Submit VCell 7.5.0.45 #637

vcdaemon · 2023-06-27T23:35:42Z

id: vcell
version: 7.5.0.45
specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.5.0.45/biosimulators.json
specificationsPatch:
version: 7.5.0.45
image:
url: ghcr.io/virtualcell/biosimulators_vcell:7.5.0.45
digest: "sha256:78ae012e68a32c2d0cb9548079eb5e62b88ab74f0b349cb5fab7580712f7a9e6"
validateImage: true
commitSimulator: true

biosimulators-daemon · 2023-06-27T23:41:54Z

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 · 2023-06-27T23:41:57Z

The specifications of your simulator is valid!

biosimulators-daemon · 2023-06-27T23:59:38Z

Summary of tests

Executed 74 test cases
Passed 38 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
- published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 0 test cases
Skipped 36 test cases:
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
- published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
- published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
- published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
- published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
- published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
- published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
- published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
- published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
- published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsComputeModelChanges
- sedml.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsRepeatedTasksWithChanges
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
- sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
- sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
- sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
- sedml.SimulatorSupportsSubstitutingAlgorithms
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

biosimulators-daemon · 2023-06-27T23:59:39Z

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (2.4 s)

Test that the inline help for a command-line interface describes the environment variables that the simulator supports.

Warnings:

The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log: None

cli.CliDisplaysHelpInline (4.1 s)

Test that a command-line interface provides inline help.

Warnings:

Command-line interfaces should display basic help when no arguments are provided.

The command-line interface displayed the following when no argument was provided:

  docker: Command recieved::<>
  <>
  Default case selected
  VCell shall execute <biosimulations >
   INFO (CLIStandalone:38) - Starting Vcell... []{}
  ERROR (BiosimulationsCommand:112) - null []{}
  java.lang.NullPointerException: null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:51) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Command-line interface should support the `-h` option for displaying help inline.

The command-line interface displayed the following when executed with `-h`:

  docker: Command recieved::<-h>
  <-h>
  Default case selected
  VCell shall execute <biosimulations -h>
   INFO (CLIStandalone:38) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit

Command-line interface should support the `--help` option for displaying help inline.

The command-line interface displayed the following when executed with `--help`:

  docker: Command recieved::<--help>
  <--help>
  Default case selected
  VCell shall execute <biosimulations --help>
   INFO (CLIStandalone:38) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             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 (0.5 s)

Test that a Docker image has BioContainers labels with metadata about the image

Warnings:

Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

biosimulators-daemon · 2023-06-27T23:59:40Z

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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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 (20.8 s)

Test that a simulator supports compute model changes

Reason for skip:

Simulator did not produce the following reports:
  - `BIOMD0000000912_sim.sedml/report`

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:38) - Starting Vcell... []{}

 INFO (PropertyLoader:577) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{}

 INFO (PropertyLoader:583) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.45 []{}

 INFO (BiosimulationsCommand:98) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:119) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:507) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{}

-----------------------------------------------------------------------------------------------------

 INFO (NativeLib:29) - Loading combinej []{}

 INFO (RunUtils:475) - TempPath Created: /tmp/vcell_temp_0de8ef30-df11-4651-95c6-5ceace680b8f5526166590520654601 []{}

 INFO (SedmlJob:107) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:120) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:156) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:161) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:165) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:177) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:238) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:330) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

ERROR (SedmlJob:253) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

 INFO (SedmlJob:273) - Generating outputs...  []{}

 INFO (SedmlJob:361) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:156) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:435) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:298) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 WARN (SedmlJob:306) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document.  []{}

ERROR (ExecutionJob:144) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@4821aa9f []{}

 INFO (NativeLib:29) - Loading jhdf5 []{}

 INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:172) - Omex archive.omex processing completed (4s) []{}

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:38) - Starting Vcell... []{}

 INFO (PropertyLoader:577) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{}

 INFO (PropertyLoader:583) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.45 []{}

 INFO (BiosimulationsCommand:98) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:119) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:507) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{}

-----------------------------------------------------------------------------------------------------

