeatedTasksWithChanges (9.4 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/tmpq4t9fqmw/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 25, 2022 12:15:27 AM 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_bc88933f-0575-40c7-b9c7-5f02996dcd886590060092121612946 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_bc88933f-0575-40c7-b9c7-5f02996dcd886590060092121612946/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) All sedml documents in this archive failed to execute Jan 25, 2022 12:15:32 AM 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_3943f23c-85f9-4cba-bed8-08605ca594c75795162334246181682 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_3943f23c-85f9-4cba-bed8-08605ca594c75795162334246181682/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (9.5 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/tmpq4t9fqmw/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 25, 2022 12:15:36 AM 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_6c60fc30-ebf1-458e-88d1-65cb1dcbe2d82268420474732832326 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_6c60fc30-ebf1-458e-88d1-65cb1dcbe2d82268420474732832326/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) All sedml documents in this archive failed to execute Jan 25, 2022 12:15:41 AM 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_06eb3010-65e6-4efe-a7a3-b6c0dafec9411988912750366441515 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_06eb3010-65e6-4efe-a7a3-b6c0dafec9411988912750366441515/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (4.6 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/tmpq4t9fqmw/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 25, 2022 12:15:46 AM 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_c51cd8e2-6aa7-4a22-a1d6-da98207ce9d69149696655725292456 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_c51cd8e2-6aa7-4a22-a1d6-da98207ce9d69149696655725292456/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (4.8 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/tmpq4t9fqmw/sedml/sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 25, 2022 12:15:51 AM 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_d81e9091-5b07-43f3-888e-25ced8a6bca34976102879311895243 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_d81e9091-5b07-43f3-888e-25ced8a6bca34976102879311895243/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (4.6 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/tmpq4t9fqmw/sedml/sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 25, 2022 12:15:55 AM 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_a3acf29d-dfe2-4b41-b212-da5b9feae6e94228503669156992004 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_a3acf29d-dfe2-4b41-b212-da5b9feae6e94228503669156992004/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (4.6 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/tmpq4t9fqmw/sedml/sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 25, 2022 12:16:00 AM 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_aa1f53f4-ca10-4eeb-85c5-a6af4af2351a3148152179880859744 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_aa1f53f4-ca10-4eeb-85c5-a6af4af2351a3148152179880859744/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (4.7 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/tmpq4t9fqmw/sedml/sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 25, 2022 12:16:05 AM 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_5972aa38-8be2-4329-84d5-0766158617244110835715180528538 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_5972aa38-8be2-4329-84d5-0766158617244110835715180528538/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (4.6 s)
Test that a simulator supports nested repeated tasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpq4t9fqmw/sedml/sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 25, 2022 12:16:09 AM 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_42f7be3f-d65a-4c74-94c0-6820a9e0ea864618462261585874040 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_42f7be3f-d65a-4c74-94c0-6820a9e0ea864618462261585874040/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) All sedml documents in this archive failed to execute ```
sedml.SimulatorSuppo ...
biosimulators-daemon commented 2 years ago

The image for your simulator is valid!

biosimulators-daemon commented 2 years ago

A member of the BioSimulators team will review your submission and publish your image before final committment to the registry.

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

  • Executed 73 test cases

  • Passed 33 test cases:

    • cli.CliDescribesSupportedEnvironmentVariablesInline
    • cli.CliDisplaysHelpInline
    • cli.CliDisplaysVersionInformationInline
    • combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
    • combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
    • combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
    • combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
    • docker_image.DeclaresSupportedEnvironmentVariables
    • docker_image.DefaultUserIsRoot
    • docker_image.HasBioContainersLabels
    • docker_image.HasOciLabels
    • docker_image.SingularityImageExecutesSimulationsSuccessfully
    • log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
    • log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
    • log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
    • log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
    • results_report.SimulatorGeneratesReportsOfSimulationResults
    • sedml.SimulatorProducesLinear2DPlots
    • sedml.SimulatorProducesLogarithmic2DPlots
    • sedml.SimulatorProducesMultiplePlots
    • sedml.SimulatorSupportsAlgorithmParameters
    • sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
    • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
    • sedml.SimulatorSupportsMultipleReportsPerSedDocument
    • sedml.SimulatorSupportsMultipleTasksPerSedDocument
    • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

