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biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
MIT License
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Submit VCell 7.4.0.68 #589

Closed vcdaemon closed 1 year ago

vcdaemon commented 2 years ago

id: vcell version: 7.4.0.68 specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.4.0.68/biosimulators.json specificationsPatch: version: 7.4.0.68 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.68 digest: "sha256:190a1eed6736057a167ff60ea3698731b157626176b7a9e9e5784c9d032c35d7" validateImage: true commitSimulator: true

biosimulators-daemon commented 2 years ago

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

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

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

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

biosimulators-daemon commented 2 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 years ago

Summary of tests

biosimulators-daemon commented 2 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (2.0 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: /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... ERROR (BiosimulationsCommand:122) - null java.lang.NullPointerException: null at org.vcell.cli.CLIRecorder.(CLIRecorder.java:43) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:39) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:35) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:46) [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:40) [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`: /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute 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`: /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute 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 (3.1 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.2 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 2 years ago

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000030 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9012`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9012) Algorithm: [`KISAO_0000669`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000669) Reason for skip: ``` Case requires model formats format_9012 and simulation algorithms KISAO_0000669 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000088`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000088 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) Reason for skip: ``` Case requires model formats format_9001 and simulation algorithms KISAO_0000057 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9010 and simulation algorithms KISAO_0000019 ``` Log: None
sedml.SimulatorProducesLinear3DPlots (0.3 s)
Test that a simulator produces linear 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (0.3 s)
Test that a simulator produces logarithmic 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsComputeModelChanges (9.7 s)
Test that a simulator supports compute model changes Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_e5165a8d-e74e-4f6e-b01d-74f24c0df0dd3376146329529883349 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - 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 (ExecuteImpl:191) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:231) - 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 (ExecuteImpl:271) - 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 INFO (SBMLImporter:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE ERROR (SEDMLImporter:562) - couldn't find SBase with sid=null in SBMLSymbolMapping WARN (SEDMLImporter:787) - could not map changeAttribute for ID null to a VCell Constant INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@3672276e INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:441) - Running simulation Caravagna2010, 75 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:543) - Ran 1 simulation jobs for 1 biomodels. INFO (ExecuteImpl:308) - Generating outputs... INFO (RunUtils:233) - Generating report `report`. INFO (ExecuteImpl:327) - Generating HDF5 file... INFO (ExecuteImpl:340) - Generating Plots... WARN (CLIPythonManager:65) - Using old style python invocation! INFO (ExecuteImpl:374) - Archiving result files ERROR (RunUtils:529) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils:533) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl:378) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl:386) - Omex archive.omex processing completed (6s) ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (7.5 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpacoklirv/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_c4ab5053-825a-457f-b278-1fccf7b7392f3709502103039362577 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - 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 (ExecuteImpl:191) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:231) - 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 (ExecuteImpl:271) - 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 INFO (SBMLImporter:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 2 taskToListOfSubTasksMap: 2 taskToVariableMap: 2 topTaskToBaseTask: 2 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@6ee8dcd3 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:441) - Running simulation Caravagna2010, 74 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@14379273 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'. INFO (SolverHandler:441) - Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 44 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:543) - Ran 2 simulation jobs for 1 biomodels. INFO (ExecuteImpl:308) - Generating outputs... INFO (RunUtils:233) - Generating report `report`. INFO (ExecuteImpl:327) - Generating HDF5 file... ERROR (ExecuteImpl:344) - 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 15, in execPlotOutputSedDoc cli.exec_plot_output_sed_doc(omexFilePath, idNamePlotsMap, baseOutPath) File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 167, in exec_plot_output_sed_doc data_set_df = pd.read_csv(report_filename, header=None).T File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 581, in _read return parser.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1255, in read index, columns, col_dict = self._engine.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 225, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 805, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1960, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 14 fields in line 5, saw 24 {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv > Result: HDF conversion failed 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 15, in execPlotOutputSedDoc cli.exec_plot_output_sed_doc(omexFilePath, idNamePlotsMap, baseOutPath) File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 167, in exec_plot_output_sed_doc data_set_df = pd.read_csv(report_filename, header=None).T File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 581, in _read return parser.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1255, in read index, columns, col_dict = self._engine.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 225, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 805, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1960, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 14 fields in line 5, saw 24 {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv > Result: HDF conversion failed at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:248) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.PythonCalls.execPlotOutputSedDoc(PythonCalls.java:29) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (4s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithChanges (9.2 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpacoklirv/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_49adceac-de84-4847-8475-21d519b1669e9008966330119623877 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_49adceac-de84-4847-8475-21d519b1669e9008966330119623877/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_28aff2b8-20e1-4f61-a09a-ee00f8c864e73116687205464130084 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_28aff2b8-20e1-4f61-a09a-ee00f8c864e73116687205464130084/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (9.2 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpacoklirv/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_862462c1-443f-4fe3-8977-9d6df6e434f91634616349953316522 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_862462c1-443f-4fe3-8977-9d6df6e434f91634616349953316522/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_2d835c0c-7bcd-4589-aab1-81ef01bb0e717179776378766722314 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_2d835c0c-7bcd-4589-aab1-81ef01bb0e717179776378766722314/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (4.5 s)
Test that a simulator supports repeated tasks over functional ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpacoklirv/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_6f12f2de-fe2c-457b-8c70-a21f99d2a0194412360308735883165 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_6f12f2de-fe2c-457b-8c70-a21f99d2a0194412360308735883165/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (4.5 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpacoklirv/sedml/sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_73a270c5-c837-49b7-8b11-3255bde6fbab8814453993034965728 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_73a270c5-c837-49b7-8b11-3255bde6fbab8814453993034965728/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (4.8 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpacoklirv/sedml/sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_c91735ed-93a9-46e3-8419-2522801719532874953373254182668 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_c91735ed-93a9-46e3-8419-2522801719532874953373254182668/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (4.5 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpacoklirv/sedml/sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_f6b91b3f-fe49-42a2-a75b-f2c8993d588d1743777807174033376 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_f6b91b3f-fe49-42a2-a75b-f2c8993d588d1743777807174033376/ ...
biosimulators-daemon commented 2 years ago