 INFO (NativeLib:29) - Loading combinej []{}

 INFO (RunUtils:475) - TempPath Created: /tmp/vcell_temp_27c1814b-26a8-4b08-b75d-9bb8b386fbda2044931051710631586 []{}

 INFO (SedmlJob:107) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:120) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:156) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:161) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:165) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:177) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:238) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:330) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

ERROR (SedmlJob:253) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

 INFO (SedmlJob:273) - Generating outputs...  []{}

 INFO (SedmlJob:361) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:156) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:435) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:298) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 WARN (SedmlJob:306) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document.  []{}

ERROR (ExecutionJob:144) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@1afd72ef []{}

 INFO (NativeLib:29) - Loading jhdf5 []{}

 INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:172) - Omex archive.omex processing completed (4s) []{}

sedml.SimulatorSupportsModelAttributeChanges (20.5 s)

Test that a simulator supports changes to the attributes of model elements

Reason for skip:

Simulator did not produce the following reports:
  - `BIOMD0000000912_sim.sedml/report`

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:38) - Starting Vcell... []{}

 INFO (PropertyLoader:577) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{}

 INFO (PropertyLoader:583) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.45 []{}

 INFO (BiosimulationsCommand:98) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:119) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:507) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{}

-----------------------------------------------------------------------------------------------------

 INFO (NativeLib:29) - Loading combinej []{}

 INFO (RunUtils:475) - TempPath Created: /tmp/vcell_temp_bbe7d9b9-0b82-46f9-94f9-a888308a6b226502031243516111474 []{}

 INFO (SedmlJob:107) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:120) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:156) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:161) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:165) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:177) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:238) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (StringTools:486) - Could not create an integer from the string x []{}

ERROR (SolverHandler:330) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:839) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

Caused by: java.lang.Exception: Errors reported:

IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:838) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

ERROR (SedmlJob:253) - Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported:

IllegalArgumentException occurred: Must be of type int!

 []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:839) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

Caused by: java.lang.Exception: Errors reported:

IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:838) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

 INFO (SedmlJob:273) - Generating outputs...  []{}

 INFO (SedmlJob:361) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:156) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:435) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:298) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 WARN (SedmlJob:306) - Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported:

IllegalArgumentException occurred: Must be of type int!

Failure executing the sed document.  []{}

ERROR (ExecutionJob:144) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@1f9d6c7b []{}

 INFO (NativeLib:29) - Loading jhdf5 []{}

 INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:172) - Omex archive.omex processing completed (3s) []{}

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:38) - Starting Vcell... []{}

 INFO (PropertyLoader:577) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{}

 INFO (PropertyLoader:583) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.45 []{}

 INFO (BiosimulationsCommand:98) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:119) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:507) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{}

-----------------------------------------------------------------------------------------------------

 INFO (NativeLib:29) - Loading combinej []{}

 INFO (RunUtils:475) - TempPath Created: /tmp/vcell_temp_597a2e7a-11d2-413c-86fe-910ed7ebacd11911019546640128750 []{}

 INFO (SedmlJob:107) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:120) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:156) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:161) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:165) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:177) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:238) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:330) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

ERROR (SedmlJob:253) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

 INFO (SedmlJob:273) - Generating outputs...  []{}

 INFO (SedmlJob:361) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:156) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:435) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:298) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [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.j ...

biosimulators-daemon · 2023-06-27T23:59:41Z

The image for your simulator is valid!

biosimulators-daemon · 2023-06-28T00:00:58Z

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 · 2023-06-28T01:45:43Z

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 · 2023-06-28T01:45:46Z

The specifications of your simulator is valid!

biosimulators-daemon · 2023-06-28T02:06:54Z

Summary of tests

Executed 74 test cases
Passed 38 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
- published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 0 test cases
Skipped 36 test cases:
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
- published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
- published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
- published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
- published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
- published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
- published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
- published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
- published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
- published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsComputeModelChanges
- sedml.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsRepeatedTasksWithChanges
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
- sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
- sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
- sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
- sedml.SimulatorSupportsSubstitutingAlgorithms
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

biosimulators-daemon · 2023-06-28T02:06:55Z

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (3.2 s)

Test that the inline help for a command-line interface describes the environment variables that the simulator supports.

