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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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Test VCell 7.5.0.127 #694

Open CodeByDrescher opened 2 months ago

CodeByDrescher commented 2 months ago

Simulation tool

Simulation tool

id: vcell version: 7.5.0.27 specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.6.0.27/biosimulators.json specificationsPatch: version: 7.5.0.127 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.5.0.127 digest: "sha256:0089380af4a4a54f7c30b5ca25dc81aa3e3130f41bb137de236cf35cbca32538" validateImage: true commitSimulator: false

Support for BioSimulators' conventions

biosimulators-daemon commented 2 months ago

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

The BioSimulators validator bot is validating the specifications of your simulator, and validating your Docker image. You have chosen not to submit your simulator to the BioSimulators registry.

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

A complete log of your simulator validation 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 months ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 months ago

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

The BioSimulators validator bot is validating the specifications of your simulator, and validating your Docker image. You have chosen not to submit your simulator to the BioSimulators registry.

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

A complete log of your simulator validation 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 months ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 months ago

Summary of tests

biosimulators-daemon commented 2 months ago

Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (0.0 s)
Test that SED documents in nested directories can be executed Exception: ``` No module named 'libsbml' ``` Log: None
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (0.0 s)
Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths Exception: ``` No module named 'libsbml' ``` Log: None
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (0.0 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file. Exception: ``` No module named 'libsbml' ``` Log: None
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (0.0 s)
Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files. Exception: ``` No module named 'libsbml' ``` Log: None
docker_image.SingularityImageExecutesSimulationsSuccessfully (0.0 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Exception: ``` No module named 'libsbml' ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (0.0 s)
Test that simulator logs the execution of COMBINE/OMEX archives Exception: ``` No module named 'libsbml' ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (0.0 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives Exception: ``` No module named 'libsbml' ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (0.0 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives Exception: ``` No module named 'libsbml' ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (0.0 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives Exception: ``` No module named 'libsbml' ``` Log: None
results_report.SimulatorGeneratesReportsOfSimulationResults (0.0 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file. Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorProducesLinear2DPlots (0.0 s)
Test that a simulator produces linear 2D plots Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorProducesLinear3DPlots (0.0 s)
Test that a simulator produces linear 3D plots Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorProducesLogarithmic2DPlots (0.0 s)
Test that a simulator produces logarithmic 2D plots Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (0.0 s)
Test that a simulator produces logarithmic 3D plots Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorProducesMultiplePlots (0.0 s)
Test that a simulator produces multiple plots Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.0 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsAlgorithmParameters (0.0 s)
Test that a simulator supports setting the values of parameters of algorithms Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports (0.0 s)
Test that a simulator supports the core elements of SED: models, simulations, tasks, data generators for individual variables, and reports Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsMultipleReportsPerSedDocument (0.0 s)
Test that a simulator supports multiple reports per SED document Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsMultipleTasksPerSedDocument (0.0 s)
Test that a simulator supports multiple tasks per SED document Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (0.0 s)
Test that a simulator supports time courses with non-zero output start times Exception: ``` No module named 'libsbml' ``` Log: None
biosimulators-daemon commented 2 months ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (3.6 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 (4.3 s)
Test that a command-line interface provides inline help. Warnings: ``` Command-line interfaces should display basic help when no arguments are provided. The command-line interface displayed the following when no argument was provided: docker: Command recieved::<> <> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} ERROR (BiosimulationsCommand:116) - Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null []{} java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null at org.vcell.cli.CLIRecorder.(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:50) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ``` ``` Command-line interface should support the `-h` option for displaying help inline. The command-line interface displayed the following when executed with `-h`: docker: Command recieved::<-h> <-h> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} Usage: CLIStandalone biosimulations [-dhqv] [-i=] [-o=] BioSimulators-compliant command-line interface to the vcell simulation program . -d, --debug full application debug mode -h, --help show this help message and exit -i, --archive= Path to a COMBINE/OMEX archive file which contains one or more SED-ML-encoded simulation experiments -o, --out-dir= Directory to save outputs -q, --quiet suppress all console output -v, --version show program's version number and exit ``` ``` Command-line interface should support the `--help` option for displaying help inline. The command-line interface displayed the following when executed with `--help`: docker: Command recieved::<--help> <--help> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} Usage: CLIStandalone biosimulations [-dhqv] [-i=] [-o=] BioSimulators-compliant command-line interface to the vcell simulation program . -d, --debug full application debug mode -h, --help show this help message and exit -i, --archive= Path to a COMBINE/OMEX archive file which contains one or more SED-ML-encoded simulation experiments -o, --out-dir= Directory to save outputs -q, --quiet suppress all console output -v, --version show program's version number and exit ``` Log: None
docker_image.DeclaresSupportedEnvironmentVariables (0.8 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - '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 (0.6 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 months 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 (0.0 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``). Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (0.0 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: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.0 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsComputeModelChanges (0.0 s)
Test that a simulator supports compute model changes Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (0.0 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsDataSetsWithDifferentShapes (0.0 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsModelAttributeChanges (0.0 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithChanges (0.0 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (0.0 s)
Test that a simulator supports repeated tasks over functional ranges Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (0.0 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (0.0 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (0.0 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (0.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (0.0 s)
Test that a simulator supports nested repeated tasks Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (0.0 s)
Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their ``order`` attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes. Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (0.0 s)
Test that a simulator supports repeated tasks over vector ranges Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsSubstitutingAlgorithms (0.0 s)
Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.SAME_METHOD`. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.NONE`. Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (0.0 s)
Test that a simulator supports multiple time courses with non-zero initial times Reason for skip: ``` No module named 'libsbml' ``` Log: None
biosimulators-daemon commented 2 months 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/10723379442). 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/10723379442).
biosimulators-daemon commented 2 months ago