The image for your simulator is valid!

biosimulators-daemon commented 2 years ago

The validation/submission of your simulator failed.

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

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

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

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

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

biosimulators-daemon commented 2 years ago

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

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

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

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

biosimulators-daemon commented 2 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 years ago

Summary of tests

biosimulators-daemon commented 2 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.9 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 (3.6 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: /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... ERROR (BiosimulationsCommand:122) - null java.lang.NullPointerException: null at org.vcell.cli.CLIRecorder.(CLIRecorder.java:43) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:39) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:35) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:46) [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:40) [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`: /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute 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`: /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute 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 (1.6 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.3 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 2 years ago

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000030 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9012`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9012) Algorithm: [`KISAO_0000669`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000669) Reason for skip: ``` Case requires model formats format_9012 and simulation algorithms KISAO_0000669 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000088`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000088 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) Reason for skip: ``` Case requires model formats format_9001 and simulation algorithms KISAO_0000057 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9010 and simulation algorithms KISAO_0000019 ``` Log: None
sedml.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 (9.2 s)
Test that a simulator supports compute model changes Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_a4c7d1e7-7b58-41b9-bb0b-e3ad108204a8445871879407616502 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - 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 (ExecuteImpl:191) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:231) - 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 (ExecuteImpl:271) - 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 INFO (SBMLImporter:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE ERROR (SEDMLImporter:562) - couldn't find SBase with sid=null in SBMLSymbolMapping WARN (SEDMLImporter:787) - could not map changeAttribute for ID null to a VCell Constant INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@3672276e INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:441) - Running simulation Caravagna2010, 68 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:543) - Ran 1 simulation jobs for 1 biomodels. INFO (ExecuteImpl:308) - Generating outputs... INFO (RunUtils:233) - Generating report `report`. INFO (ExecuteImpl:327) - Generating HDF5 file... INFO (ExecuteImpl:340) - Generating Plots... WARN (CLIPythonManager:65) - Using old style python invocation! INFO (ExecuteImpl:374) - Archiving result files ERROR (RunUtils:529) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils:533) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl:378) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl:386) - Omex archive.omex processing completed (6s) ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (7.3 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpaz0q4gha/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_45212c5c-0069-469d-932c-1178aae5251f131172385569003968 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - 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 (ExecuteImpl:191) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:231) - 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 (ExecuteImpl:271) - 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 INFO (SBMLImporter:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 2 taskToListOfSubTasksMap: 2 taskToVariableMap: 2 topTaskToBaseTask: 2 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@6ee8dcd3 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:441) - Running simulation Caravagna2010, 76 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@14379273 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'. INFO (SolverHandler:441) - Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 49 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:543) - Ran 2 simulation jobs for 1 biomodels. INFO (ExecuteImpl:308) - Generating outputs... INFO (RunUtils:233) - Generating report `report`. INFO (ExecuteImpl:327) - Generating HDF5 file... ERROR (ExecuteImpl:344) - 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 15, in execPlotOutputSedDoc cli.exec_plot_output_sed_doc(omexFilePath, idNamePlotsMap, baseOutPath) File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 167, in exec_plot_output_sed_doc data_set_df = pd.read_csv(report_filename, header=None).T File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 581, in _read return parser.