Submit VCell 7.5.0.99
Closed this issue · 7 comments
id: vcell
version: 7.5.0.99
specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.5.0.99/biosimulators.json
specificationsPatch:
version: 7.5.0.99
image:
url: ghcr.io/virtualcell/biosimulators_vcell:7.5.0.99
digest: "sha256:84c1cf7409ef07ea53a220e85cff6b182694b6f781d8f3502a908486d406b97e"
validateImage: true
commitSimulator: true
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.
The specifications of your simulator is valid!
Summary of tests
-
Executed 74 test cases
-
Passed 38 test cases:
cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
docker_image.SingularityImageExecutesSimulationsSuccessfully
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
sedml.SimulatorSupportsDataSetsWithDifferentShapes
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
-
Failed 0 test cases
-
Skipped 36 test cases:
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsComputeModelChanges
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsRepeatedTasksWithChanges
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
sedml.SimulatorSupportsSubstitutingAlgorithms
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline
(3.6 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.
The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
- 'ALGORITHM_SUBSTITUTION_POLICY'
- 'BUNDLE_OUTPUTS'
- 'COLLECT_COMBINE_ARCHIVE_RESULTS'
- 'COLLECT_SED_DOCUMENT_RESULTS'
- 'DEBUG'
- 'H5_REPORTS_PATH'
- 'KEEP_INDIVIDUAL_OUTPUTS'
- 'LOG_PATH'
- 'OMEX_METADATA_INPUT_FORMAT'
- 'OMEX_METADATA_OUTPUT_FORMAT'
- 'OMEX_METADATA_SCHEMA'
- 'PLOTS_PATH'
- 'REPORTS_PATH'
- 'REPORT_FORMATS'
- 'SAVE_PLOT_DATA'
- 'VALIDATE_IMAGES'
- 'VALIDATE_IMPORTED_MODEL_FILES'
- 'VALIDATE_OMEX_MANIFESTS'
- 'VALIDATE_OMEX_METADATA'
- 'VALIDATE_RESULTS'
- 'VALIDATE_SEDML'
- 'VALIDATE_SEDML_MODELS'
- 'VERBOSE'
- 'VIZ_FORMATS'
If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.
Note, support for these environment variables is optional. Simulation tools are not required to support these variables.
Log: None
cli.CliDisplaysHelpInline
(4.1 s)
Test that a command-line interface provides inline help.
Warnings:
Command-line interfaces should display basic help when no arguments are provided.
The command-line interface displayed the following when no argument was provided:
docker: Command recieved::<>
<>
Default case selected
VCell shall execute <biosimulations >
WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
INFO (CLIStandalone:36) - Starting Vcell... []{}
ERROR (BiosimulationsCommand:116) - Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null []{}
java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null
at org.vcell.cli.CLIRecorder.<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:50) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
Command-line interface should support the `-h` option for displaying help inline.
The command-line interface displayed the following when executed with `-h`:
docker: Command recieved::<-h>
<-h>
Default case selected
VCell shall execute <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
(0.7 s)
Test if a Docker image declares the environment variables that is supports
Warnings:
Docker images for simulation tools should declare the environment variables that they support.
The Docker image does not declare the following standard environment variables recognized by BioSimulators:
- 'BUNDLE_OUTPUTS'
- 'COLLECT_COMBINE_ARCHIVE_RESULTS'
- 'COLLECT_SED_DOCUMENT_RESULTS'
- 'DEBUG'
- 'H5_REPORTS_PATH'
- 'KEEP_INDIVIDUAL_OUTPUTS'
- 'LOG_PATH'
- 'OMEX_METADATA_INPUT_FORMAT'
- 'OMEX_METADATA_OUTPUT_FORMAT'
- 'OMEX_METADATA_SCHEMA'
- 'PLOTS_PATH'
- 'REPORTS_PATH'
- 'REPORT_FORMATS'
- 'SAVE_PLOT_DATA'
- 'VALIDATE_IMAGES'
- 'VALIDATE_IMPORTED_MODEL_FILES'
- 'VALIDATE_OMEX_MANIFESTS'
- 'VALIDATE_OMEX_METADATA'
- 'VALIDATE_RESULTS'
- 'VALIDATE_SEDML'
- 'VALIDATE_SEDML_MODELS'
- 'VERBOSE'
- 'VIZ_FORMATS'
If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.
