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Submit VCell 7.7.0.7 #707

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jcschaff opened this issue Nov 7, 2024 · 29 comments
Closed

Submit VCell 7.7.0.7 #707

jcschaff opened this issue Nov 7, 2024 · 29 comments
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Approved Validate/submit simulator Validate a simulation tool or request its submission to the BioSimulators registry Validated

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@jcschaff
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jcschaff commented Nov 7, 2024 •
edited by CodeByDrescher
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id: vcell
version: 7.7.0.7
specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.7.0.7/biosimulators.json
specificationsPatch:
version: 7.7.0.7
image:
url: ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7
digest: "sha256:47620241d9f45eef4bc2ae4579869dacaea1ea629520ab166cd8778afc658293"
validateImage: true
commitSimulator: true
@jcschaff jcschaff added the Validate/submit simulator Validate a simulation tool or request its submission to the BioSimulators registry label Nov 7, 2024
@biosimulators-daemon
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Thank you @jcschaff 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
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The specifications of your simulator is valid!

@biosimulators-daemon
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Summary of tests

  • Executed 74 test cases

  • Passed 8 test cases:

    • cli.CliDescribesSupportedEnvironmentVariablesInline
    • cli.CliDisplaysHelpInline
    • cli.CliDisplaysVersionInformationInline
    • docker_image.DeclaresSupportedEnvironmentVariables
    • docker_image.DefaultUserIsRoot
    • docker_image.HasBioContainersLabels
    • docker_image.HasOciLabels
    • docker_image.SingularityImageExecutesSimulationsSuccessfully

  • Failed 26 test cases:

    • combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
    • combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
    • combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
    • combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
    • 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/Parmar-BMC-Syst-Biol-2017-iron-distribution
    • 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.SimulatorProducesLinear2DPlots
    • sedml.SimulatorProducesLogarithmic2DPlots
    • sedml.SimulatorProducesMultiplePlots
    • sedml.SimulatorSupportsAlgorithmParameters
    • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
    • sedml.SimulatorSupportsMultipleReportsPerSedDocument
    • sedml.SimulatorSupportsMultipleTasksPerSedDocument
    • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

  • Skipped 40 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/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.SimulatorCanResolveModelSourcesDefinedByUriFragments
    • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
    • sedml.SimulatorProducesLinear3DPlots
    • sedml.SimulatorProducesLogarithmic3DPlots
    • sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
    • sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
    • sedml.SimulatorSupportsComputeModelChanges
    • sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
    • sedml.SimulatorSupportsDataSetsWithDifferentShapes
    • 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

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Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (6.0 s)

Test that SED documents in nested directories can be executed

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_6c08b14f-c79a-436a-b701-1eb050ffc74814460595282573942265 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (6.0 s)

Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_ac6d685f-07e5-4c9d-ae6d-d4068b8778726995872997310686966 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (6.0 s)

Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_540bbcac-3ccf-42a9-b9a2-ebd87f6a38e311678898603710670896 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (6.0 s)

Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files.

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_2494aaff-299a-420c-a621-465afa046ada3992512678325046624 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (6.0 s)

Test that simulator logs the execution of COMBINE/OMEX archives

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_be88e133-7bff-47a8-a659-91e867c923f817212834272546219466 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (5.9 s)

Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_d1db1e22-6fdd-4944-9e9c-284273f273981138305137471505004 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (5.9 s)

Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_3374f42e-3c30-4c95-83f8-89399b15f19916650803482323609533 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (5.9 s)

Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_ce648b54-3b65-4b65-85d2-13f97842dbcf15920455319487380012 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (5.9 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_e1c0dff8-5536-4604-8c69-479a9702373313131275715174480900 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex []{}

 | Root(root) | OMEX_EXECUTE(Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (6.1 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_793609b7-f5fe-4c42-a270-1868f056bd075322912117424875926 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex []{}

 | Root(root) | OMEX_EXECUTE(Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (6.0 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_9ad2b029-98c1-4b68-bac5-1c2370a537ae15621726241964701802 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex []{}

 | Root(root) | OMEX_EXECUTE(Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (5.8 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/Elowitz-Nature-2000-Repressilator.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Elowitz-Nature-2000-Repressilator.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate pl ...

@biosimulators-daemon
Copy link

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.7 s)

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

Warnings:

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

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

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

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

Log: None

cli.CliDisplaysHelpInline (4.2 s)

Test that a command-line interface provides inline help.

Warnings:

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

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

  docker: Command recieved::<>
  <>
  Default case selected
  VCell shall execute <biosimulations >
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  ERROR (BiosimulationsCommand:118) - Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null []{}
  java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:53) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  

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

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

  docker: Command recieved::<-h>
  <-h>
  Default case selected
  VCell shall execute <biosimulations -h>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[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>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[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 (0.3 s)

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

Warnings:

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

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

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

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

Log: None

docker_image.HasBioContainersLabels (0.3 s)

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

Warnings:

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

Log: None

@biosimulators-daemon
Copy link

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

Required model formats and simulation algorithms for SED tasks:

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:

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:

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:

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:

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:

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:

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:

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:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:

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:

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:

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:

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:

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:

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:

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:

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:

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (6.0 s)

Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1).

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_897b9540-783b-423d-89d0-e99d5a0969b42590833688905727990 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (5.9 s)

Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1) and inherit the changes of the model.

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_58d032d9-b66f-4493-afd9-a2cf9421a45711357371195743966648 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
sedml.SimulatorProducesLinear3DPlots (0.3 s)

Test that a simulator produces linear 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.3 s)

Test that a simulator produces logarithmic 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (11.9 s)

Test that a simulator supports model changes that involve adding, replacing, and removing model elements.

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_7aa7ea53-5e0a-4a74-92cf-7d378845ae9a7823832000886853925 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

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>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_177f7599-0c83-4e19-940d-01537d12af8a3641130053861013962 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
sedml.SimulatorSupportsComputeModelChanges (12.0 s)

Test that a simulator supports compute model changes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_2de80205-ecda-418d-833f-5c673cb14d0f1021106735253169347 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

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>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_650d55c2-b570-43b8-8c6f-e4022f6dfd885262109790751499754 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (5.9 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_80677158-90d3-4c09-9ed0-3ac9767814b115304312591928566782 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
sedml.SimulatorSupportsDataSetsWithDifferentShapes (5.9 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_e2f928be-b0d8-4693-9033-1abd749645d317050529008376326207 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
sedml.SimulatorSupportsModelAttributeChanges (12.1 s)

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

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_539ea365-bb04-4546-8a0d-4df85845e5a38695807706606524269 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at [email protected]/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

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>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_86828b63-717e-44b5-b3ed-0a14037cb3395688182611506956163 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli ...

@biosimulators-daemon
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- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/11729180129). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/11729180129).

@biosimulators-daemon biosimulators-daemon added the Invalid This doesn't seem right label Nov 7, 2024
@biosimulators-daemon
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Thank you @jcschaff 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 biosimulators-daemon removed the Invalid This doesn't seem right label Nov 11, 2024
@biosimulators-daemon
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The specifications of your simulator is valid!