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1255, in read index, columns, col_dict = self._engine.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 225, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 805, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1960, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 14 fields in line 5, saw 24 {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv > Result: HDF conversion failed 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 15, in execPlotOutputSedDoc cli.exec_plot_output_sed_doc(omexFilePath, idNamePlotsMap, baseOutPath) File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 167, in exec_plot_output_sed_doc data_set_df = pd.read_csv(report_filename, header=None).T File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 581, in _read return parser.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1255, in read index, columns, col_dict = self._engine.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 225, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 805, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1960, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 14 fields in line 5, saw 24 {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv > Result: HDF conversion failed at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:248) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.PythonCalls.execPlotOutputSedDoc(PythonCalls.java:29) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (4s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithChanges (8.6 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpaz0q4gha/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_0d3f9c4a-0c49-42de-9805-cb7431ce5aff6132386816852463863 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_0d3f9c4a-0c49-42de-9805-cb7431ce5aff6132386816852463863/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_9274921d-d784-45b0-827c-0a696f5b605a8483171700412345202 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_9274921d-d784-45b0-827c-0a696f5b605a8483171700412345202/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (8.7 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpaz0q4gha/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_041c57f8-a1c6-4f2c-a7fa-3b4c46baae946654979560468393045 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_041c57f8-a1c6-4f2c-a7fa-3b4c46baae946654979560468393045/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_c5c94058-d724-4801-8d28-a4e69e6caf2a7341707128173641923 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_c5c94058-d724-4801-8d28-a4e69e6caf2a7341707128173641923/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (4.2 s)
Test that a simulator supports repeated tasks over functional ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpaz0q4gha/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_5b0eb889-9bea-441d-abc5-4156c68aa6e87065346231788222029 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_5b0eb889-9bea-441d-abc5-4156c68aa6e87065346231788222029/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (4.2 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpaz0q4gha/sedml/sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_c6719480-f0a0-499a-b1e9-99a525c8c06b1012858991880157713 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_c6719480-f0a0-499a-b1e9-99a525c8c06b1012858991880157713/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (4.3 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpaz0q4gha/sedml/sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_4f9a2a10-9504-4a8b-8c7a-bc366f845e664869877278072008004 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_4f9a2a10-9504-4a8b-8c7a-bc366f845e664869877278072008004/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (4.3 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpaz0q4gha/sedml/sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_fc8cca1a-d05f-4148-b091-d557d497c11a2284377142081920051 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_fc8cca1a-d05f-4148-b091-d557d497c11a2284377142081920051/BI ...
biosimulators-daemon commented 2 years ago

The image for your simulator is valid!

biosimulators-daemon commented 2 years ago

The validation/submission of your simulator failed.

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

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

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

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

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

biosimulators-daemon commented 2 years ago

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

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

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

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

biosimulators-daemon commented 2 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 years ago

Summary of tests

biosimulators-daemon commented 2 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (3.0 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 (4.7 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: /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... ERROR (BiosimulationsCommand:122) - null java.lang.NullPointerException: null at org.vcell.cli.CLIRecorder.(CLIRecorder.java:43) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:39) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:35) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:46) [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:40) [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`: /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute 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`: /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute 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 (0.7 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.3 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 2 years ago