  • Failed 0 test cases

  • Skipped 40 test cases:

    • published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
    • published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
    • published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
    • published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
    • published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
    • published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
    • published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
    • published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
    • published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
    • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
    • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
    • published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
    • published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
    • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
    • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
    • sedml.SimulatorProducesLinear3DPlots
    • sedml.SimulatorProducesLogarithmic3DPlots
    • sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
    • sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
    • sedml.SimulatorSupportsComputeModelChanges
    • sedml.SimulatorSupportsDataSetsWithDifferentShapes
    • sedml.SimulatorSupportsModelAttributeChanges
    • sedml.SimulatorSupportsRepeatedTasksWithChanges
    • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
    • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
    • sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
    • sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
    • sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
    • sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
    • sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
    • sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
    • sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
    • sedml.SimulatorSupportsSubstitutingAlgorithms
    • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
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 (1.9 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 (1.5 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 (0.3 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.SimulatorCanResolveModelSourcesDefinedByUriFragments (9.6 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``). Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` Jan 25, 2022 5:08:56 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_dcb12bdf-220d-4e42-a09e-fdf46b8101462875855458915126508 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 2 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 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=#__source__] Model [id=__source__, name=null, language=urn:sedml:language:sbml, src=Caravagna2010.xml] 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@4b14918a, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@6d1ef78d, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@1a6c1270, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@18a136ac, 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 [Fatal Error] :1:1: Content is not allowed in prolog. [Fatal Error] :1:1: Content is not allowed in prolog. java.lang.RuntimeException: Error importing from SBML : no SBML source. at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:449) at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:704) at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:74) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:375) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Error importing from SBML : no SBML source. Generating report `report`. java.lang.NullPointerException at org.vcell.cli.CLIUtils.generateReportsAsCSV(CLIUtils.java:530) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:404) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) HDF conversion successful All sedml documents in this archive failed to execute ```
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (9.8 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``) and inherit the changes of the model. Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` Jan 25, 2022 5:09:06 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_c33f4aad-c2ef-44c2-b0f1-ce2c911ef3f75291085768099881280 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 2 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 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=#__source__] Model [id=__source__, name=null, language=urn:sedml:language:sbml, src=Caravagna2010.xml] 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@18a136ac, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@77d67cf3, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@6dee4f1b, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@176b3f44, 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 [Fatal Error] :1:1: Content is not allowed in prolog. [Fatal Error] :1:1: Content is not allowed in prolog. java.lang.RuntimeException: Error importing from SBML : no SBML source. at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:449) at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:704) at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:74) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:375) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Error importing from SBML : no SBML source. Generating report `report`. java.lang.NullPointerException at org.vcell.cli.CLIUtils.generateReportsAsCSV(CLIUtils.java:530) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:404) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) HDF conversion successful All sedml documents in this archive failed to execute ```
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 (14.8 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: ``` Jan 25, 2022 5:10:53 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_a8b8e275-277c-4298-b56e-7799dbf06f455532646831603842383 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 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] 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@1a6c1270, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@18a136ac, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@77d67cf3, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@6dee4f1b, 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/temp3964106521942898269.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@65f00478 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 110 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsComputeModelChanges (15.4 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: ``` Jan 25, 2022 5:11:22 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_01bba65b-6db2-48bf-a1d8-a2e14deca5c66431138240332611079 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 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] 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@1d0d6318, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@4bc28c33, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@4409e975, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@5c153b9e, 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/temp8027521531900425886.