@biosimulators-daemon
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Summary of tests

  • Executed 74 test cases

  • Passed 8 test cases:

    • cli.CliDescribesSupportedEnvironmentVariablesInline
    • cli.CliDisplaysHelpInline
    • cli.CliDisplaysVersionInformationInline
    • docker_image.DeclaresSupportedEnvironmentVariables
    • docker_image.DefaultUserIsRoot
    • docker_image.HasBioContainersLabels
    • docker_image.HasOciLabels
    • docker_image.SingularityImageExecutesSimulationsSuccessfully

  • Failed 26 test cases:

    • combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
    • combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
    • combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
    • combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
    • 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/Parmar-BMC-Syst-Biol-2017-iron-distribution
    • 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.SimulatorProducesLinear2DPlots
    • sedml.SimulatorProducesLogarithmic2DPlots
    • sedml.SimulatorProducesMultiplePlots
    • sedml.SimulatorSupportsAlgorithmParameters
    • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
    • sedml.SimulatorSupportsMultipleReportsPerSedDocument
    • sedml.SimulatorSupportsMultipleTasksPerSedDocument
    • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

  • Skipped 40 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/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.SimulatorCanResolveModelSourcesDefinedByUriFragments
    • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
    • sedml.SimulatorProducesLinear3DPlots
    • sedml.SimulatorProducesLogarithmic3DPlots
    • sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
    • sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
    • sedml.SimulatorSupportsComputeModelChanges
    • sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
    • sedml.SimulatorSupportsDataSetsWithDifferentShapes
    • 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

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Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (5.7 s)

Test that SED documents in nested directories can be executed

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_c5cacb5e-a861-4b2f-88c1-9c5915cef8ec6617940894336030963 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (5.7 s)

Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_6e18182f-23d1-4b59-be88-aaa10b2e985e6320236766812143475 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (5.8 s)

Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_2f2052bd-b975-47ce-bdb8-a6909f3167b1299266976637282585 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (5.7 s)

Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files.

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_32cd924d-4a78-446c-a7f4-5dfac2d50b6615258777481382463246 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (5.7 s)

Test that simulator logs the execution of COMBINE/OMEX archives

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_ae36da09-b3de-44f3-97bd-f53c46de831212898257477189804307 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (5.6 s)

Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_e05498d5-6ac6-4d85-b7f4-7fc7b47935d07732693997066960068 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (5.7 s)

Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_77aaf1ff-f96a-4c0a-b113-52a163fd849610776622899569038347 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (5.6 s)

Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_37be1fb8-6ea3-4f8a-af03-45aef9a86c2a8558011410236314223 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (5.6 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_df1a649e-ef4c-473a-9883-3029c48ee28212339538195913141463 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex` can not be written to., error for archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex []{}

 | Root(root) | OMEX_EXECUTE(Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex` can not be written to., error for archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex` can not be written to., error for archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (5.6 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_99aad180-c2c6-4a55-b1ff-1c4d1c4f0e674501138301655509629 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex` can not be written to., error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex []{}

 | Root(root) | OMEX_EXECUTE(Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex` can not be written to., error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex` can not be written to., error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (5.6 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_c556ecd2-43d2-4221-a064-a51e3da9f77d17505993282818066414 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex` can not be written to., error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex []{}

 | Root(root) | OMEX_EXECUTE(Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex` can not be written to., error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex` can not be written to., error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (5.6 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/Elowitz-Nature-2000-Repressilator.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Elowitz-Nature-2000-Repressilator.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/Elowitz-Nature-2000-Repressilator.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_c9939bbf-4453-4a4c-8ea3-c4ff232781633939007531968256379 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/Elowitz-Nature-2000-Repressilator.omex` can not be written to., error for archive /tmp/in/Elowitz-Nature-2000-Repressilator.omex []{}

 | Root(root) | OMEX_EXECUTE(Elowitz-Nature-2000-Repressilator.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/Elowitz-Nature-2000-Repressilator.omex` can not be written to., error for archive /tmp/in/Elowitz-Nature-2000-Repressilator.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/Elowitz-Nature-2000-Repressilator.omex` can not be written to., error for archive /tmp/in/Elowitz-Nature-2000-Repressilator.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/Elowitz-Nature-2000-Repressilator.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (5.7 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_b8c88855-45e4-4600-b395-b457a743ff6d16427276601628653523 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex` can not be written to., error for archive /tmp/in/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex []{}

 | Root(root) | OMEX_EXECUTE(Parmar-BMC-Syst-Biol-2017-iron-distribution.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex` can not be written to., error for archive /tmp/in/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex` can not be written to., error for archive /tmp/in/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (5.6 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_ef7990da-e7b0-4df4-b50a-63710ae61a157466861021288300021 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex` can not be written to., error for archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex []{}

 | Root(root) | OMEX_EXECUTE(Vilar-PNAS-2002-minimal-circardian-clock.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex` can not be written to., error for archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex` can not be written to., error for archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (5.6 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in  ...

@biosimulators-daemon
Copy link

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.5 s)

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

Warnings:

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

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

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

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

Log: None

cli.CliDisplaysHelpInline (4.0 s)

Test that a command-line interface provides inline help.

Warnings:

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

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

  docker: Command recieved::<>
  <>
  Default case selected
  VCell shall execute <biosimulations >
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  ERROR (BiosimulationsCommand:118) - Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null []{}
  java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:53) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  

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

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

  docker: Command recieved::<-h>
  <-h>
  Default case selected
  VCell shall execute <biosimulations -h>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[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>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[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 (0.3 s)

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

Warnings:

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

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

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

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

Log: None

docker_image.HasBioContainersLabels (0.2 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
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Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

Required model formats and simulation algorithms for SED tasks:

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:

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:

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:

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:

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:

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:

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:

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:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:

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:

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:

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:

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:

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:

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:

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:

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:

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (5.7 s)

Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1).

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_4d982847-11b7-4ea7-8052-6079bcfbbc7213903971816403119749 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (5.7 s)

Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1) and inherit the changes of the model.

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_a63dd070-1b13-4b18-a8b8-4e09311c6fff5719518865447754535 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
sedml.SimulatorProducesLinear3DPlots (0.3 s)

Test that a simulator produces linear 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.3 s)

Test that a simulator produces logarithmic 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (11.3 s)

Test that a simulator supports model changes that involve adding, replacing, and removing model elements.

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_62cc4d29-25f7-45f4-af11-1505cff85d2a9282755218381829690 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

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>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_84da8ca9-2efb-4b9c-9668-6c35d02d27e711506064895717537430 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
sedml.SimulatorSupportsComputeModelChanges (11.4 s)

Test that a simulator supports compute model changes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_3c9088de-d39f-4e7c-ad65-8032d10196653052588679591081513 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

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>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_d4e082b1-022f-4c38-a2c2-32e0dbe2f8305201489019583848596 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (5.7 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_ff3a349a-f07d-4bcc-a2cb-282f3eaf767711806111798919677447 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
sedml.SimulatorSupportsDataSetsWithDifferentShapes (5.8 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_306f308d-d4cc-46d0-9d49-f05a360893ca4897383425761892311 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
sedml.SimulatorSupportsModelAttributeChanges (11.4 s)

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

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_efaae49f-dc15-4ce3-b2c3-bddf438bd8a44877558334689637207 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

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>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_a767fb8f-0daf-4ca4-89cc-406daaf7f49215038827888380631965 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
sedml.SimulatorSupportsRepeatedTasksWithChanges (11.4 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_514ffa3e-92bf-4fbd-91ea-fe9f0ec2f7739347736276136774260 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

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>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_030d080a-fc7f-4c60-be49-857e9ee2778115192891345122755697 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArgumentException: ZipFile at `/tmp/in/archive.omex` can not be written to.