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000030 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9012`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9012) Algorithm: [`KISAO_0000669`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000669) Reason for skip: ``` Case requires model formats format_9012 and simulation algorithms KISAO_0000669 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000088`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000088 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) Reason for skip: ``` Case requires model formats format_9001 and simulation algorithms KISAO_0000057 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9010 and simulation algorithms KISAO_0000019 ``` Log: None
sedml.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 (11.1 s)
Test that a simulator supports compute model changes Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_0843ab31-0269-4175-ae79-7827a4740d302989734413456027785 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - 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 (ExecuteImpl:191) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:231) - 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 (ExecuteImpl:271) - 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 INFO (SBMLImporter:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE ERROR (SEDMLImporter:562) - couldn't find SBase with sid=null in SBMLSymbolMapping WARN (SEDMLImporter:787) - could not map changeAttribute for ID null to a VCell Constant INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@3672276e INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:441) - Running simulation Caravagna2010, 87 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:543) - Ran 1 simulation jobs for 1 biomodels. INFO (ExecuteImpl:308) - Generating outputs... INFO (RunUtils:233) - Generating report `report`. INFO (ExecuteImpl:327) - Generating HDF5 file... INFO (ExecuteImpl:340) - Generating Plots... WARN (CLIPythonManager:65) - Using old style python invocation! INFO (ExecuteImpl:374) - Archiving result files ERROR (RunUtils:529) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils:533) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl:378) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl:386) - Omex archive.omex processing completed (7s) ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (8.6 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpk2i_ewl8/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_44b94efe-bcd2-430c-b1a3-ed6dc93932fd8820308804588177947 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - 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 (ExecuteImpl:191) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:231) - 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 (ExecuteImpl:271) - 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 INFO (SBMLImporter:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 2 taskToListOfSubTasksMap: 2 taskToVariableMap: 2 topTaskToBaseTask: 2 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@6ee8dcd3 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:441) - Running simulation Caravagna2010, 86 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@14379273 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'. INFO (SolverHandler:441) - Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 46 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:543) - Ran 2 simulation jobs for 1 biomodels. INFO (ExecuteImpl:308) - Generating outputs... INFO (RunUtils:233) - Generating report `report`. INFO (ExecuteImpl:327) - Generating HDF5 file... ERROR (ExecuteImpl:344) - 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 15, in execPlotOutputSedDoc cli.exec_plot_output_sed_doc(omexFilePath, idNamePlotsMap, baseOutPath) File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 167, in exec_plot_output_sed_doc data_set_df = pd.read_csv(report_filename, header=None).T File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 581, in _read return parser.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1255, in read index, columns, col_dict = self._engine.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 225, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 805, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1960, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 14 fields in line 5, saw 24 {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv > Result: HDF conversion failed 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 15, in execPlotOutputSedDoc cli.exec_plot_output_sed_doc(omexFilePath, idNamePlotsMap, baseOutPath) File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 167, in exec_plot_output_sed_doc data_set_df = pd.read_csv(report_filename, header=None).T File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 581, in _read return parser.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1255, in read index, columns, col_dict = self._engine.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 225, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 805, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1960, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 14 fields in line 5, saw 24 {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv > Result: HDF conversion failed at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:248) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.PythonCalls.execPlotOutputSedDoc(PythonCalls.java:29) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (4s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithChanges (10.7 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpk2i_ewl8/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_0265f2d2-ac6e-4cb9-bab7-688a4bb698553723921088454895573 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_0265f2d2-ac6e-4cb9-bab7-688a4bb698553723921088454895573/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_b1eb0a57-df96-46f3-af86-6914ef24dc677669351892785627859 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_b1eb0a57-df96-46f3-af86-6914ef24dc677669351892785627859/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (10.6 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpk2i_ewl8/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_14e821ae-7d40-4f65-bdf1-77c2cf3c9d6f7540915807035546290 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_14e821ae-7d40-4f65-bdf1-77c2cf3c9d6f7540915807035546290/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_5dabfd89-6b32-4c26-9754-9a886dab7e401443125080653310309 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_5dabfd89-6b32-4c26-9754-9a886dab7e401443125080653310309/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (5.2 s)
Test that a simulator supports repeated tasks over functional ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpk2i_ewl8/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_6fbdeb08-74ae-4dbf-8ea8-8403c0f2c63d4597071961875400927 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_6fbdeb08-74ae-4dbf-8ea8-8403c0f2c63d4597071961875400927/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (5.2 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpk2i_ewl8/sedml/sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_f2150a39-fd6f-492e-9384-cdcfe273d8cf2797432126703485690 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_f2150a39-fd6f-492e-9384-cdcfe273d8cf2797432126703485690/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (5.2 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpk2i_ewl8/sedml/sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_65354b22-30db-4c88-9592-96293df621a1605108360163553706 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_65354b22-30db-4c88-9592-96293df621a1605108360163553706/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (5.2 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpk2i_ewl8/sedml/sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_90d7f53f-02c3-428b-89a6-5b5cef9845446880560548946803025 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_90d7f53f-02c3-428b-89a6-5b5cef9845446880560548946803025 ...
biosimulators-daemon commented 2 years ago

The image for your simulator is valid!

biosimulators-daemon commented 2 years ago

The validation/submission of your simulator failed.