Warnings:

The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log: None

cli.CliDisplaysHelpInline (4.7 s)

Test that a command-line interface provides inline help.

Warnings:

Command-line interfaces should display basic help when no arguments are provided.

The command-line interface displayed the following when no argument was provided:

  docker: Command recieved::<>
  <>
  Default case selected
  VCell shall execute <biosimulations >
   INFO (CLIStandalone:38) - Starting Vcell... []{}
  ERROR (BiosimulationsCommand:112) - null []{}
  java.lang.NullPointerException: null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:51) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Command-line interface should support the `-h` option for displaying help inline.

The command-line interface displayed the following when executed with `-h`:

  docker: Command recieved::<-h>
  <-h>
  Default case selected
  VCell shall execute <biosimulations -h>
   INFO (CLIStandalone:38) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit

Command-line interface should support the `--help` option for displaying help inline.

The command-line interface displayed the following when executed with `--help`:

  docker: Command recieved::<--help>
  <--help>
  Default case selected
  VCell shall execute <biosimulations --help>
   INFO (CLIStandalone:38) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit

Log: None

docker_image.DeclaresSupportedEnvironmentVariables (0.5 s)

Test if a Docker image declares the environment variables that is supports

Warnings:

Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log: None

docker_image.HasBioContainersLabels (0.2 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 · 2023-06-28T02:06:56Z

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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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 (25.4 s)

Test that a simulator supports compute model changes

Reason for skip:

Simulator did not produce the following reports:
  - `BIOMD0000000912_sim.sedml/report`

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:38) - Starting Vcell... []{}

 INFO (PropertyLoader:577) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{}

 INFO (PropertyLoader:583) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.45 []{}

 INFO (BiosimulationsCommand:98) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:119) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:507) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{}

-----------------------------------------------------------------------------------------------------

 INFO (NativeLib:29) - Loading combinej []{}

 INFO (RunUtils:475) - TempPath Created: /tmp/vcell_temp_d078b6af-7fbf-4129-addf-85392aa3b338974094712981555231 []{}

 INFO (SedmlJob:107) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:120) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:156) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:161) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:165) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:177) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:238) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:330) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

ERROR (SedmlJob:253) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

 INFO (SedmlJob:273) - Generating outputs...  []{}

 INFO (SedmlJob:361) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:156) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:435) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:298) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 WARN (SedmlJob:306) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document.  []{}

ERROR (ExecutionJob:144) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@4821aa9f []{}

 INFO (NativeLib:29) - Loading jhdf5 []{}

 INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:172) - Omex archive.omex processing completed (5s) []{}

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:38) - Starting Vcell... []{}

 INFO (PropertyLoader:577) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{}

 INFO (PropertyLoader:583) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.45 []{}

 INFO (BiosimulationsCommand:98) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:119) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:507) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{}

-----------------------------------------------------------------------------------------------------

 INFO (NativeLib:29) - Loading combinej []{}

 INFO (RunUtils:475) - TempPath Created: /tmp/vcell_temp_8f96fee4-fda1-434d-8f73-3d82609dc4a45502113055809360890 []{}

 INFO (SedmlJob:107) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:120) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:156) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:161) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:165) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:177) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:238) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:330) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

ERROR (SedmlJob:253) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

 INFO (SedmlJob:273) - Generating outputs...  []{}

 INFO (SedmlJob:361) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:156) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:435) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:298) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 WARN (SedmlJob:306) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document.  []{}

ERROR (ExecutionJob:144) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@1afd72ef []{}

 INFO (NativeLib:29) - Loading jhdf5 []{}

 INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:172) - Omex archive.omex processing completed (6s) []{}

sedml.SimulatorSupportsModelAttributeChanges (24.6 s)

Test that a simulator supports changes to the attributes of model elements

Reason for skip:

Simulator did not produce the following reports:
  - `BIOMD0000000912_sim.sedml/report`

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:38) - Starting Vcell... []{}

 INFO (PropertyLoader:577) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{}

 INFO (PropertyLoader:583) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.45 []{}

 INFO (BiosimulationsCommand:98) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:119) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:507) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{}