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:63) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:45) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (11.4 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_0fcf846f-917c-4577-9daa-db5e331d8d9016765677823894994477 []{}

ERROR (ExecutionJob:101) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:118) - ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: ZipFile at `/tmp/in/archive.omex` can not be written to., error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.IllegalArg ...

@biosimulators-daemon
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- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/11780127539). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/11780127539).

@biosimulators-daemon biosimulators-daemon added the Invalid This doesn't seem right label Nov 11, 2024
@biosimulators-daemon
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The validation/submission of your simulator failed.

- expected a single document in the stream
-   in "<unicode string>", line 2, column 1:
-     id: vcell
-     ^
- but found another document
-   in "<unicode string>", line 12, column 1:
-     --- 
-     ^

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
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Thank you @jcschaff 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 biosimulators-daemon removed the Invalid This doesn't seem right label Nov 12, 2024
@biosimulators-daemon
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The specifications of your simulator is valid!

@biosimulators-daemon
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Summary of tests

  • Executed 74 test cases

  • Passed 36 test cases:

    • cli.CliDescribesSupportedEnvironmentVariablesInline
    • cli.CliDisplaysHelpInline
    • cli.CliDisplaysVersionInformationInline
    • 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/Parmar-BMC-Syst-Biol-2017-iron-distribution
    • 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.SimulatorSupportsAddReplaceRemoveModelElementChanges
    • sedml.SimulatorSupportsAlgorithmParameters
    • sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
    • sedml.SimulatorSupportsDataSetsWithDifferentShapes
    • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
    • sedml.SimulatorSupportsMultipleReportsPerSedDocument
    • sedml.SimulatorSupportsMultipleTasksPerSedDocument
    • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

  • Failed 3 test cases:

    • combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
    • combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
    • sedml.SimulatorProducesMultiplePlots

  • Skipped 35 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/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

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Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (8.7 s)

Test that SED documents in nested directories can be executed

Exception:

Simulator did not generate the following expected reports
  - `subdir/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>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_b3ec0b93-ff9a-46e1-8461-ee0e4e5ba31e3583676880360308879 []{}

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_b858028e-1458-41c6-97dd-9f7999d2bcf012263307443879508779 []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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 []{}

taskToSimulationMap: 1

taskToListOfSubTasksMap: 1

taskToVariableMap: 1

topTaskToBaseTask: 1

 INFO (SolverHandler:430) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@3a11c0eb []{}

 INFO (SolverHandler:431) - Status: Finished: SOLVER_FINISHED:completed []{}

 INFO (SolverHandler:477) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. []{}

 INFO (SolverHandler:489) - Running simulation Caravagna2010, 81 ms []{}

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

 INFO (SolverHandler:613) - Ran 1 simulation jobs for 1 biomodels. []{}

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:353) - Generating CSV file...  []{}

 INFO (RunUtils:202) - Generating report `report`. []{}

 INFO (RunUtils:381) - created csv file for report report: /tmp/VCell_CLI_193217ef7d41374789805205609857/subdir/BIOMD0000000912_sim.sedml/report.csv []{}

 INFO (SedmlJob:376) - Generating Plots...  []{}

 INFO (SedmlJob:387) - Generating HDF5 file...  []{}

 INFO (SedmlJob:339) - Archiving result files []{}

 WARN (RunUtils:446) - No PDF files found, skipping archiving `plots.zip` files []{}

 INFO (RunUtils:450) - Archiving resultant CSV files to `reports.zip`. []{}

 INFO (SedmlJob:346) - SED-ML : BIOMD0000000912_sim.sedml successfully completed []{}

 INFO (ExecutionJob:144) - Processing of SedML succeeded.

	> 1 model

	> 1 simulation

	> 1 task

	> 1 output

		>> 1 report

		>> 0 2D plots

		>> 0 3D plots

	> Does not have Math Overrides

	> Does not have Parameter Scans []{}

 INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_193217ef7d41374789805205609857 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:114) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive.omex processing completed (3s) []{}
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (9.2 s)

Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths

Exception:

Simulator did not generate the following expected reports
  - `subdir/BIOMD0000000912_sim.sedml/report`
  - `subdir__copy/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>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_8e24ec2a-1a4b-4261-a5f2-e1f478e5101015956623896362725233 []{}

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_093b75bd-4434-4b1a-a13f-424253653de218046976517442899602 []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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 []{}

taskToSimulationMap: 1

taskToListOfSubTasksMap: 1

taskToVariableMap: 1

topTaskToBaseTask: 1

 INFO (SolverHandler:430) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@7b18658a []{}

 INFO (SolverHandler:431) - Status: Finished: SOLVER_FINISHED:completed []{}

 INFO (SolverHandler:477) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. []{}

 INFO (SolverHandler:489) - Running simulation Caravagna2010, 70 ms []{}

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

 INFO (SolverHandler:613) - Ran 1 simulation jobs for 1 biomodels. []{}

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:353) - Generating CSV file...  []{}

 INFO (RunUtils:202) - Generating report `report`. []{}

 INFO (RunUtils:381) - created csv file for report report: /tmp/VCell_CLI_193217f194a5303066254240240596/subdir/BIOMD0000000912_sim.sedml/report.csv []{}

 INFO (SedmlJob:376) - Generating Plots...  []{}

 INFO (SedmlJob:387) - Generating HDF5 file...  []{}

 INFO (SedmlJob:339) - Archiving result files []{}

 WARN (RunUtils:446) - No PDF files found, skipping archiving `plots.zip` files []{}

 INFO (RunUtils:450) - Archiving resultant CSV files to `reports.zip`. []{}

 INFO (SedmlJob:346) - SED-ML : BIOMD0000000912_sim.sedml successfully completed []{}

 INFO (ExecutionJob:144) - Processing of SedML succeeded.

	> 1 model

	> 1 simulation

	> 1 task

	> 1 output

		>> 1 report

		>> 0 2D plots

		>> 0 3D plots

	> Does not have Math Overrides

	> Does not have Parameter Scans []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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 []{}

taskToSimulationMap: 1

taskToListOfSubTasksMap: 1

taskToVariableMap: 1

topTaskToBaseTask: 1

 INFO (SolverHandler:430) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@7b7068d8 []{}

 INFO (SolverHandler:431) - Status: Finished: SOLVER_FINISHED:completed []{}

 INFO (SolverHandler:477) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. []{}

 INFO (SolverHandler:489) - Running simulation Caravagna2010, 34 ms []{}

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

 INFO (SolverHandler:613) - Ran 1 simulation jobs for 1 biomodels. []{}

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:353) - Generating CSV file...  []{}

 INFO (RunUtils:202) - Generating report `report`. []{}

 INFO (RunUtils:381) - created csv file for report report: /tmp/VCell_CLI_193217f194a5303066254240240596/subdir__copy/BIOMD0000000912_sim.sedml/report.csv []{}

 INFO (SedmlJob:376) - Generating Plots...  []{}

 INFO (SedmlJob:387) - Generating HDF5 file...  []{}

 INFO (SedmlJob:339) - Archiving result files []{}

 WARN (RunUtils:446) - No PDF files found, skipping archiving `plots.zip` files []{}

 INFO (RunUtils:450) - Archiving resultant CSV files to `reports.zip`. []{}

 INFO (SedmlJob:346) - SED-ML : BIOMD0000000912_sim.sedml successfully completed []{}

 INFO (ExecutionJob:144) - Processing of SedML succeeded.