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

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

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

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

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

biosimulators-daemon commented 2 years ago

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

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

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

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

biosimulators-daemon commented 2 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 years ago

Summary of tests

biosimulators-daemon commented 2 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (2.7 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 (4.0 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: /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... ERROR (BiosimulationsCommand:122) - null java.lang.NullPointerException: null at org.vcell.cli.CLIRecorder.(CLIRecorder.java:43) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:39) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:35) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:46) [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:40) [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`: /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute 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`: /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute 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 (0.4 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.3 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 2 years ago

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000030 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9012`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9012) Algorithm: [`KISAO_0000669`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000669) Reason for skip: ``` Case requires model formats format_9012 and simulation algorithms KISAO_0000669 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000088`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000088 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) Reason for skip: ``` Case requires model formats format_9001 and simulation algorithms KISAO_0000057 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9010 and simulation algorithms KISAO_0000019 ``` Log: None
sedml.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 (0.3 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 (10.1 s)
Test that a simulator supports compute model changes Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_f61b6612-ddee-4e86-9068-bdc78f70459c3893215672602225377 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - 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 (ExecuteImpl:191) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:231) - 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 (ExecuteImpl:271) - 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 INFO (SBMLImporter:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE ERROR (SEDMLImporter:562) - couldn't find SBase with sid=null in SBMLSymbolMapping WARN (SEDMLImporter:787) - could not map changeAttribute for ID null to a VCell Constant INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@3672276e INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:441) - Running simulation Caravagna2010, 85 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:543) - Ran 1 simulation jobs for 1 biomodels. INFO (ExecuteImpl:308) - Generating outputs... INFO (RunUtils:233) - Generating report `report`. INFO (ExecuteImpl:327) - Generating HDF5 file... INFO (ExecuteImpl:340) - Generating Plots... WARN (CLIPythonManager:65) - Using old style python invocation! INFO (ExecuteImpl:374) - Archiving result files ERROR (RunUtils:529) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils:533) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl:378) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl:386) - Omex archive.omex processing completed (6s) ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (7.5 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmppe5vlr10/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_56ae9be6-73b5-4197-bedf-13acc69ece7b784267666532515222 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - 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 (ExecuteImpl:191) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:231) - 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 (ExecuteImpl:271) - 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 INFO (SBMLImporter:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 2 taskToListOfSubTasksMap: 2 taskToVariableMap: 2 topTaskToBaseTask: 2 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@6ee8dcd3 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:441) - Running simulation Caravagna2010, 71 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@14379273 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'. INFO (SolverHandler:441) - Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 37 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:543) - Ran 2 simulation jobs for 1 biomodels. INFO (ExecuteImpl:308) - Generating outputs... INFO (RunUtils:233) - Generating report `report`. INFO (ExecuteImpl:327) - Generating HDF5 file... ERROR (ExecuteImpl:344) - 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 15, in execPlotOutputSedDoc cli.exec_plot_output_sed_doc(omexFilePath, idNamePlotsMap, baseOutPath) File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 167, in exec_plot_output_sed_doc data_set_df = pd.read_csv(report_filename, header=None).T File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 581, in _read return parser.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1255, in read index, columns, col_dict = self._engine.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 225, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 805, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1960, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 14 fields in line 5, saw 24 {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv > Result: HDF conversion failed 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 15, in execPlotOutputSedDoc cli.exec_plot_output_sed_doc(omexFilePath, idNamePlotsMap, baseOutPath) File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 167, in exec_plot_output_sed_doc data_set_df = pd.read_csv(report_filename, header=None).T File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 581, in _read return parser.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1255, in read index, columns, col_dict = self._engine.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 225, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 805, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1960, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 14 fields in line 5, saw 24 {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv > Result: HDF conversion failed at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:248) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.PythonCalls.execPlotOutputSedDoc(PythonCalls.java:29) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (4s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithChanges (9.1 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmppe5vlr10/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_bdda6aae-0d71-42a2-ab9e-27a24da556389153883222339185404 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_bdda6aae-0d71-42a2-ab9e-27a24da556389153883222339185404/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_34843931-7a19-4714-b764-b75856272cec1450867022620374607 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_34843931-7a19-4714-b764-b75856272cec1450867022620374607/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (9.1 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmppe5vlr10/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_4078346b-4151-4099-94dc-cdd6e13688811644388099436354718 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_4078346b-4151-4099-94dc-cdd6e13688811644388099436354718/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_6ece7b69-0972-444b-93f6-b1c4de79c3e65806050898441496224 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_6ece7b69-0972-444b-93f6-b1c4de79c3e65806050898441496224/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (4.4 s)
Test that a simulator supports repeated tasks over functional ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmppe5vlr10/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_085a5286-b0db-43e2-8ffa-ed399b7e199b5095312702794570051 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_085a5286-b0db-43e2-8ffa-ed399b7e199b5095312702794570051/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (4.5 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmppe5vlr10/sedml/sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_0343b0d0-1eb3-416b-875a-5ad82f5a58264787156128399698810 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_0343b0d0-1eb3-416b-875a-5ad82f5a58264787156128399698810/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (4.5 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmppe5vlr10/sedml/sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_eea969db-e67b-4aac-9526-ed25df4b34d01571752082043874215 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_eea969db-e67b-4aac-9526-ed25df4b34d01571752082043874215/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (4.4 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmppe5vlr10/sedml/sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_dd552dd6-70b9-459c-b23e-2ea001c461846446898103524571826 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_dd552dd6-70b9-459c-b23e-2ea001c461846446898103524571826/ ...
biosimulators-daemon commented 2 years ago