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

The BioSimulators validator bot is validating the specifications of your simulator, and validating your Docker image. You have chosen not to submit your simulator to the BioSimulators registry.

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

A complete log of your simulator validation 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 months ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 months ago

Summary of tests

biosimulators-daemon commented 2 months ago

Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (0.0 s)
Test that SED documents in nested directories can be executed Exception: ``` No module named 'libsbml' ``` Log: None
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (0.0 s)
Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths Exception: ``` No module named 'libsbml' ``` Log: None
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (0.0 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file. Exception: ``` No module named 'libsbml' ``` Log: None
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (0.0 s)
Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files. Exception: ``` No module named 'libsbml' ``` Log: None
docker_image.SingularityImageExecutesSimulationsSuccessfully (0.0 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Exception: ``` No module named 'libsbml' ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (0.0 s)
Test that simulator logs the execution of COMBINE/OMEX archives Exception: ``` No module named 'libsbml' ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (0.0 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives Exception: ``` No module named 'libsbml' ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (0.0 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives Exception: ``` No module named 'libsbml' ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (0.0 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives Exception: ``` No module named 'libsbml' ``` Log: None
results_report.SimulatorGeneratesReportsOfSimulationResults (0.0 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file. Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorProducesLinear2DPlots (0.0 s)
Test that a simulator produces linear 2D plots Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorProducesLinear3DPlots (0.0 s)
Test that a simulator produces linear 3D plots Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorProducesLogarithmic2DPlots (0.0 s)
Test that a simulator produces logarithmic 2D plots Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (0.0 s)
Test that a simulator produces logarithmic 3D plots Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorProducesMultiplePlots (0.0 s)
Test that a simulator produces multiple plots Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.0 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsAlgorithmParameters (0.0 s)
Test that a simulator supports setting the values of parameters of algorithms Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports (0.0 s)
Test that a simulator supports the core elements of SED: models, simulations, tasks, data generators for individual variables, and reports Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsMultipleReportsPerSedDocument (0.0 s)
Test that a simulator supports multiple reports per SED document Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsMultipleTasksPerSedDocument (0.0 s)
Test that a simulator supports multiple tasks per SED document Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (0.0 s)
Test that a simulator supports time courses with non-zero output start times Exception: ``` No module named 'libsbml' ``` Log: None
biosimulators-daemon commented 2 months ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (3.2 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 (4.1 s)
Test that a command-line interface provides inline help. Warnings: ``` Command-line interfaces should display basic help when no arguments are provided. The command-line interface displayed the following when no argument was provided: docker: Command recieved::<> <> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} ERROR (BiosimulationsCommand:116) - Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null []{} java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null at org.vcell.cli.CLIRecorder.(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:50) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ``` ``` Command-line interface should support the `-h` option for displaying help inline. The command-line interface displayed the following when executed with `-h`: docker: Command recieved::<-h> <-h> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} Usage: CLIStandalone biosimulations [-dhqv] [-i=] [-o=] BioSimulators-compliant command-line interface to the vcell simulation program . -d, --debug full application debug mode -h, --help show this help message and exit -i, --archive= Path to a COMBINE/OMEX archive file which contains one or more SED-ML-encoded simulation experiments -o, --out-dir= Directory to save outputs -q, --quiet suppress all console output -v, --version show program's version number and exit ``` ``` Command-line interface should support the `--help` option for displaying help inline. The command-line interface displayed the following when executed with `--help`: docker: Command recieved::<--help> <--help> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} Usage: CLIStandalone biosimulations [-dhqv] [-i=] [-o=] BioSimulators-compliant command-line interface to the vcell simulation program . -d, --debug full application debug mode -h, --help show this help message and exit -i, --archive= Path to a COMBINE/OMEX archive file which contains one or more SED-ML-encoded simulation experiments -o, --out-dir= Directory to save outputs -q, --quiet suppress all console output -v, --version show program's version number and exit ``` Log: None
docker_image.DeclaresSupportedEnvironmentVariables (0.2 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.2 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 2 months 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 (0.0 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``). Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (0.0 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: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.0 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsComputeModelChanges (0.0 s)
Test that a simulator supports compute model changes Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (0.0 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsDataSetsWithDifferentShapes (0.0 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsModelAttributeChanges (0.0 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithChanges (0.0 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (0.0 s)
Test that a simulator supports repeated tasks over functional ranges Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (0.0 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (0.0 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (0.0 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (0.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (0.0 s)
Test that a simulator supports nested repeated tasks Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (0.0 s)
Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their ``order`` attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes. Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (0.0 s)
Test that a simulator supports repeated tasks over vector ranges Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsSubstitutingAlgorithms (0.0 s)
Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.SAME_METHOD`. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.NONE`. Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (0.0 s)
Test that a simulator supports multiple time courses with non-zero initial times Reason for skip: ``` No module named 'libsbml' ``` Log: None
biosimulators-daemon commented 2 months 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/10723742251). 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/10723742251).
biosimulators-daemon commented 2 months ago