Note, support for these environment variables is optional. Simulation tools are not required to support these variables.
Log: None
docker_image.HasBioContainersLabels
(0.6 s)
Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
Docker images are encouraged to have the following BioContainers labels:
extra.identifiers.biotools
Log: None
Skips
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
(0.0 s)
Required model formats and simulation algorithms for SED tasks:
- Format:
format_3972
Algorithm:KISAO_0000263
Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000263
Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
(0.0 s)
Required model formats and simulation algorithms for SED tasks:
- Format:
format_3972
Algorithm:KISAO_0000019
Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000019
Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
(0.0 s)
Required model formats and simulation algorithms for SED tasks:
- Format:
format_3240
Algorithm:KISAO_0000019
Reason for skip:
Case requires model formats format_3240 and simulation algorithms KISAO_0000019
Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
(0.0 s)
Required model formats and simulation algorithms for SED tasks:
- Format:
format_3240
Algorithm:KISAO_0000019
Reason for skip:
Case requires model formats format_3240 and simulation algorithms KISAO_0000019
Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
(0.0 s)
Required model formats and simulation algorithms for SED tasks:
- Format:
format_2585
Algorithm:KISAO_0000019
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019
Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
(0.0 s)
Required model formats and simulation algorithms for SED tasks:
- Format:
format_9004
Algorithm:KISAO_0000019
Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000019
Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
(0.0 s)
Required model formats and simulation algorithms for SED tasks:
- Format:
format_9004
Algorithm:KISAO_0000030
Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000030
Log: None
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
(0.0 s)
Required model formats and simulation algorithms for SED tasks:
- Format:
format_9012
Algorithm:KISAO_0000669
Reason for skip:
Case requires model formats format_9012 and simulation algorithms KISAO_0000669
Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
(0.0 s)
Required model formats and simulation algorithms for SED tasks:
- Format:
format_2585
Algorithm:KISAO_0000088
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000088
Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
(0.0 s)
Required model formats and simulation algorithms for SED tasks:
- Format:
format_2585
Algorithm:KISAO_000019
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_000019
Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
(0.0 s)
Required model formats and simulation algorithms for SED tasks:
- Format:
format_2585
Algorithm:KISAO_0000496
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000496
Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
(0.0 s)
Required model formats and simulation algorithms for SED tasks:
- Format:
format_2585
Algorithm:KISAO_0000560
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560
Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
(0.0 s)
Required model formats and simulation algorithms for SED tasks:
- Format:
format_2585
Algorithm:KISAO_0000560
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560
Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
(0.0 s)
Required model formats and simulation algorithms for SED tasks:
- Format:
format_2585
Algorithm:KISAO_0000029
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000029
Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
(0.0 s)
Required model formats and simulation algorithms for SED tasks:
- Format:
format_2585
Algorithm:KISAO_0000437
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000437
Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
(0.0 s)
Required model formats and simulation algorithms for SED tasks:
- Format:
format_2585
Algorithm:KISAO_0000449
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000449
Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
(0.0 s)
Required model formats and simulation algorithms for SED tasks:
- Format:
format_2585
Algorithm:KISAO_0000449
Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000449
Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
(0.0 s)
Required model formats and simulation algorithms for SED tasks:
- Format:
format_9001
Algorithm:KISAO_0000057
Reason for skip:
Case requires model formats format_9001 and simulation algorithms KISAO_0000057
Log: None
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
(0.0 s)
Required model formats and simulation algorithms for SED tasks:
- Format:
format_9010
Algorithm:KISAO_0000019
Reason for skip:
Case requires model formats format_9010 and simulation algorithms KISAO_0000019
Log: None
sedml.SimulatorProducesLinear3DPlots
(0.2 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
(0.2 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing
Log: None
sedml.SimulatorSupportsComputeModelChanges
(17.7 s)
Test that a simulator supports compute model changes
Reason for skip:
The image 'ghcr.io/virtualcell/biosimulators_vcell:7.5.0.99' 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:92) - Beginning execution []{}
INFO (CLIPythonManager:116) - Initializing Python... []{}
INFO (CLIPythonManager:136) - Python initialization success! []{}
INFO (ExecuteImpl:126) - Preparing output directory... []{}
ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}
ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}
INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{}
-----------------------------------------------------------------------------------------------------
INFO (NativeLib:33) - Loading combinej []{}
INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_9c8f34b6-9a17-4794-afbf-fe0dbd25a2ab12427587753286010664 []{}
INFO (SedmlJob:109) - 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:124) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}
INFO (SedmlJob:160) - 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:165) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}
-----------------------------------------------------------------------------------------------------
INFO (SedmlJob:169) - Creating pseudo SED-ML for HDF5 conversion... []{}
INFO (SedmlJob:181) - 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:256) - 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:258) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:229) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:134) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:147) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import
at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
... 18 more
ERROR (SedmlJob:272) - 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:258) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:229) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:134) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:147) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import
at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
... 18 more
INFO (SedmlJob:297) - Generating outputs... []{}
INFO (SedmlJob:387) - Generating HDF5 file... []{}
WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}
WARN (SpatialResultsConverter:56) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (SpatialResultsConverter:56) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (SpatialResultsConverter:56) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (SpatialResultsConverter:56) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (SpatialResultsConverter:118) - We encountered non-compatible (or non-existent) data. 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:322) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:243) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:134) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:147) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
WARN (SedmlJob:331) - Unable to initialize bioModel for the given selection
Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document. []{}
ERROR (ExecutionJob:144) - Processing of SedML has failed.