The image for your simulator is valid!

biosimulators-daemon commented 2 years ago

The validation/submission of your simulator failed.

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

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

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

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

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

moraru commented 2 years ago

After passing validation final step of building and uploading the singularity image fails due to https://github.com/biosimulators/Biosimulators_test_suite/issues/64

should be re-run after fixing above

biosimulators-daemon commented 2 years ago

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

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

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

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

biosimulators-daemon commented 2 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 years ago

Summary of tests

biosimulators-daemon commented 2 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (4.0 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 (5.8 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: /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... ERROR (BiosimulationsCommand:122) - null java.lang.NullPointerException: null at org.vcell.cli.CLIRecorder.(CLIRecorder.java:43) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:39) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:35) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:46) [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:40) [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`: /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute 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`: /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute 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 (1.4 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (1.1 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 2 years ago

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000030 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9012`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9012) Algorithm: [`KISAO_0000669`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000669) Reason for skip: ``` Case requires model formats format_9012 and simulation algorithms KISAO_0000669 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000088`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000088 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) Reason for skip: ``` Case requires model formats format_9001 and simulation algorithms KISAO_0000057 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9010 and simulation algorithms KISAO_0000019 ``` Log: None
sedml.SimulatorProducesLinear3DPlots (0.5 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 (13.0 s)
Test that a simulator supports compute model changes Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_5fb88cec-31e1-46de-80c5-cbb43ceca4525735342145614217077 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - 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 (ExecuteImpl:191) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:231) - 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 (ExecuteImpl:271) - 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 INFO (SBMLImporter:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE ERROR (SEDMLImporter:562) - couldn't find SBase with sid=null in SBMLSymbolMapping WARN (SEDMLImporter:787) - could not map changeAttribute for ID null to a VCell Constant INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@3672276e INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:441) - Running simulation Caravagna2010, 103 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:543) - Ran 1 simulation jobs for 1 biomodels. INFO (ExecuteImpl:308) - Generating outputs... INFO (RunUtils:233) - Generating report `report`. INFO (ExecuteImpl:327) - Generating HDF5 file... INFO (ExecuteImpl:340) - Generating Plots... WARN (CLIPythonManager:65) - Using old style python invocation! INFO (ExecuteImpl:374) - Archiving result files ERROR (RunUtils:529) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils:533) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl:378) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl:386) - Omex archive.omex processing completed (7s) ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (9.7 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmphmfmjwn8/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_bc866238-0aeb-44e4-9be9-4d177926938a7516058548143991960 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - 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 (ExecuteImpl:191) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:215) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:219) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:231) - 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 (ExecuteImpl:271) - 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 INFO (SBMLImporter:3242) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:217) - Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 2 taskToListOfSubTasksMap: 2 taskToVariableMap: 2 topTaskToBaseTask: 2 INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@6ee8dcd3 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:441) - Running simulation Caravagna2010, 93 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:384) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@14379273 INFO (SolverHandler:385) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:429) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'. INFO (SolverHandler:441) - Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 47 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:543) - Ran 2 simulation jobs for 1 biomodels. INFO (ExecuteImpl:308) - Generating outputs... INFO (RunUtils:233) - Generating report `report`. INFO (ExecuteImpl:327) - Generating HDF5 file... ERROR (ExecuteImpl:344) - 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 15, in execPlotOutputSedDoc cli.exec_plot_output_sed_doc(omexFilePath, idNamePlotsMap, baseOutPath) File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 167, in exec_plot_output_sed_doc data_set_df = pd.read_csv(report_filename, header=None).T File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 581, in _read return parser.