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

The BioSimulators validator bot is validating the specifications of your simulator, and validating your Docker image. You have chosen not to submit your simulator to the BioSimulators registry.

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

A complete log of your simulator validation 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 months ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 months ago

Summary of tests

biosimulators-daemon commented 2 months ago

Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (0.0 s)
Test that SED documents in nested directories can be executed Exception: ``` No module named 'libsbml' ``` Log: None
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (0.0 s)
Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths Exception: ``` No module named 'libsbml' ``` Log: None
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (0.0 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file. Exception: ``` No module named 'libsbml' ``` Log: None
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (0.0 s)
Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files. Exception: ``` No module named 'libsbml' ``` Log: None
docker_image.SingularityImageExecutesSimulationsSuccessfully (0.0 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Exception: ``` No module named 'libsbml' ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (0.0 s)
Test that simulator logs the execution of COMBINE/OMEX archives Exception: ``` No module named 'libsbml' ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (0.0 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives Exception: ``` No module named 'libsbml' ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (0.0 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives Exception: ``` No module named 'libsbml' ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (0.0 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives Exception: ``` No module named 'libsbml' ``` Log: None
results_report.SimulatorGeneratesReportsOfSimulationResults (0.0 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file. Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorProducesLinear2DPlots (0.0 s)
Test that a simulator produces linear 2D plots Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorProducesLinear3DPlots (0.0 s)
Test that a simulator produces linear 3D plots Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorProducesLogarithmic2DPlots (0.0 s)
Test that a simulator produces logarithmic 2D plots Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (0.0 s)
Test that a simulator produces logarithmic 3D plots Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorProducesMultiplePlots (0.0 s)
Test that a simulator produces multiple plots Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.0 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsAlgorithmParameters (0.0 s)
Test that a simulator supports setting the values of parameters of algorithms Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports (0.0 s)
Test that a simulator supports the core elements of SED: models, simulations, tasks, data generators for individual variables, and reports Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsMultipleReportsPerSedDocument (0.0 s)
Test that a simulator supports multiple reports per SED document Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsMultipleTasksPerSedDocument (0.0 s)
Test that a simulator supports multiple tasks per SED document Exception: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (0.0 s)
Test that a simulator supports time courses with non-zero output start times Exception: ``` No module named 'libsbml' ``` Log: None
biosimulators-daemon commented 2 months ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (3.6 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 (4.2 s)
Test that a command-line interface provides inline help. Warnings: ``` Command-line interfaces should display basic help when no arguments are provided. The command-line interface displayed the following when no argument was provided: docker: Command recieved::<> <> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} ERROR (BiosimulationsCommand:116) - Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null []{} java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null at org.vcell.cli.CLIRecorder.(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:50) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ``` ``` Command-line interface should support the `-h` option for displaying help inline. The command-line interface displayed the following when executed with `-h`: docker: Command recieved::<-h> <-h> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} Usage: CLIStandalone biosimulations [-dhqv] [-i=] [-o=] BioSimulators-compliant command-line interface to the vcell simulation program . -d, --debug full application debug mode -h, --help show this help message and exit -i, --archive= Path to a COMBINE/OMEX archive file which contains one or more SED-ML-encoded simulation experiments -o, --out-dir= Directory to save outputs -q, --quiet suppress all console output -v, --version show program's version number and exit ``` ``` Command-line interface should support the `--help` option for displaying help inline. The command-line interface displayed the following when executed with `--help`: docker: Command recieved::<--help> <--help> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} Usage: CLIStandalone biosimulations [-dhqv] [-i=] [-o=] BioSimulators-compliant command-line interface to the vcell simulation program . -d, --debug full application debug mode -h, --help show this help message and exit -i, --archive= Path to a COMBINE/OMEX archive file which contains one or more SED-ML-encoded simulation experiments -o, --out-dir= Directory to save outputs -q, --quiet suppress all console output -v, --version show program's version number and exit ``` Log: None
docker_image.DeclaresSupportedEnvironmentVariables (0.5 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.5 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 2 months 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 (0.0 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``). Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (0.0 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: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.0 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsComputeModelChanges (0.0 s)
Test that a simulator supports compute model changes Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (0.0 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsDataSetsWithDifferentShapes (0.0 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsModelAttributeChanges (0.0 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithChanges (0.0 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (0.0 s)
Test that a simulator supports repeated tasks over functional ranges Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (0.0 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (0.0 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (0.0 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (0.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (0.0 s)
Test that a simulator supports nested repeated tasks Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (0.0 s)
Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their ``order`` attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes. Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (0.0 s)
Test that a simulator supports repeated tasks over vector ranges Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsSubstitutingAlgorithms (0.0 s)
Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.SAME_METHOD`. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.NONE`. Reason for skip: ``` No module named 'libsbml' ``` Log: None
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (0.0 s)
Test that a simulator supports multiple time courses with non-zero initial times Reason for skip: ``` No module named 'libsbml' ``` Log: None
biosimulators-daemon commented 2 months 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/10723742251). 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/10723742251).
biosimulators-daemon commented 2 months ago