-----------------------------------------------------------------------------------------------------

 INFO (NativeLib:29) - Loading combinej []{}

 INFO (RunUtils:475) - TempPath Created: /tmp/vcell_temp_8be864ee-1cea-4fcd-9d5f-2a208bd8846c491570514760659240 []{}

 INFO (SedmlJob:107) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:120) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:156) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:161) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:165) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:177) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:238) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (StringTools:486) - Could not create an integer from the string x []{}

ERROR (SolverHandler:330) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:839) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

Caused by: java.lang.Exception: Errors reported:

IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:838) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

ERROR (SedmlJob:253) - Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported:

IllegalArgumentException occurred: Must be of type int!

 []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:839) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

Caused by: java.lang.Exception: Errors reported:

IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:838) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

 INFO (SedmlJob:273) - Generating outputs...  []{}

 INFO (SedmlJob:361) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:156) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:435) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:298) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

 WARN (SedmlJob:306) - Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported:

IllegalArgumentException occurred: Must be of type int!

Failure executing the sed document.  []{}

ERROR (ExecutionJob:144) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@1f9d6c7b []{}

 INFO (NativeLib:29) - Loading jhdf5 []{}

 INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:172) - Omex archive.omex processing completed (4s) []{}

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

 INFO (CLIStandalone:38) - Starting Vcell... []{}

 INFO (PropertyLoader:577) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{}

 INFO (PropertyLoader:583) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.45 []{}

 INFO (BiosimulationsCommand:98) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:119) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:507) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{}

-----------------------------------------------------------------------------------------------------

 INFO (NativeLib:29) - Loading combinej []{}

 INFO (RunUtils:475) - TempPath Created: /tmp/vcell_temp_c1bab306-edc9-4877-af12-a48e2474a42a1461440962591846241 []{}

 INFO (SedmlJob:107) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:120) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:156) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:161) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:165) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:177) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:238) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:330) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

ERROR (SedmlJob:253) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:358) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:891) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:303) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	... 18 more

 INFO (SedmlJob:273) - Generating outputs...  []{}

 INFO (SedmlJob:361) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:69) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:156) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:435) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:298) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:204) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:127) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:137) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [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.jav ...

biosimulators-daemon · 2023-06-28T02:06:57Z

The image for your simulator is valid!

biosimulators-daemon · 2023-06-28T02:08:07Z

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).

vcdaemon added the Validate/submit simulator Validate a simulation tool or request its submission to the BioSimulators registry label Jun 27, 2023

biosimulators-daemon added Validated Approved labels Jun 27, 2023

biosimulators-daemon added the Invalid This doesn't seem right label Jun 28, 2023

biosimulators-daemon removed Invalid This doesn't seem right Validated labels Jun 28, 2023

biosimulators-daemon added Validated Invalid This doesn't seem right labels Jun 28, 2023

luciansmith closed this as completed Oct 18, 2024

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Submit VCell 7.5.0.45 #637

Submit VCell 7.5.0.45 #637

vcdaemon commented Jun 27, 2023

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biosimulators-daemon commented Jun 28, 2023

biosimulators-daemon commented Jun 28, 2023

biosimulators-daemon commented Jun 28, 2023

Submit VCell 7.5.0.45 #637

Submit VCell 7.5.0.45 #637

Comments

vcdaemon commented Jun 27, 2023

biosimulators-daemon commented Jun 27, 2023

biosimulators-daemon commented Jun 27, 2023

biosimulators-daemon commented Jun 27, 2023

Summary of tests

biosimulators-daemon commented Jun 27, 2023

Warnings

biosimulators-daemon commented Jun 27, 2023

Skips

biosimulators-daemon commented Jun 27, 2023

biosimulators-daemon commented Jun 28, 2023

biosimulators-daemon commented Jun 28, 2023

biosimulators-daemon commented Jun 28, 2023

biosimulators-daemon commented Jun 28, 2023

Summary of tests

biosimulators-daemon commented Jun 28, 2023

Warnings

biosimulators-daemon commented Jun 28, 2023

Skips

biosimulators-daemon commented Jun 28, 2023

biosimulators-daemon commented Jun 28, 2023