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1255, in read index, columns, col_dict = self._engine.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 225, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 805, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1960, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 14 fields in line 5, saw 24 {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv > Result: HDF conversion failed 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 15, in execPlotOutputSedDoc cli.exec_plot_output_sed_doc(omexFilePath, idNamePlotsMap, baseOutPath) File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 167, in exec_plot_output_sed_doc data_set_df = pd.read_csv(report_filename, header=None).T File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 581, in _read return parser.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1255, in read index, columns, col_dict = self._engine.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 225, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 805, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1960, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 14 fields in line 5, saw 24 {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv > Result: HDF conversion failed at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:248) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.PythonCalls.execPlotOutputSedDoc(PythonCalls.java:29) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (4s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithChanges (12.3 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmphmfmjwn8/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_eb9f8d49-1e24-4a27-81e8-e3e7a9b75a1e3639528374154117278 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_eb9f8d49-1e24-4a27-81e8-e3e7a9b75a1e3639528374154117278/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_10866051-6675-4899-ad26-3db8a0618b9b1372628713589121055 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_10866051-6675-4899-ad26-3db8a0618b9b1372628713589121055/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (14.1 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmphmfmjwn8/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_7bb3d18f-8972-440a-8794-4c45950987134803198280904479394 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_7bb3d18f-8972-440a-8794-4c45950987134803198280904479394/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_aa1d4c8c-0289-462a-ae02-8501522a16522016147036215399891 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_aa1d4c8c-0289-462a-ae02-8501522a16522016147036215399891/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (6.4 s)
Test that a simulator supports repeated tasks over functional ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmphmfmjwn8/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_2ff4998e-8360-4434-b722-ef2b327a366e2487726734354716853 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_2ff4998e-8360-4434-b722-ef2b327a366e2487726734354716853/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (6.7 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmphmfmjwn8/sedml/sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_8f5b2746-197e-4163-a8ad-9739d84a9f391277534808561115017 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_8f5b2746-197e-4163-a8ad-9739d84a9f391277534808561115017/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (6.5 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmphmfmjwn8/sedml/sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_7d7b8fbf-2ad6-4bad-9f6b-11b515fa5c531670896892910677298 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_7d7b8fbf-2ad6-4bad-9f6b-11b515fa5c531670896892910677298/BIOMD0000000912_sim.sedml failed with error: org.jlibsedml.XMLException: Error reading archive: Error loading sed-ml document : null at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:333) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) [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:40) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:386) - Omex archive.omex processing completed (1s) ERROR (ExecuteImpl:396) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (6.5 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmphmfmjwn8/sedml/sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` /usr/local/app/vcell/installDir/docker_run.sh: line 3: raw_command: command not found VCell shall execute INFO (CLIStandalone:36) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.68 INFO (BiosimulationsCommand:109) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:142) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:559) - TempPath Created: /tmp/vcell_temp_d3abeae1-6c9a-4f30-80d2-cc0bd3c673de594302512492200082 INFO (ExecuteImpl:164) - Preparing output directory... INFO (ExecuteImpl:174) - Initializing SED-ML document... SED-ML version level not supported, import may fail java.lang.NullPointerException at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:290) at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:787) at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:201) at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:364) at org.jlibsedml.Libsedml.readSEDMLArchive(Libsedml.java:317) at org.vcell.cli.run.ExecuteImpl.getSedMLFile(ExecuteImpl.java:415) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:188) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:112) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:40) ERROR (ExecuteImpl:249) - SED-ML processing for /tmp/vcell_temp_d3abeae1-6c9a-4f30-80d2-cc0bd3c673de59430251249220008 ...
biosimulators-daemon commented 2 years ago

The image for your simulator is valid!

biosimulators-daemon commented 2 years ago

The validation/submission of your simulator failed.

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

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

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

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

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