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

The BioSimulators validator bot is validating the specifications of your simulator, and validating your Docker image. You have chosen not to submit your simulator to the BioSimulators registry.

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

A complete log of your simulator validation 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 months ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 months ago

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

The BioSimulators validator bot is validating the specifications of your simulator, and validating your Docker image. You have chosen not to submit your simulator to the BioSimulators registry.

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

A complete log of your simulator validation 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 months ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 months ago

Summary of tests

biosimulators-daemon commented 2 months ago

Failures

docker_image.SingularityImageExecutesSimulationsSuccessfully (19.4 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Exception: ``` The Docker image could not be successfully executed as a Singularity image: ``` Log: None
biosimulators-daemon commented 2 months ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (2.3 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 (4.1 s)
Test that a command-line interface provides inline help. Warnings: ``` Command-line interfaces should display basic help when no arguments are provided. The command-line interface displayed the following when no argument was provided: docker: Command recieved::<> <> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} ERROR (BiosimulationsCommand:116) - Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null []{} java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null at org.vcell.cli.CLIRecorder.(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:50) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ``` ``` Command-line interface should support the `-h` option for displaying help inline. The command-line interface displayed the following when executed with `-h`: docker: Command recieved::<-h> <-h> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} Usage: CLIStandalone biosimulations [-dhqv] [-i=] [-o=] BioSimulators-compliant command-line interface to the vcell simulation program . -d, --debug full application debug mode -h, --help show this help message and exit -i, --archive= Path to a COMBINE/OMEX archive file which contains one or more SED-ML-encoded simulation experiments -o, --out-dir= Directory to save outputs -q, --quiet suppress all console output -v, --version show program's version number and exit ``` ``` Command-line interface should support the `--help` option for displaying help inline. The command-line interface displayed the following when executed with `--help`: docker: Command recieved::<--help> <--help> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} Usage: CLIStandalone biosimulations [-dhqv] [-i=] [-o=] BioSimulators-compliant command-line interface to the vcell simulation program . -d, --debug full application debug mode -h, --help show this help message and exit -i, --archive= Path to a COMBINE/OMEX archive file which contains one or more SED-ML-encoded simulation experiments -o, --out-dir= Directory to save outputs -q, --quiet suppress all console output -v, --version show program's version number and exit ``` Log: None
docker_image.DeclaresSupportedEnvironmentVariables (0.2 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.2 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 2 months ago

