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biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
MIT License
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Submit VCell 7.5.0.37 #631

Closed vcdaemon closed 1 year ago

vcdaemon commented 1 year ago

id: vcell version: 7.5.0.37 specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.5.0.37/biosimulators.json specificationsPatch: version: 7.5.0.37 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.5.0.37 digest: "sha256:47979e5c16f910fcc0cc08f6ef57d109d89245573d31ef4b41ad52bb924bb72c" validateImage: true commitSimulator: true

biosimulators-daemon commented 1 year ago

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

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

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

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

biosimulators-daemon commented 1 year ago

The specifications of your simulator is valid!

biosimulators-daemon commented 1 year ago

Summary of tests

biosimulators-daemon commented 1 year ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (2.8 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 (4.5 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 INFO (CLIStandalone:38) - Starting Vcell... []{} ERROR (BiosimulationsCommand:113) - null []{} java.lang.NullPointerException: null at org.vcell.cli.CLIRecorder.(CLIRecorder.java:68) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:57) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:46) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:51) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ``` ``` 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 INFO (CLIStandalone:38) - 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 INFO (CLIStandalone:38) - 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 (0.5 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 1 year ago

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000030 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9012`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9012) Algorithm: [`KISAO_0000669`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000669) Reason for skip: ``` Case requires model formats format_9012 and simulation algorithms KISAO_0000669 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000088`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000088 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-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 (0.4 s)
Test that a simulator produces linear 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (0.4 s)
Test that a simulator produces logarithmic 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.4 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsComputeModelChanges (24.6 s)
Test that a simulator supports compute model changes Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute INFO (CLIStandalone:38) - Starting Vcell... []{} INFO (PropertyLoader:578) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{} INFO (PropertyLoader:584) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.37 []{} INFO (BiosimulationsCommand:98) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:100) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:507) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej []{} INFO (RunUtils:475) - TempPath Created: /tmp/vcell_temp_c5de0b99-2183-4970-8e3a-56886b18e62b645528340349454135 []{} INFO (SedmlJob:104) - 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:117) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:153) - 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:158) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:162) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:174) - 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:235) - 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:330) - 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:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:237) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:217) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:185) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:118) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 18 more ERROR (SedmlJob:248) - 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:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:237) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:217) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:185) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:118) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 18 more INFO (SedmlJob:268) - Generating outputs... []{} INFO (SedmlJob:356) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:156) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:430) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:293) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:224) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:185) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:118) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] WARN (SedmlJob:301) - 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:143) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@6f911326 []{} INFO (NativeLib:29) - Loading jhdf5 []{} INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{} INFO (ExecutionJob:171) - Omex archive.omex processing completed (5s) []{} docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute INFO (CLIStandalone:38) - Starting Vcell... []{} INFO (PropertyLoader:578) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{} INFO (PropertyLoader:584) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.37 []{} INFO (BiosimulationsCommand:98) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:100) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:507) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej []{} INFO (RunUtils:475) - TempPath Created: /tmp/vcell_temp_1193be8d-0bf5-4ddd-b1aa-6c98fd23ba536111647097444065520 []{} INFO (SedmlJob:104) - 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:117) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:153) - 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:158) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:162) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:174) - 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:235) - 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:330) - 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:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:237) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:217) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:185) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:118) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 18 more ERROR (SedmlJob:248) - 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:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:237) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:217) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:185) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:118) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 18 more INFO (SedmlJob:268) - Generating outputs... []{} INFO (SedmlJob:356) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:156) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:430) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:293) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:224) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:185) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:118) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] WARN (SedmlJob:301) - 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:143) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@7b122839 []{} INFO (NativeLib:29) - Loading jhdf5 []{} INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{} INFO (ExecutionJob:171) - Omex archive.omex processing completed (5s) []{} ```
sedml.SimulatorSupportsModelAttributeChanges (24.5 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute INFO (CLIStandalone:38) - Starting Vcell... []{} INFO (PropertyLoader:578) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{} INFO (PropertyLoader:584) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.37 []{} INFO (BiosimulationsCommand:98) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:100) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:507) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej []{} INFO (RunUtils:475) - TempPath Created: /tmp/vcell_temp_cd963f7e-09f3-414f-a200-dcc78c67c2ab2244786209461183886 []{} INFO (SedmlJob:104) - 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:117) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:153) - 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:158) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:162) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:174) - 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:235) - 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:330) - 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:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:237) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:217) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:185) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:118) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:839) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 18 more Caused by: java.lang.Exception: Errors reported: IllegalArgumentException occurred: Must be of type int! at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:838) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 18 more ERROR (SedmlJob:248) - 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:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:237) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:217) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:185) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:118) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:839) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 18 more Caused by: java.lang.Exception: Errors reported: IllegalArgumentException occurred: Must be of type int! at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:838) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 18 more INFO (SedmlJob:268) - Generating outputs... []{} INFO (SedmlJob:356) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:156) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:430) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:293) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:224) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:185) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:118) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] WARN (SedmlJob:301) - 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:143) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@73386d72 []{} INFO (NativeLib:29) - Loading jhdf5 []{} INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{} INFO (ExecutionJob:171) - Omex archive.omex processing completed (4s) []{} docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute INFO (CLIStandalone:38) - Starting Vcell... []{} INFO (PropertyLoader:578) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{} INFO (PropertyLoader:584) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.37 []{} INFO (BiosimulationsCommand:98) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:100) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:507) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej []{} INFO (RunUtils:475) - TempPath Created: /tmp/vcell_temp_c68e720e-c981-4ceb-aa2f-6a29e923d3042922586069589371360 []{} INFO (SedmlJob:104) - 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:117) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:153) - 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:158) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:162) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:174) - 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:235) - 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:330) - 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:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:237) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:217) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:185) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:118) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 18 more ERROR (SedmlJob:248) - 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:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:237) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:217) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:185) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:118) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] 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:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 18 more INFO (SedmlJob:268) - Generating outputs... []{} INFO (SedmlJob:356) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (NonspatialResultsConverter:156) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{} WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{} WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{} ERROR (SedmlJob:430) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:293) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:224) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:185) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:118) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:102) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.ja ...
biosimulators-daemon commented 1 year ago

The image for your simulator is valid!

biosimulators-daemon commented 1 year ago

The validation/submission of your simulator failed.

- 504 Server Error: Gateway Time-out for url: https://api.biosimulations.org/images/refresh

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).