	> 1 model

	> 1 simulation

	> 1 task

	> 1 output

		>> 1 report

		>> 0 2D plots

		>> 0 3D plots

	> Does not have Math Overrides

	> Does not have Parameter Scans []{}

 INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_193217f194a5303066254240240596 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:114) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive.omex processing completed (4s) []{}
sedml.SimulatorProducesMultiplePlots (8.8 s)

Test that a simulator produces multiple plots

Exception:

Simulator did not produce the following plots:
  - `BIOMD0000000912_sim.sedml/plot_0.pdf`

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>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_1826e9d8-a510-44e9-98cd-e526e655dff316723351163857953396 []{}

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_1e0f0393-f656-4121-9ef7-1cf8c3464f482114367475265864888 []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 0  report(s),  2 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

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

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

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

taskToSimulationMap: 1

taskToListOfSubTasksMap: 1

taskToVariableMap: 1

topTaskToBaseTask: 1

 INFO (SolverHandler:430) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@7ab2a07e []{}

 INFO (SolverHandler:431) - Status: Finished: SOLVER_FINISHED:completed []{}

 INFO (SolverHandler:477) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. []{}

 INFO (SolverHandler:489) - Running simulation Caravagna2010, 66 ms []{}

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

 INFO (SolverHandler:613) - Ran 1 simulation jobs for 1 biomodels. []{}

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:353) - Generating CSV file...  []{}

 INFO (RunUtils:196) - Ignoring unsupported output `plot_0` while CSV generation. []{}

 INFO (RunUtils:196) - Ignoring unsupported output `plot_1` while CSV generation. []{}

 INFO (RunUtils:202) - Generating report `__plot__plot_0`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__plot_0: /tmp/VCell_CLI_1932180536f14567245091867755389/BIOMD0000000912_sim.sedml/__plot__plot_0.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__plot_1`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__plot_1: /tmp/VCell_CLI_1932180536f14567245091867755389/BIOMD0000000912_sim.sedml/__plot__plot_1.csv []{}

 INFO (SedmlJob:376) - Generating Plots...  []{}

 INFO (SedmlJob:387) - Generating HDF5 file...  []{}

 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `plot_0` while CSV generation. []{}

 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `plot_1` while CSV generation. []{}

 INFO (SedmlJob:339) - Archiving result files []{}

 INFO (RunUtils:450) - Archiving resultant PDF files to `plots.zip`. []{}

 INFO (RunUtils:450) - Archiving resultant CSV files to `reports.zip`. []{}

 INFO (SedmlJob:346) - SED-ML : BIOMD0000000912_sim.sedml successfully completed []{}

 INFO (ExecutionJob:144) - Processing of SedML succeeded.

	> 1 model

	> 1 simulation

	> 1 task

	> 2 outputs

		>> 0 reports

		>> 2 2D plots

		>> 0 3D plots

	> Does not have Math Overrides

	> Does not have Parameter Scans []{}

 INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_1932180536f14567245091867755389 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:114) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive.omex processing completed (4s) []{}

@biosimulators-daemon
Copy link

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.5 s)

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

Warnings:

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

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

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

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

Log: None

cli.CliDisplaysHelpInline (4.0 s)

Test that a command-line interface provides inline help.

Warnings:

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

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

  docker: Command recieved::<>
  <>
  Default case selected
  VCell shall execute <biosimulations >
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  ERROR (BiosimulationsCommand:118) - Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null []{}
  java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:53) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  

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

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

  docker: Command recieved::<-h>
  <-h>
  Default case selected
  VCell shall execute <biosimulations -h>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[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>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[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 (0.2 s)

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

Warnings:

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

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

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

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

Log: None

docker_image.HasBioContainersLabels (0.2 s)

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

Warnings:

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

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (11.8 s)

Required model formats and simulation algorithms for SED tasks:

Warnings:

Plots were not produced:
  simulation_1.sedml/Figure_3a
  simulation_1.sedml/Figure_3b
  simulation_1.sedml/Figure_3c

Log:

docker: Command recieved::<-i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_a0f6fba7-a321-403b-8b22-5e94556422967969417356350890724 []{}

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_81b6f345-976e-4ab3-947a-1dd8dbfb653718348788115314948224 []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: simulation_1.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  4 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : simulation_1.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R1 to distributed: linear factor was null, lumped reaction R1 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R2 to distributed: linear factor was null, lumped reaction R2 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R3 to distributed: linear factor was null, lumped reaction R3 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R4 to distributed: linear factor was null, lumped reaction R4 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R5 to distributed: linear factor was null, lumped reaction R5 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R6 to distributed: linear factor was null, lumped reaction R6 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R7 to distributed: linear factor was null, lumped reaction R7 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R8 to distributed: linear factor was null, lumped reaction R8 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R9 to distributed: linear factor was null, lumped reaction R9 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R10 to distributed: linear factor was null, lumped reaction R10 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R11 to distributed: linear factor was null, lumped reaction R11 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R12 to distributed: linear factor was null, lumped reaction R12 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R13 to distributed: linear factor was null, lumped reaction R13 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R14 to distributed: linear factor was null, lumped reaction R14 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R15 to distributed: linear factor was null, lumped reaction R15 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R16 to distributed: linear factor was null, lumped reaction R16 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R18 to distributed: linear factor was null, lumped reaction R18 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R19 to distributed: linear factor was null, lumped reaction R19 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R20 to distributed: linear factor was null, lumped reaction R20 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R21 to distributed: linear factor was null, lumped reaction R21 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R22 to distributed: linear factor was null, lumped reaction R22 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R23 to distributed: linear factor was null, lumped reaction R23 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R24 to distributed: linear factor was null, lumped reaction R24 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R25 to distributed: linear factor was null, lumped reaction R25 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R26 to distributed: linear factor was null, lumped reaction R26 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R27 to distributed: linear factor was null, lumped reaction R27 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R28 to distributed: linear factor was null, lumped reaction R28 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R29 to distributed: linear factor was null, lumped reaction R29 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30 to distributed: linear factor was null, lumped reaction R30 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R31 to distributed: linear factor was null, lumped reaction R31 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R32 to distributed: linear factor was null, lumped reaction R32 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R33 to distributed: linear factor was null, lumped reaction R33 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R34 to distributed: linear factor was null, lumped reaction R34 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R35 to distributed: linear factor was null, lumped reaction R35 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R36 to distributed: linear factor was null, lumped reaction R36 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R37 to distributed: linear factor was null, lumped reaction R37 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R38 to distributed: linear factor was null, lumped reaction R38 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R39 to distributed: linear factor was null, lumped reaction R39 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R40 to distributed: linear factor was null, lumped reaction R40 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R41 to distributed: linear factor was null, lumped reaction R41 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R42 to distributed: linear factor was null, lumped reaction R42 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R43 to distributed: linear factor was null, lumped reaction R43 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R44 to distributed: linear factor was null, lumped reaction R44 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R45 to distributed: linear factor was null, lumped reaction R45 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R46 to distributed: linear factor was null, lumped reaction R46 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R47 to distributed: linear factor was null, lumped reaction R47 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R48 to distributed: linear factor was null, lumped reaction R48 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R49 to distributed: linear factor was null, lumped reaction R49 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R50 to distributed: linear factor was null, lumped reaction R50 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R51 to distributed: linear factor was null, lumped reaction R51 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R52 to distributed: linear factor was null, lumped reaction R52 could not be transformed to distributed []{}

 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='task_1') is compatible, solver match found in ontology: 'KISAO:0000086' matched to RungeKuttaFehlberg []{}

taskToSimulationMap: 1

taskToListOfSubTasksMap: 1

taskToVariableMap: 1

topTaskToBaseTask: 1

 INFO (SolverHandler:477) - Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg_simulation_1.sedml_Ciliberto2003_Morphogenesis' Task 'simulation 1'. []{}