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000030 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9012`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9012) Algorithm: [`KISAO_0000669`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000669) Reason for skip: ``` Case requires model formats format_9012 and simulation algorithms KISAO_0000669 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000088`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000088 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) Reason for skip: ``` Case requires model formats format_9001 and simulation algorithms KISAO_0000057 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9010 and simulation algorithms KISAO_0000019 ``` Log: None
sedml.SimulatorProducesLinear3DPlots (0.3 s)
Test that a simulator produces linear 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (0.3 s)
Test that a simulator produces logarithmic 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsComputeModelChanges (18.3 s)
Test that a simulator supports compute model changes Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.5.0.127' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:92) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:133) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:87) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_a906e78c-75f4-4a59-875e-5ed1f904097717930462654316447638 []{} INFO (SedmlJob:110) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more INFO (SedmlJob:298) - Generating outputs... []{} INFO (SedmlJob:388) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:134) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:462) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document. []{} ERROR (ExecutionJob:145) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@113dcaf8 []{} INFO (NativeLib:33) - Loading jhdf5 []{} INFO (Hdf5Writer:44) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:117) - HDF5 file successfully written to. []{} INFO (ExecutionJob:173) - Omex archive.omex processing completed (4s) []{} ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{} | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:92) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:133) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:87) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_b097ca99-3293-41ce-9df0-ace1e5f6dad014058611461565614616 []{} INFO (SedmlJob:110) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more INFO (SedmlJob:298) - Generating outputs... []{} INFO (SedmlJob:388) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:134) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:462) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document. []{} ERROR (ExecutionJob:145) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@5b44318 []{} INFO (NativeLib:33) - Loading jhdf5 []{} INFO (Hdf5Writer:44) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:117) - HDF5 file successfully written to. []{} INFO (ExecutionJob:173) - Omex archive.omex processing completed (4s) []{} ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{} | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: ```
sedml.SimulatorSupportsModelAttributeChanges (18.2 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.5.0.127' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:92) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:133) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:87) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_89c92c36-5189-4315-b7c7-9a642104359c9779641646668195496 []{} INFO (SedmlJob:110) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (StringTools:486) - Could not create an integer from the string x []{} ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more Caused by: java.lang.Exception: Errors reported: IllegalArgumentException occurred: Must be of type int! at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported: IllegalArgumentException occurred: Must be of type int! []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more Caused by: java.lang.Exception: Errors reported: IllegalArgumentException occurred: Must be of type int! at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more INFO (SedmlJob:298) - Generating outputs... []{} INFO (SedmlJob:388) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:134) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:462) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported: IllegalArgumentException occurred: Must be of type int! Failure executing the sed document. []{} ERROR (ExecutionJob:145) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@6e4599c0 []{} INFO (NativeLib:33) - Loading jhdf5 []{} INFO (Hdf5Writer:44) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:117) - HDF5 file successfully written to. []{} INFO (ExecutionJob:173) - Omex archive.omex processing completed (3s) []{} ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{} | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:92) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:133) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:87) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_bd8298f0-0dce-431f-b94d-fb778c1f8d5f15330840965029161799 []{} INFO (SedmlJob:110) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more INFO (SedmlJob:298) - Generating outputs... []{} INFO (SedmlJob:388) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:134) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:462) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(C ...
biosimulators-daemon commented 2 months 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/10730325347). 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/10730325347).
biosimulators-daemon commented 2 months ago

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

The BioSimulators validator bot is validating the specifications of your simulator, and validating your Docker image. You have chosen not to submit your simulator to the BioSimulators registry.

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

A complete log of your simulator validation 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 months ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 months ago

Summary of tests

biosimulators-daemon commented 2 months ago

Failures

docker_image.SingularityImageExecutesSimulationsSuccessfully (19.0 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Exception: ``` The Docker image could not be successfully executed as a Singularity image (error code 1: docker: Command recieved::<-i /root/archive.omex -o /root> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:92) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} ERROR (BiosimulationsCommand:116) - Python error caught: < Traceback (most recent call last): File "", line 1, in File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/wrapper.py", line 5, in from deprecated import deprecated ModuleNotFoundError: No module named 'deprecated' > []{} org.vcell.cli.PythonStreamException: Python error caught: < Traceback (most recent call last): File "", line 1, in File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/wrapper.py", line 5, in from deprecated import deprecated ModuleNotFoundError: No module named 'deprecated' > at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:287) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:263) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIPythonManager.executeThroughPython(CLIPythonManager.java:192) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIPythonManager.instantiatePythonProcess(CLIPythonManager.java:135) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:94) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ``` Log: None
biosimulators-daemon commented 2 months ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.6 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 (3.9 s)
Test that a command-line interface provides inline help. Warnings: ``` Command-line interfaces should display basic help when no arguments are provided. The command-line interface displayed the following when no argument was provided: docker: Command recieved::<> <> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} ERROR (BiosimulationsCommand:116) - Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null []{} java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null at org.vcell.cli.CLIRecorder.(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:50) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ``` ``` Command-line interface should support the `-h` option for displaying help inline. The command-line interface displayed the following when executed with `-h`: docker: Command recieved::<-h> <-h> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} Usage: CLIStandalone biosimulations [-dhqv] [-i=] [-o=] BioSimulators-compliant command-line interface to the vcell simulation program . -d, --debug full application debug mode -h, --help show this help message and exit -i, --archive= Path to a COMBINE/OMEX archive file which contains one or more SED-ML-encoded simulation experiments -o, --out-dir= Directory to save outputs -q, --quiet suppress all console output -v, --version show program's version number and exit ``` ``` Command-line interface should support the `--help` option for displaying help inline. The command-line interface displayed the following when executed with `--help`: docker: Command recieved::<--help> <--help> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} Usage: CLIStandalone biosimulations [-dhqv] [-i=] [-o=] BioSimulators-compliant command-line interface to the vcell simulation program . -d, --debug full application debug mode -h, --help show this help message and exit -i, --archive= Path to a COMBINE/OMEX archive file which contains one or more SED-ML-encoded simulation experiments -o, --out-dir= Directory to save outputs -q, --quiet suppress all console output -v, --version show program's version number and exit ``` 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 months ago