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@178270b2 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 88 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (16.0 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/tmpa4frfani/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 25, 2022 5:11:54 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_054d5879-c587-4865-873c-5d97094acd9a4013475001083024524 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 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] 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@3f270e0a, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@1a760689, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@7241a47d, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@70f59913, name=I, getId()=data_gen_I] DataGenerator [math=org.jmathml.ASTRootNode@77258e59, name=null, getId()=data_gen_time__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@5dcd8c7a, name=null, getId()=data_gen_T__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@2250b9f2, name=null, getId()=data_gen_E__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@7e3181aa, 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/temp4544820513054994309.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@4564e94b Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 96 ms ----------------------------------------------------------------------------------------------------- /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@7af1cd63 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'. Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 38 ms ----------------------------------------------------------------------------------------------------- Ran 2 simulations for 1 biomodels. Generating report `report`. 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 421, 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 155, 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 1250, 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 (15.9 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: ``` Jan 25, 2022 5:12:10 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_33a0bbdf-1292-41b0-830f-65286f176a2f1642849174436584748 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 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] 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@1a6c1270, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@18a136ac, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@77d67cf3, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@6dee4f1b, 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/temp5203079885447895645.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@3c017078 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 116 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsRepeatedTasksWithChanges (8.9 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/tmpa4frfani/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 25, 2022 5:13:13 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_0f7afda5-858b-4797-878e-3076841f35634691630283302478707 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_0f7afda5-858b-4797-878e-3076841f35634691630283302478707/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) All sedml documents in this archive failed to execute Jan 25, 2022 5:13:17 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_b4899c76-f769-46b6-9ce0-e7938b0adb681362826914950457120 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_b4899c76-f769-46b6-9ce0-e7938b0adb681362826914950457120/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (8.9 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/tmpa4frfani/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 25, 2022 5:13:22 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_5b3585ca-8fa1-4bde-9e8f-ef07be4141715028721031140563506 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_5b3585ca-8fa1-4bde-9e8f-ef07be4141715028721031140563506/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) All sedml documents in this archive failed to execute Jan 25, 2022 5:13:26 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_ea19bc87-bc00-4a84-bee0-22f7ec477c457307977871792261442 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_ea19bc87-bc00-4a84-bee0-22f7ec477c457307977871792261442/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (4.3 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/tmpa4frfani/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 25, 2022 5:13:31 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_9f3d2b47-5ea1-468d-aa83-c48fe2618a4d1639181303152911814 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_9f3d2b47-5ea1-468d-aa83-c48fe2618a4d1639181303152911814/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (4.3 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/tmpa4frfani/sedml/sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 25, 2022 5:13:35 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_91b69dfc-4a4a-4899-89e9-29d80fc1a84c4039238850676403499 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_91b69dfc-4a4a-4899-89e9-29d80fc1a84c4039238850676403499/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) 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/tmpa4frfani/sedml/sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 25, 2022 5:13:39 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_d1e9ce81-53ab-4829-b204-f0fa480fbc2c7984773450552284072 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_d1e9ce81-53ab-4829-b204-f0fa480fbc2c7984773450552284072/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (4.2 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/tmpa4frfani/sedml/sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 25, 2022 5:13:44 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_708dfb01-6dde-44c8-a610-4c27b23fcffa5151385226449130031 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_708dfb01-6dde-44c8-a610-4c27b23fcffa5151385226449130031/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (4.3 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/tmpa4frfani/sedml/sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 25, 2022 5:13:48 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_958df898-e9fb-4201-9c0e-2679d623687b3997708651055444440 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_958df898-e9fb-4201-9c0e-2679d623687b3997708651055444440/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (4.3 s)
Test that a simulator supports nested repeated tasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpa4frfani/sedml/sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 25, 2022 5:13:52 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_59c191b6-5f18-46ac-aebb-774a806936458542762124179992319 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) SED-ML processing for /tmp/vcell_temp_59c191b6-5f18-46ac-aebb-774a806936458542762124179992319/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:298) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:148) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksW ...
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.

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