 INFO (SolverHandler:489) - Running simulation simulation 1, 680 ms []{}

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

 INFO (SolverHandler:613) - Ran 1 simulation jobs for 1 biomodels. []{}

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:353) - Generating CSV file...  []{}

 INFO (RunUtils:196) - Ignoring unsupported output `Figure_3a` while CSV generation. []{}

 INFO (RunUtils:196) - Ignoring unsupported output `Figure_3b` while CSV generation. []{}

 INFO (RunUtils:196) - Ignoring unsupported output `Figure_3c` while CSV generation. []{}

 INFO (RunUtils:196) - Ignoring unsupported output `Figure_3d` while CSV generation. []{}

 INFO (RunUtils:202) - Generating report `report`. []{}

 INFO (RunUtils:381) - created csv file for report report: /tmp/VCell_CLI_193218549fb11886901492316223430/simulation_1.sedml/report.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__Figure_3a`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__Figure_3a: /tmp/VCell_CLI_193218549fb11886901492316223430/simulation_1.sedml/__plot__Figure_3a.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__Figure_3b`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__Figure_3b: /tmp/VCell_CLI_193218549fb11886901492316223430/simulation_1.sedml/__plot__Figure_3b.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__Figure_3c`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__Figure_3c: /tmp/VCell_CLI_193218549fb11886901492316223430/simulation_1.sedml/__plot__Figure_3c.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__Figure_3d`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__Figure_3d: /tmp/VCell_CLI_193218549fb11886901492316223430/simulation_1.sedml/__plot__Figure_3d.csv []{}

 INFO (SedmlJob:376) - Generating Plots...  []{}

 INFO (SedmlJob:387) - Generating HDF5 file...  []{}

 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `Figure_3a` while CSV generation. []{}

 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `Figure_3b` while CSV generation. []{}

 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `Figure_3c` while CSV generation. []{}

 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `Figure_3d` while CSV generation. []{}

 INFO (SedmlJob:339) - Archiving result files []{}

 INFO (RunUtils:450) - Archiving resultant PDF files to `plots.zip`. []{}

 INFO (RunUtils:450) - Archiving resultant CSV files to `reports.zip`. []{}

 INFO (SedmlJob:346) - SED-ML : simulation_1.sedml successfully completed []{}

 INFO (ExecutionJob:144) - Processing of SedML succeeded.

	> 1 model

	> 1 simulation

	> 1 task

	> 5 outputs

		>> 1 report

		>> 4 2D plots

		>> 0 3D plots

	> Does not have Math Overrides

	> Does not have Parameter Scans []{}

 INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_193218549fb11886901492316223430 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:114) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex processing completed (7s) []{}
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (11.4 s)

Required model formats and simulation algorithms for SED tasks:

Warnings:

Plots were not produced:
  simulation_1.sedml/Figure_3a
  simulation_1.sedml/Figure_3b
  simulation_1.sedml/Figure_3c

Log:

docker: Command recieved::<-i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_b12b435e-2129-4a73-a925-68d14abbc1ac13326701895993570924 []{}

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_f919fe65-3865-4e74-bb19-a022dd15821511956563350962297266 []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: simulation_1.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  4 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : simulation_1.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R1 to distributed: linear factor was null, lumped reaction R1 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R2 to distributed: linear factor was null, lumped reaction R2 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R3 to distributed: linear factor was null, lumped reaction R3 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R4 to distributed: linear factor was null, lumped reaction R4 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R5 to distributed: linear factor was null, lumped reaction R5 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R6 to distributed: linear factor was null, lumped reaction R6 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R7 to distributed: linear factor was null, lumped reaction R7 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R8 to distributed: linear factor was null, lumped reaction R8 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R9 to distributed: linear factor was null, lumped reaction R9 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R10 to distributed: linear factor was null, lumped reaction R10 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R11 to distributed: linear factor was null, lumped reaction R11 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R12 to distributed: linear factor was null, lumped reaction R12 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R13 to distributed: linear factor was null, lumped reaction R13 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R14 to distributed: linear factor was null, lumped reaction R14 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R15 to distributed: linear factor was null, lumped reaction R15 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R16 to distributed: linear factor was null, lumped reaction R16 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R18 to distributed: linear factor was null, lumped reaction R18 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R19 to distributed: linear factor was null, lumped reaction R19 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R20 to distributed: linear factor was null, lumped reaction R20 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R21 to distributed: linear factor was null, lumped reaction R21 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R22 to distributed: linear factor was null, lumped reaction R22 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R23 to distributed: linear factor was null, lumped reaction R23 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R24 to distributed: linear factor was null, lumped reaction R24 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R25 to distributed: linear factor was null, lumped reaction R25 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R26 to distributed: linear factor was null, lumped reaction R26 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R27 to distributed: linear factor was null, lumped reaction R27 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R28 to distributed: linear factor was null, lumped reaction R28 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R29 to distributed: linear factor was null, lumped reaction R29 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R30 to distributed: linear factor was null, lumped reaction R30 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R31 to distributed: linear factor was null, lumped reaction R31 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R32 to distributed: linear factor was null, lumped reaction R32 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R33 to distributed: linear factor was null, lumped reaction R33 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R34 to distributed: linear factor was null, lumped reaction R34 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R35 to distributed: linear factor was null, lumped reaction R35 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R36 to distributed: linear factor was null, lumped reaction R36 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R37 to distributed: linear factor was null, lumped reaction R37 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R38 to distributed: linear factor was null, lumped reaction R38 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R39 to distributed: linear factor was null, lumped reaction R39 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R40 to distributed: linear factor was null, lumped reaction R40 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R41 to distributed: linear factor was null, lumped reaction R41 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R42 to distributed: linear factor was null, lumped reaction R42 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R43 to distributed: linear factor was null, lumped reaction R43 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R44 to distributed: linear factor was null, lumped reaction R44 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R45 to distributed: linear factor was null, lumped reaction R45 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R46 to distributed: linear factor was null, lumped reaction R46 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R47 to distributed: linear factor was null, lumped reaction R47 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R48 to distributed: linear factor was null, lumped reaction R48 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R49 to distributed: linear factor was null, lumped reaction R49 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R50 to distributed: linear factor was null, lumped reaction R50 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R51 to distributed: linear factor was null, lumped reaction R51 could not be transformed to distributed []{}

 WARN (SBMLImporter:2877) - failed to transform lumped reaction R52 to distributed: linear factor was null, lumped reaction R52 could not be transformed to distributed []{}

 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='task_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

taskToSimulationMap: 1

taskToListOfSubTasksMap: 1

taskToVariableMap: 1

topTaskToBaseTask: 1

 INFO (SolverHandler:430) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@4529b266 []{}

 INFO (SolverHandler:431) - Status: Finished: SOLVER_FINISHED:completed []{}

 INFO (SolverHandler:477) - Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous_simulation_1.sedml_Ciliberto2003_Morphogenesis' Task 'simulation 1'. []{}

 INFO (SolverHandler:489) - Running simulation simulation 1, 152 ms []{}

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

 INFO (SolverHandler:613) - Ran 1 simulation jobs for 1 biomodels. []{}

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:353) - Generating CSV file...  []{}

 INFO (RunUtils:196) - Ignoring unsupported output `Figure_3a` while CSV generation. []{}

 INFO (RunUtils:196) - Ignoring unsupported output `Figure_3b` while CSV generation. []{}