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000030 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9012`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9012) Algorithm: [`KISAO_0000669`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000669) Reason for skip: ``` Case requires model formats format_9012 and simulation algorithms KISAO_0000669 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000088`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000088 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) Reason for skip: ``` Case requires model formats format_9001 and simulation algorithms KISAO_0000057 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9010 and simulation algorithms KISAO_0000019 ``` Log: None
sedml.SimulatorProducesLinear3DPlots (0.3 s)
Test that a simulator produces linear 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (0.3 s)
Test that a simulator produces logarithmic 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsComputeModelChanges (18.7 s)
Test that a simulator supports compute model changes Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.5.0.127' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:92) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:133) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:87) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_939836f2-0b5c-4615-975c-a90858d6980c3533592077522611061 []{} INFO (SedmlJob:110) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more INFO (SedmlJob:298) - Generating outputs... []{} INFO (SedmlJob:388) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:134) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:462) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document. []{} ERROR (ExecutionJob:145) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@113dcaf8 []{} INFO (NativeLib:33) - Loading jhdf5 []{} INFO (Hdf5Writer:44) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:117) - HDF5 file successfully written to. []{} INFO (ExecutionJob:173) - Omex archive.omex processing completed (4s) []{} ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{} | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:92) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:133) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:87) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_49cb24c2-f21d-4031-b241-9eea2a923aa0163950296337306671 []{} INFO (SedmlJob:110) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more INFO (SedmlJob:298) - Generating outputs... []{} INFO (SedmlJob:388) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:134) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:462) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document. []{} ERROR (ExecutionJob:145) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@389a5022 []{} INFO (NativeLib:33) - Loading jhdf5 []{} INFO (Hdf5Writer:44) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:117) - HDF5 file successfully written to. []{} INFO (ExecutionJob:173) - Omex archive.omex processing completed (4s) []{} ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{} | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: ```
sedml.SimulatorSupportsModelAttributeChanges (18.0 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.5.0.127' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:92) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:133) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:87) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_70fafc3f-c96e-4bd0-ab64-27f93d26e91212718491599402430933 []{} INFO (SedmlJob:110) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (StringTools:486) - Could not create an integer from the string x []{} ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more Caused by: java.lang.Exception: Errors reported: IllegalArgumentException occurred: Must be of type int! at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported: IllegalArgumentException occurred: Must be of type int! []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more Caused by: java.lang.Exception: Errors reported: IllegalArgumentException occurred: Must be of type int! at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more INFO (SedmlJob:298) - Generating outputs... []{} INFO (SedmlJob:388) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:134) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:462) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported: IllegalArgumentException occurred: Must be of type int! Failure executing the sed document. []{} ERROR (ExecutionJob:145) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@3d1f558a []{} INFO (NativeLib:33) - Loading jhdf5 []{} INFO (Hdf5Writer:44) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:117) - HDF5 file successfully written to. []{} INFO (ExecutionJob:173) - Omex archive.omex processing completed (3s) []{} ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{} | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:92) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:133) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:87) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_41d25c04-e49e-42f7-a17a-5d22c043b1e64352386626755526100 []{} INFO (SedmlJob:110) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more INFO (SedmlJob:298) - Generating outputs... []{} INFO (SedmlJob:388) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:134) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:462) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(Com ...
biosimulators-daemon commented 2 months 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/10730325347). 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/10730325347).
biosimulators-daemon commented 2 months ago

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

The BioSimulators validator bot is validating the specifications of your simulator, and validating your Docker image. You have chosen not to submit your simulator to the BioSimulators registry.

