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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 7.4.0.32 #535

Closed vcdaemon closed 2 years ago

vcdaemon commented 2 years ago

id: vcell version: 7.4.0.32 specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.4.0.32/biosimulators.json specificationsPatch: version: 7.4.0.32 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.32 digest: "sha256:bc16d6c585fd05f88a57dd37f001d766b6613989fbaf43327bc2aa3d9a639e48" 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

Failures

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (13.6 s)
Test that simulator logs the execution of COMBINE/OMEX archives Exception: ``` The execution status report produced by the simulator is not valid. By the end of the execution of a COMBINE/OMEX archive, the status of the archive, each SED document, and each SED element should be `SUCCEEDED`, `SKIPPED`, or `FAILED`. ``` Log: ``` Jan 24, 2022 3:39:10 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_27e52239-b1f0-455c-8ab4-4b4039de920d9031460812361295574 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@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 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/temp1532649741405728634.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@4a60ee36 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 109 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`. ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (13.4 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives Exception: ``` The execution status report produced by the simulator is not valid. By the end of the execution of a COMBINE/OMEX archive, the status of the archive, each SED document, and each SED element should be `SUCCEEDED`, `SKIPPED`, or `FAILED`. ``` Log: ``` Jan 24, 2022 3:39:24 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_0512423d-a22f-42d1-918f-885b3ff4ee031508868645884546399 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@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 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/temp6794436777788480224.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@4a60ee36 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 82 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /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`. ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (13.4 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives Exception: ``` The execution status report produced by the simulator is not valid. By the end of the execution of a COMBINE/OMEX archive, the status of the archive, each SED document, and each SED element should be `SUCCEEDED`, `SKIPPED`, or `FAILED`. ``` Log: ``` Jan 24, 2022 3:39:37 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_4f8f2176-d1d2-4d34-ab99-d0395442875d4463740975884771875 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@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 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/temp3383000916374250225.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@4a60ee36 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 114 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`. ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (13.4 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives Exception: ``` The execution status report produced by the simulator is not valid. By the end of the execution of a COMBINE/OMEX archive, the status of the archive, each SED document, and each SED element should be `SUCCEEDED`, `SKIPPED`, or `FAILED`. ``` Log: ``` Jan 24, 2022 3:39:51 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_c52438d5-a071-4344-b4e2-814bb38451839071485364788304490 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@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 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/temp5465236412480515040.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@4a60ee36 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 98 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`. ```
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 (1.8 s)
Test that a command-line interface provides inline help. Warnings: ``` Command-line interface should support the `-h` option for displaying help inline. The command-line interface displayed the following when executed with `-h`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` ``` Command-line interface should support the `--help` option for displaying help inline. The command-line interface displayed the following when executed with `--help`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` Log: None
cli.CliDisplaysVersionInformationInline (1.4 s)
Test that a command-line interface provides version information inline. Warnings: ``` Command-line interface should support the `-v` option for displaying version information inline. The command-line interface displayed the following when executed with `-v`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` ``` Command-line interface should support the `--version` option for displaying version information inline. The command-line interface displayed the following when executed with `--version`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` Log: None
docker_image.DeclaresSupportedEnvironmentVariables (0.4 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.3 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 (8.5 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 24, 2022 3:33:38 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_23c0b8bb-2eca-410e-b9a9-94843b1398fb1950254386560749671 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 (8.5 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 24, 2022 3:33:47 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_04be2f0d-156b-4699-bfa7-acf25d00967f2476632439028757222 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 (0.3 s)
Test that a simulator produces linear 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (0.3 s)
Test that a simulator produces logarithmic 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (13.2 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 24, 2022 3:35:23 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_b02f4fe9-c5c4-48cb-8116-c9945b19c1692538715062393766389 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/temp3565117875563467742.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, 90 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 (14.4 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 24, 2022 3:35:49 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_6afb82e3-2a8e-4046-95fa-67544429b4141227567804378581737 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/temp4209340262010032587.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, 91 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 (14.2 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/tmpwwkknl7q/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 24, 2022 3:36:18 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_250a8695-5f29-4126-bdda-f90dab4adfc67017961536612157713 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/temp7833285387773248282.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, 118 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, 44 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 (14.4 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 24, 2022 3:36:32 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_bcfd3560-7064-4e9a-b98f-3d787365a0534871269483363637089 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/temp4666682844924185144.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, 87 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 (8.1 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpwwkknl7q/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 24, 2022 3:37:29 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_a54550ce-37e3-440d-ab7c-e2fc1e019a8c2248742714293461354 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_a54550ce-37e3-440d-ab7c-e2fc1e019a8c2248742714293461354/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 24, 2022 3:37:33 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_c6347c1f-fa45-42cd-9e66-ff045af119bf7867641260697840150 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_c6347c1f-fa45-42cd-9e66-ff045af119bf7867641260697840150/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 (8.2 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/tmpwwkknl7q/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 24, 2022 3:37:37 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_0b3d84a8-c029-4834-b2a2-393f6e5173f5877302542295369672 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_0b3d84a8-c029-4834-b2a2-393f6e5173f5877302542295369672/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 24, 2022 3:37:41 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_92ff4ebf-75e0-4899-9207-f275efe10b378541081378399502993 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_92ff4ebf-75e0-4899-9207-f275efe10b378541081378399502993/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 (4.0 s)
Test that a simulator supports repeated tasks over functional ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpwwkknl7q/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 24, 2022 3:37:45 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_2b3d80e5-c0c3-4ffc-b1b1-9d208a168ac12096833501688897583 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_2b3d80e5-c0c3-4ffc-b1b1-9d208a168ac12096833501688897583/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 (4.0 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpwwkknl7q/sedml/sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 24, 2022 3:37:49 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_1e0f06b0-8854-4c75-b7d5-2a4bc58b428a7059268953354109697 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_1e0f06b0-8854-4c75-b7d5-2a4bc58b428a7059268953354109697/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 (3.9 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/tmpwwkknl7q/sedml/sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 24, 2022 3:37:53 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_62d30f41-9050-4d3d-9f81-59e1c35e6fa87018942925378230296 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_62d30f41-9050-4d3d-9f81-59e1c35e6fa87018942925378230296/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 (4.0 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/tmpwwkknl7q/sedml/sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 24, 2022 3:37:57 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_f2d64eba-5688-4a86-9ad2-a6b171e0d1a2101651265798126510 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_f2d64eba-5688-4a86-9ad2-a6b171e0d1a2101651265798126510/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 (4.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpwwkknl7q/sedml/sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 24, 2022 3:38:01 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_f891181b-2420-48dd-9b1c-7664bbe6e3db20420615023268679 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_f891181b-2420-48dd-9b1c-7664bbe6e3db20420615023268679/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 (4.0 s)
Test that a simulator supports nested repeated tasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpwwkknl7q/sedml/sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 24, 2022 3:38:05 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_09f799dc-2c6c-413a-8284-f224529effb71580563186522775186 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_09f799dc-2c6c-413a-8284-f224529effb71580563186522775186/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.SimulatorSupportsRepeatedTasksWithSubTas ...
biosimulators-daemon commented 2 years ago 
- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/1737909322). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/1737909322).
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