 INFO (RunUtils:196) - Ignoring unsupported output `Figure_3c` while CSV generation. []{}

 INFO (RunUtils:196) - Ignoring unsupported output `Figure_3d` while CSV generation. []{}

 INFO (RunUtils:202) - Generating report `report`. []{}

 INFO (RunUtils:381) - created csv file for report report: /tmp/VCell_CLI_193218577fa10289878122042280774/simulation_1.sedml/report.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__Figure_3a`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__Figure_3a: /tmp/VCell_CLI_193218577fa10289878122042280774/simulation_1.sedml/__plot__Figure_3a.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__Figure_3b`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__Figure_3b: /tmp/VCell_CLI_193218577fa10289878122042280774/simulation_1.sedml/__plot__Figure_3b.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__Figure_3c`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__Figure_3c: /tmp/VCell_CLI_193218577fa10289878122042280774/simulation_1.sedml/__plot__Figure_3c.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__Figure_3d`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__Figure_3d: /tmp/VCell_CLI_193218577fa10289878122042280774/simulation_1.sedml/__plot__Figure_3d.csv []{}

 INFO (SedmlJob:376) - Generating Plots...  []{}

 INFO (SedmlJob:387) - Generating HDF5 file...  []{}

 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `Figure_3a` while CSV generation. []{}

 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `Figure_3b` while CSV generation. []{}

 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `Figure_3c` while CSV generation. []{}

 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `Figure_3d` while CSV generation. []{}

 INFO (SedmlJob:339) - Archiving result files []{}

 INFO (RunUtils:450) - Archiving resultant PDF files to `plots.zip`. []{}

 INFO (RunUtils:450) - Archiving resultant CSV files to `reports.zip`. []{}

 INFO (SedmlJob:346) - SED-ML : simulation_1.sedml successfully completed []{}

 INFO (ExecutionJob:144) - Processing of SedML succeeded.

	> 1 model

	> 1 simulation

	> 1 task

	> 5 outputs

		>> 1 report

		>> 4 2D plots

		>> 0 3D plots

	> Does not have Math Overrides

	> Does not have Parameter Scans []{}

 INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_193218577fa10289878122042280774 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:114) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex processing completed (6s) []{}
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (11.0 s)

Required model formats and simulation algorithms for SED tasks:

Warnings:

Plots were not produced:
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3b
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3c
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3d
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3e
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3f
  Parmar2017_Deficient_Rich_tracer.sedml/Figure_3g

Log:

docker: Command recieved::<-i /tmp/in/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_b6e098cb-671e-48f3-87bd-9f5a5895d7121849785798159125231 []{}

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_7fceaa75-805b-43db-a9dc-f8c33158bad81981562721252590588 []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

 INFO (SedmlJob:125) - Processing SED-ML: Parmar2017_Deficient_Rich_tracer.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  7 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : Parmar2017_Deficient_Rich_tracer.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

 INFO (SBMLImporter:966) - adjustExpression(): replacing '___TIME_SYMBOL___' with 't' in (___TIME_SYMBOL___ >= 35.0) []{}

 INFO (AbstractMathMapping:1457) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}

 INFO (AbstractMathMapping:1457) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}

 INFO (AbstractMathMapping:1457) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}

 INFO (AbstractMathMapping:1457) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}

 INFO (AbstractMathMapping:1457) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}

 INFO (AbstractMathMapping:1457) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}

 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='task_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

taskToSimulationMap: 1

taskToListOfSubTasksMap: 1

taskToVariableMap: 1

topTaskToBaseTask: 1

 INFO (SolverHandler:430) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@3dded90a []{}

 INFO (SolverHandler:431) - Status: Finished: SOLVER_FINISHED:completed []{}

 INFO (SolverHandler:477) - Succesful execution: Model 'Parmar-BMC-Syst-Biol-2017-iron-distribution_Parmar2017_Deficient_Rich_tracer.sedml_model' Task 'task_1'. []{}

 INFO (SolverHandler:489) - Running simulation task_1_task_1, 145 ms []{}

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

 INFO (SolverHandler:613) - Ran 1 simulation jobs for 1 biomodels. []{}

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:353) - Generating CSV file...  []{}

 INFO (RunUtils:196) - Ignoring unsupported output `Figure_3b` while CSV generation. []{}

 INFO (RunUtils:196) - Ignoring unsupported output `Figure_3c` while CSV generation. []{}

 INFO (RunUtils:196) - Ignoring unsupported output `Figure_3d` while CSV generation. []{}

 INFO (RunUtils:196) - Ignoring unsupported output `Figure_3e` while CSV generation. []{}

 INFO (RunUtils:196) - Ignoring unsupported output `Figure_3f` while CSV generation. []{}

 INFO (RunUtils:196) - Ignoring unsupported output `Figure_3g` while CSV generation. []{}

 INFO (RunUtils:196) - Ignoring unsupported output `Figure_3h` while CSV generation. []{}

 INFO (RunUtils:202) - Generating report `report`. []{}

 INFO (RunUtils:381) - created csv file for report report: /tmp/VCell_CLI_1932185c90d4951469476099313461/Parmar2017_Deficient_Rich_tracer.sedml/report.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__Figure_3b`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__Figure_3b: /tmp/VCell_CLI_1932185c90d4951469476099313461/Parmar2017_Deficient_Rich_tracer.sedml/__plot__Figure_3b.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__Figure_3c`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__Figure_3c: /tmp/VCell_CLI_1932185c90d4951469476099313461/Parmar2017_Deficient_Rich_tracer.sedml/__plot__Figure_3c.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__Figure_3d`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__Figure_3d: /tmp/VCell_CLI_1932185c90d4951469476099313461/Parmar2017_Deficient_Rich_tracer.sedml/__plot__Figure_3d.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__Figure_3e`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__Figure_3e: /tmp/VCell_CLI_1932185c90d4951469476099313461/Parmar2017_Deficient_Rich_tracer.sedml/__plot__Figure_3e.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__Figure_3f`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__Figure_3f: /tmp/VCell_CLI_1932185c90d4951469476099313461/Parmar2017_Deficient_Rich_tracer.sedml/__plot__Figure_3f.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__Figure_3g`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__Figure_3g: /tmp/VCell_CLI_1932185c90d4951469476099313461/Parmar2017_Deficient_Rich_tracer.sedml/__plot__Figure_3g.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__Figure_3h`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__Figure_3h: /tmp/VCell_CLI_1932185c90d4951469476099313461/Parmar2017_Deficient_Rich_tracer.sedml/__plot__Figure_3h.csv []{}

 INFO (SedmlJob:376) - Generating Plots...  []{}

 INFO (SedmlJob:387) - Generating HDF5 file...  []{}

 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `Figure_3b` while CSV generation. []{}

 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `Figure_3c` while CSV generation. []{}

 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `Figure_3d` while CSV generation. []{}

 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `Figure_3e` while CSV generation. []{}

 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `Figure_3f` while CSV generation. []{}

 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `Figure_3g` while CSV generation. []{}

 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `Figure_3h` while CSV generation. []{}

 INFO (SedmlJob:339) - Archiving result files []{}

 INFO (RunUtils:450) - Archiving resultant PDF files to `plots.zip`. []{}

 INFO (RunUtils:450) - Archiving resultant CSV files to `reports.zip`. []{}

 INFO (SedmlJob:346) - SED-ML : Parmar2017_Deficient_Rich_tracer.sedml successfully completed []{}

 INFO (ExecutionJob:144) - Processing of SedML succeeded.