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

A complete log of your simulator validation 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 months ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 months ago

Summary of tests

biosimulators-daemon commented 2 months ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.5 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 (3.7 s)
Test that a command-line interface provides inline help. Warnings: ``` Command-line interfaces should display basic help when no arguments are provided. The command-line interface displayed the following when no argument was provided: docker: Command recieved::<> <> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} ERROR (BiosimulationsCommand:116) - Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null []{} java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null at org.vcell.cli.CLIRecorder.(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:50) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ``` ``` Command-line interface should support the `-h` option for displaying help inline. The command-line interface displayed the following when executed with `-h`: docker: Command recieved::<-h> <-h> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} Usage: CLIStandalone biosimulations [-dhqv] [-i=] [-o=] BioSimulators-compliant command-line interface to the vcell simulation program . -d, --debug full application debug mode -h, --help show this help message and exit -i, --archive= Path to a COMBINE/OMEX archive file which contains one or more SED-ML-encoded simulation experiments -o, --out-dir= Directory to save outputs -q, --quiet suppress all console output -v, --version show program's version number and exit ``` ``` Command-line interface should support the `--help` option for displaying help inline. The command-line interface displayed the following when executed with `--help`: docker: Command recieved::<--help> <--help> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} Usage: CLIStandalone biosimulations [-dhqv] [-i=] [-o=] BioSimulators-compliant command-line interface to the vcell simulation program . -d, --debug full application debug mode -h, --help show this help message and exit -i, --archive= Path to a COMBINE/OMEX archive file which contains one or more SED-ML-encoded simulation experiments -o, --out-dir= Directory to save outputs -q, --quiet suppress all console output -v, --version show program's version number and exit ``` 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 months 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/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) Reason for skip: ``` Case requires model formats format_9001 and simulation algorithms KISAO_0000057 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9010 and simulation algorithms KISAO_0000019 ``` Log: None
sedml.SimulatorProducesLinear3DPlots (0.3 s)
Test that a simulator produces linear 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (0.3 s)
Test that a simulator produces logarithmic 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsComputeModelChanges (18.7 s)
Test that a simulator supports compute model changes Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.5.0.127' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:92) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:133) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:87) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_e70d6f10-b1e2-4838-9351-314640d1ee3d1132066174296478264 []{} INFO (SedmlJob:110) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more INFO (SedmlJob:298) - Generating outputs... []{} INFO (SedmlJob:388) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:134) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:462) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document. []{} ERROR (ExecutionJob:145) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@1600a8a2 []{} INFO (NativeLib:33) - Loading jhdf5 []{} INFO (Hdf5Writer:44) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:117) - HDF5 file successfully written to. []{} INFO (ExecutionJob:173) - Omex archive.omex processing completed (4s) []{} ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{} | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:92) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:133) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:87) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_74c1d8e5-bfb2-496e-849b-41f68ec7d7e914642700589990380592 []{} INFO (SedmlJob:110) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more INFO (SedmlJob:298) - Generating outputs... []{} INFO (SedmlJob:388) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:134) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:462) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document. []{} ERROR (ExecutionJob:145) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@4217bce6 []{} INFO (NativeLib:33) - Loading jhdf5 []{} INFO (Hdf5Writer:44) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:117) - HDF5 file successfully written to. []{} INFO (ExecutionJob:173) - Omex archive.omex processing completed (4s) []{} ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{} | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: ```
sedml.SimulatorSupportsModelAttributeChanges (17.9 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.5.0.127' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:92) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:133) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:87) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_466cd8b0-2563-421f-aa44-0c883f6ee0de16019010358496739173 []{} INFO (SedmlJob:110) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (StringTools:486) - Could not create an integer from the string x []{} ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more Caused by: java.lang.Exception: Errors reported: IllegalArgumentException occurred: Must be of type int! at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported: IllegalArgumentException occurred: Must be of type int! []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more Caused by: java.lang.Exception: Errors reported: IllegalArgumentException occurred: Must be of type int! at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more INFO (SedmlJob:298) - Generating outputs... []{} INFO (SedmlJob:388) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:134) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:462) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported: IllegalArgumentException occurred: Must be of type int! Failure executing the sed document. []{} ERROR (ExecutionJob:145) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@765d55d5 []{} INFO (NativeLib:33) - Loading jhdf5 []{} INFO (Hdf5Writer:44) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:117) - HDF5 file successfully written to. []{} INFO (ExecutionJob:173) - Omex archive.omex processing completed (3s) []{} ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{} | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:92) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:133) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:87) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_6c74ce0b-1b41-42a2-8b2d-f693d103686816192275852969288955 []{} INFO (SedmlJob:110) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more INFO (SedmlJob:298) - Generating outputs... []{} INFO (SedmlJob:388) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:134) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:462) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@lev ...
biosimulators-daemon commented 2 months ago

The image for your simulator is valid!

biosimulators-daemon commented 2 months ago

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

The BioSimulators validator bot is validating the specifications of your simulator, and validating your Docker image. You have chosen not to submit your simulator to the BioSimulators registry.