	> 1 model

	> 1 simulation

	> 1 task

	> 8 outputs

		>> 1 report

		>> 7 2D plots

		>> 0 3D plots

	> Does not have Math Overrides

	> Does not have Parameter Scans []{}

 INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_1932185c90d4951469476099313461 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:114) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex Parmar-BMC-Syst-Biol-2017-iron-distribution.omex processing completed (6s) []{}
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (23.4 s)

Required model formats and simulation algorithms for SED tasks:

Warnings:

Plots were not produced:
  simulation.sedml/plot2d_Euler_small_step_size
  simulation.sedml/plot2d_Fig_1_c
  simulation.sedml/plot2d_Fig_1a
  simulation.sedml/plot2d_low_delta_R_det

Log:

docker: Command recieved::<-i /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_4ebfdd97-599e-4be8-9547-9e6c58c5e60315685216776569772451 []{}

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_35239e56-8f29-4c0a-9389-f63b1dec25813692974956272852788 []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: simulation.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 4 model(s), 5 simulation(s), 5 task(s), 5  report(s),  5 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : simulation.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (AbstractMathMapping:1457) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}

 INFO (AbstractMathMapping:1457) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}

 INFO (AbstractMathMapping:1457) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}

 INFO (AbstractMathMapping:1457) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}

 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='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

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

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

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

 INFO (SEDMLImporter:182) - Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

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

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

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

 INFO (SEDMLImporter:182) - Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler []{}

 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='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson []{}

 WARN (AbstractMathMapping:1740) - expected unit=molecules.s-1, found=tbd []{}

 WARN (AbstractMathMapping:1740) - expected unit=molecules.s-1, found=tbd []{}

 WARN (AbstractMathMapping:1740) - expected unit=molecules.s-1, found=tbd []{}

 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='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson []{}

 WARN (AbstractMathMapping:1740) - expected unit=molecules.s-1, found=tbd []{}

 WARN (AbstractMathMapping:1740) - expected unit=molecules.s-1, found=tbd []{}

 WARN (AbstractMathMapping:1740) - expected unit=molecules.s-1, found=tbd []{}

----comparing model from----BioModel@2d4fb0d8(Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_deterministic) with model from BioModel@52c27d53(Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_stochastic_0)

false

taskToSimulationMap: 5

taskToListOfSubTasksMap: 5

taskToVariableMap: 5

topTaskToBaseTask: 5

 INFO (SolverHandler:430) - Solver: cbit.vcell.solver.stoch.GibsonSolver@7c5c2b17 []{}

 INFO (SolverHandler:431) - Status: Finished: SOLVER_FINISHED:completed []{}

 INFO (SolverHandler:477) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_stochastic_0' Task 'tsk_1_1'. []{}

 INFO (SolverHandler:489) - Running simulation tsk_1_1, 188 ms []{}

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

 INFO (SolverHandler:430) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@2a191f83 []{}

 INFO (SolverHandler:431) - Status: Finished: SOLVER_FINISHED:completed []{}

 INFO (SolverHandler:477) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_deterministic' Task 'tsk_0_0'. []{}

 INFO (SolverHandler:489) - Running simulation tsk_0_0, 89 ms []{}

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

 INFO (SolverHandler:477) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_deterministic' Task 'tsk_0_3'. []{}

 INFO (SolverHandler:489) - Running simulation tsk_0_3, 5504 ms []{}

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

 INFO (SolverHandler:430) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@42150951 []{}

 INFO (SolverHandler:431) - Status: Finished: SOLVER_FINISHED:completed []{}

 INFO (SolverHandler:477) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_deterministic_0' Task 'tsk_0_1'. []{}

 INFO (SolverHandler:489) - Running simulation tsk_0_1, 62 ms []{}

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

 INFO (SolverHandler:430) - Solver: cbit.vcell.solver.stoch.GibsonSolver@5cc152f9 []{}

 INFO (SolverHandler:431) - Status: Finished: SOLVER_FINISHED:completed []{}

 INFO (SolverHandler:477) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_stochastic' Task 'tsk_1_0'. []{}

 INFO (SolverHandler:489) - Running simulation tsk_1_0, 189 ms []{}

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

 INFO (SolverHandler:613) - Ran 5 simulation jobs for 4 biomodels. []{}

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:353) - Generating CSV file...  []{}

 INFO (RunUtils:196) - Ignoring unsupported output `plot2d_Fig_1a` while CSV generation. []{}

 INFO (RunUtils:196) - Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation. []{}

 INFO (RunUtils:196) - Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation. []{}

 INFO (RunUtils:196) - Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation. []{}

 INFO (RunUtils:196) - Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation. []{}

 INFO (RunUtils:202) - Generating report `report_Fig_1a`. []{}

 INFO (RunUtils:381) - created csv file for report report_Fig_1a: /tmp/VCell_CLI_193218652089299241645424527064/simulation.sedml/report_Fig_1a.csv []{}

 INFO (RunUtils:202) - Generating report `report_low_delta_R_det`. []{}

 INFO (RunUtils:381) - created csv file for report report_low_delta_R_det: /tmp/VCell_CLI_193218652089299241645424527064/simulation.sedml/report_low_delta_R_det.csv []{}

 INFO (RunUtils:202) - Generating report `report_Euler_small_step_size`. []{}

 INFO (RunUtils:381) - created csv file for report report_Euler_small_step_size: /tmp/VCell_CLI_193218652089299241645424527064/simulation.sedml/report_Euler_small_step_size.csv []{}

 INFO (RunUtils:202) - Generating report `report_Fig_1_c`. []{}

 INFO (RunUtils:381) - created csv file for report report_Fig_1_c: /tmp/VCell_CLI_193218652089299241645424527064/simulation.sedml/report_Fig_1_c.csv []{}

 INFO (RunUtils:202) - Generating report `report_low_delta_R_stoch`. []{}

 INFO (RunUtils:381) - created csv file for report report_low_delta_R_stoch: /tmp/VCell_CLI_193218652089299241645424527064/simulation.sedml/report_low_delta_R_stoch.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__plot2d_Fig_1a`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__plot2d_Fig_1a: /tmp/VCell_CLI_193218652089299241645424527064/simulation.sedml/__plot__plot2d_Fig_1a.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__plot2d_low_delta_R_det`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__plot2d_low_delta_R_det: /tmp/VCell_CLI_193218652089299241645424527064/simulation.sedml/__plot__plot2d_low_delta_R_det.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__plot2d_Euler_small_step_size`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__plot2d_Euler_small_step_size: /tmp/VCell_CLI_193218652089299241645424527064/simulation.sedml/__plot__plot2d_Euler_small_step_size.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__plot2d_Fig_1_c`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__plot2d_Fig_1_c: /tmp/VCell_CLI_193218652089299241645424527064/simulation.sedml/__plot__plot2d_Fig_1_c.csv []{}

 INFO (RunUtils:202) - Generating report `__plot__plot2d_low_delta_R_stoch`. []{}

 INFO (RunUtils:381) - created csv file for report __plot__plot2d_low_delta_R_stoch: /tmp/VCell_CLI_193218652089299241645424527064/simulation.sedml/__plot__plot2d_low_delt ...