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

A complete log of your simulator validation 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 months ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 months ago

Summary of tests

biosimulators-daemon commented 2 months ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.4 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 (3.5 s)
Test that a command-line interface provides inline help. Warnings: ``` Command-line interfaces should display basic help when no arguments are provided. The command-line interface displayed the following when no argument was provided: docker: Command recieved::<> <> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} ERROR (BiosimulationsCommand:116) - Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null []{} java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null at org.vcell.cli.CLIRecorder.(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:50) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ``` ``` Command-line interface should support the `-h` option for displaying help inline. The command-line interface displayed the following when executed with `-h`: docker: Command recieved::<-h> <-h> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} Usage: CLIStandalone biosimulations [-dhqv] [-i=] [-o=] BioSimulators-compliant command-line interface to the vcell simulation program . -d, --debug full application debug mode -h, --help show this help message and exit -i, --archive= Path to a COMBINE/OMEX archive file which contains one or more SED-ML-encoded simulation experiments -o, --out-dir= Directory to save outputs -q, --quiet suppress all console output -v, --version show program's version number and exit ``` ``` Command-line interface should support the `--help` option for displaying help inline. The command-line interface displayed the following when executed with `--help`: docker: Command recieved::<--help> <--help> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} Usage: CLIStandalone biosimulations [-dhqv] [-i=] [-o=] BioSimulators-compliant command-line interface to the vcell simulation program . -d, --debug full application debug mode -h, --help show this help message and exit -i, --archive= Path to a COMBINE/OMEX archive file which contains one or more SED-ML-encoded simulation experiments -o, --out-dir= Directory to save outputs -q, --quiet suppress all console output -v, --version show program's version number and exit ``` Log: None
docker_image.DeclaresSupportedEnvironmentVariables (0.2 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.2 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 2 months 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/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) Reason for skip: ``` Case requires model formats format_9001 and simulation algorithms KISAO_0000057 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9010 and simulation algorithms KISAO_0000019 ``` Log: None
sedml.SimulatorProducesLinear3DPlots (0.3 s)
Test that a simulator produces linear 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (0.3 s)
Test that a simulator produces logarithmic 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsComputeModelChanges (17.8 s)
Test that a simulator supports compute model changes Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.5.0.127' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:92) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:133) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:87) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_5cb34aa7-eec8-4f60-9d30-75a421d338751054240623270125592 []{} INFO (SedmlJob:110) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more INFO (SedmlJob:298) - Generating outputs... []{} INFO (SedmlJob:388) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:134) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:462) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document. []{} ERROR (ExecutionJob:145) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@1600a8a2 []{} INFO (NativeLib:33) - Loading jhdf5 []{} INFO (Hdf5Writer:44) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:117) - HDF5 file successfully written to. []{} INFO (ExecutionJob:173) - Omex archive.omex processing completed (4s) []{} ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{} | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:92) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:133) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:87) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_fb709f79-76a2-4d19-a9db-2a3e45f6886a16570027545987153061 []{} INFO (SedmlJob:110) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more INFO (SedmlJob:298) - Generating outputs... []{} INFO (SedmlJob:388) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:134) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:462) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document. []{} ERROR (ExecutionJob:145) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@4217bce6 []{} INFO (NativeLib:33) - Loading jhdf5 []{} INFO (Hdf5Writer:44) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:117) - HDF5 file successfully written to. []{} INFO (ExecutionJob:173) - Omex archive.omex processing completed (4s) []{} ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{} | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: ```
sedml.SimulatorSupportsModelAttributeChanges (17.5 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.5.0.127' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:92) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:133) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:87) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_57f6247e-3a27-46d1-83ed-99d4241f271c16544908983757957682 []{} INFO (SedmlJob:110) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (StringTools:486) - Could not create an integer from the string x []{} ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more Caused by: java.lang.Exception: Errors reported: IllegalArgumentException occurred: Must be of type int! at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported: IllegalArgumentException occurred: Must be of type int! []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more Caused by: java.lang.Exception: Errors reported: IllegalArgumentException occurred: Must be of type int! at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more INFO (SedmlJob:298) - Generating outputs... []{} INFO (SedmlJob:388) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:134) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:462) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported: IllegalArgumentException occurred: Must be of type int! Failure executing the sed document. []{} ERROR (ExecutionJob:145) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@2bfb583b []{} INFO (NativeLib:33) - Loading jhdf5 []{} INFO (Hdf5Writer:44) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:117) - HDF5 file successfully written to. []{} INFO (ExecutionJob:173) - Omex archive.omex processing completed (3s) []{} ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{} | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:92) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:133) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:87) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_4d285b5e-7ecc-4468-9339-123a2bedf11a3195949555806686379 []{} INFO (SedmlJob:110) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 18 more INFO (SedmlJob:298) - Generating outputs... []{} INFO (SedmlJob:388) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:61) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:134) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:462) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:141) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:158) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection Xpath for SBML Level (/sbml:sbml[1]/@leve ...