@biosimulators-daemon
Copy link

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

Required model formats and simulation algorithms for SED tasks:

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:

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:

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:

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:

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:

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:

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:

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:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:

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:

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:

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:

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:

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:

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:

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:

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:

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorProducesLinear3DPlots (0.3 s)

Test that a simulator produces linear 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.3 s)

Test that a simulator produces logarithmic 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsComputeModelChanges (18.8 s)

Test that a simulator supports compute model changes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_8f6f7548-7940-4a9d-8aa7-fb3fed500ed75088709189562740748 []{}

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_73992483-ea5e-4d31-b9cf-eb662b44aada14337707271859851403 []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

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

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

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

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

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

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

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

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

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

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

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

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:387) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:461) - Failure executing the sed document.  []{}

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

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

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

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@566c1e71 []{}

 INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_1932180f7bf8589913353286976170 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:114) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive.omex processing completed (4s) []{}

ERROR (BiosimulationsCommand:103) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: 

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_7eb270b4-64d6-4e23-9c14-ecb9589e5b698473522481859898793 []{}

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_85a83381-e7bd-452d-8606-3f2532e377301085410404400698596 []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

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

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

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

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

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

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

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

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

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

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

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

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:387) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:461) - Failure executing the sed document.  []{}

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

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

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

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@1b1252c8 []{}

 INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_19321811bed3397794048633774105 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:114) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive.omex processing completed (4s) []{}

ERROR (BiosimulationsCommand:103) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error:
sedml.SimulatorSupportsModelAttributeChanges (18.3 s)

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

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

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

<-i>

Default case selected

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

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

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

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

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_cd4de931-f300-486f-9af5-e7ac613acc8c3762450252831334376 []{}

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_01c098e7-9e25-4a88-bd20-e3280fa0fb9a11842682223579095050 []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

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

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

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

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

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

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

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

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

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

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

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

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

	... 18 more

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

IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported:

IllegalArgumentException occurred: Must be of type int!

 []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

Caused by: java.lang.Exception: Errors reported:

IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:387) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:461) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported:

IllegalArgumentException occurred: Must be of type int!

Failure executing the sed document.  []{}

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@78a515e4 []{}

 INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_1932181832b7960848086588114549 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:114) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive.omex processing completed (3s) []{}

ERROR (BiosimulationsCommand:103) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: 

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

-----------------------------------------------------------------------------------------------------

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_a869efb4-49e8-42eb-b75a-d28f0350744617913420604256352933 []{}

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_8d80b091-829a-4a85-9820-4e4cc74d7d7b1948006932398106746 []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:387) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:461) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document.  []{}

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@29c1249a []{}

 INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_1932181a3c75218627153004253554 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:114) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive.omex processing completed (5s) []{}

ERROR (BiosimulationsCommand:103) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error:
sedml.SimulatorSupportsRepeatedTasksWithChanges (20.7 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

-----------------------------------------------------------------------------------------------------

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_a54aa4ce-5a91-44d3-b1f6-34867f7623fa16929508273601836645 []{}

 INFO (RunUtils:476) - TempPath  ...

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- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/11802770437). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/11802770437).

@biosimulators-daemon biosimulators-daemon added the Invalid This doesn't seem right label Nov 12, 2024
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Thank you @jcschaff 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 biosimulators-daemon removed the Invalid This doesn't seem right label Nov 15, 2024
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The specifications of your simulator is valid!

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Summary of tests

  • Executed 74 test cases

  • Passed 39 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/Parmar-BMC-Syst-Biol-2017-iron-distribution
    • 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 35 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/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

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Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.5 s)

Test that the inline help for a command-line interface describes the environment variables that the simulator supports.

Warnings:

The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log: None

cli.CliDisplaysHelpInline (4.0 s)

Test that a command-line interface provides inline help.

Warnings:

Command-line interfaces should display basic help when no arguments are provided.

The command-line interface displayed the following when no argument was provided:

  docker: Command recieved::<>
  <>
  Default case selected
  VCell shall execute <biosimulations >
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  ERROR (BiosimulationsCommand:118) - Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null []{}
  java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:53) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  

Command-line interface should support the `-h` option for displaying help inline.

The command-line interface displayed the following when executed with `-h`:

  docker: Command recieved::<-h>
  <-h>
  Default case selected
  VCell shall execute <biosimulations -h>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[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>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[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 (0.2 s)

Test if a Docker image declares the environment variables that is supports

Warnings:

Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log: None

docker_image.HasBioContainersLabels (0.2 s)

Test that a Docker image has BioContainers labels with metadata about the image

Warnings:

Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

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Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

Required model formats and simulation algorithms for SED tasks:

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:

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:

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:

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:

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:

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:

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:

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:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:

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:

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:

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:

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:

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:

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:

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:

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:

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorProducesLinear3DPlots (0.3 s)

Test that a simulator produces linear 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.3 s)

Test that a simulator produces logarithmic 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsComputeModelChanges (18.2 s)

Test that a simulator supports compute model changes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

-----------------------------------------------------------------------------------------------------

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_28cdddc5-0ac7-43a3-846e-29d3776b91462981991617727350536 []{}

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_af5f5a04-6436-4613-b3c6-007f40ff351315946521994805113740 []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:387) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:461) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document.  []{}

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@43c39321 []{}

 INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_19331fe8f923441052858698727281 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:122) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive.omex processing completed (4s) []{}

ERROR (BiosimulationsCommand:103) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: 

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

-----------------------------------------------------------------------------------------------------

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_1ffe3449-a0e6-4ec5-8002-54ae8200efe618299804871291956572 []{}

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_fe0d909f-26d5-464f-bc53-1846c38cf5a715549305267502016812 []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:387) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:461) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document.  []{}

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@652e345 []{}

 INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_19331feb32011744746448924320939 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:122) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive.omex processing completed (4s) []{}

ERROR (BiosimulationsCommand:103) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error:
sedml.SimulatorSupportsModelAttributeChanges (17.2 s)

Test that a simulator supports changes to the attributes of model elements

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

-----------------------------------------------------------------------------------------------------

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_58d76e74-5aed-4254-b1bf-0719a79ff01c90730489515088434 []{}

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_7133807d-97ad-49c9-b841-b56e7aeba4f514608649659632876634 []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (StringTools:486) - Could not create an integer from the string x []{}

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

Caused by: java.lang.Exception: Errors reported:

IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported:

IllegalArgumentException occurred: Must be of type int!

 []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

Caused by: java.lang.Exception: Errors reported:

IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:387) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:461) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported:

IllegalArgumentException occurred: Must be of type int!

Failure executing the sed document.  []{}

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@1fc713c9 []{}

 INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_19331ff17f911497448473974274570 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:122) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive.omex processing completed (3s) []{}

ERROR (BiosimulationsCommand:103) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: 

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

-----------------------------------------------------------------------------------------------------

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_f8cf9420-f0c2-4255-b885-6a759073a7f810617425591774519236 []{}

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_32bb4e80-69ec-4c50-b813-cffc2bc227b97583494619583455521 []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

-----------------------------------------------------------------------------------------------------

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:387) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:461) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document.  []{}

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@4c5f7b4f []{}

 INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_19331ff36ba9796306752960140333 []{}

 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}

 INFO (BiosimulationsHdf5Writer:122) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive.omex processing completed (4s) []{}

ERROR (BiosimulationsCommand:103) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error:
sedml.SimulatorSupportsRepeatedTasksWithChanges (20.0 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:95) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

-----------------------------------------------------------------------------------------------------

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_24db7b5c-aa08-4ea4-b8d0-1272ad451f4f14337294224034587164 []{}

 INFO (RunUtils:476) - TempPath ...

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The image for your simulator is valid!

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Your submission was committed to the BioSimulators registry. Thank you!

Future submissions of subsequent versions of VCell to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.

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