org.vcell.cli.run.SedmlStatistics@177ede17 []{}
INFO (NativeLib:33) - Loading jhdf5 []{}
INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/tmp/out []{}
INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{}
INFO (ExecutionJob:172) - Omex archive.omex processing completed (4s) []{}
ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{}
| Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error:
docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>
<-i>
Default case selected
VCell shall execute <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:92) - Beginning execution []{}
INFO (CLIPythonManager:116) - Initializing Python... []{}
INFO (CLIPythonManager:136) - Python initialization success! []{}
INFO (ExecuteImpl:126) - Preparing output directory... []{}
ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}
ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}
INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{}
-----------------------------------------------------------------------------------------------------
INFO (NativeLib:33) - Loading combinej []{}
INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_50ce68a2-8d66-4140-8084-6587348438798601307137464035124 []{}
INFO (SedmlJob:109) - 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:124) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}
INFO (SedmlJob:160) - 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:165) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}
-----------------------------------------------------------------------------------------------------
INFO (SedmlJob:169) - Creating pseudo SED-ML for HDF5 conversion... []{}
INFO (SedmlJob:181) - 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:256) - 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:258) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:229) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:134) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:147) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import
at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
... 18 more
ERROR (SedmlJob:272) - 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:258) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:229) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:134) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:147) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import
at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
... 18 more
INFO (SedmlJob:297) - Generating outputs... []{}
INFO (SedmlJob:387) - Generating HDF5 file... []{}
WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}
WARN (SpatialResultsConverter:56) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (SpatialResultsConverter:56) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (SpatialResultsConverter:56) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (SpatialResultsConverter:56) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (SpatialResultsConverter:118) - We encountered non-compatible (or non-existent) data. 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:322) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:243) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:134) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:147) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
WARN (SedmlJob:331) - Unable to initialize bioModel for the given selection
Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document. []{}
ERROR (ExecutionJob:144) - Processing of SedML has failed.
org.vcell.cli.run.SedmlStatistics@1e721583 []{}
INFO (NativeLib:33) - Loading jhdf5 []{}
INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/tmp/out []{}
INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{}
INFO (ExecutionJob:172) - Omex archive.omex processing completed (4s) []{}
ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{}
| Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error:
sedml.SimulatorSupportsModelAttributeChanges
(17.1 s)
Test that a simulator supports changes to the attributes of model elements
Reason for skip:
The image 'ghcr.io/virtualcell/biosimulators_vcell:7.5.0.99' 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:92) - Beginning execution []{}
INFO (CLIPythonManager:116) - Initializing Python... []{}
INFO (CLIPythonManager:136) - Python initialization success! []{}
INFO (ExecuteImpl:126) - Preparing output directory... []{}
ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}
ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}
INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{}
-----------------------------------------------------------------------------------------------------
INFO (NativeLib:33) - Loading combinej []{}
INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_a179eab8-7e5e-4cb5-9fce-502412009cbb6271637861813967934 []{}
INFO (SedmlJob:109) - 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:124) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}
INFO (SedmlJob:160) - 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:165) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}
-----------------------------------------------------------------------------------------------------
INFO (SedmlJob:169) - Creating pseudo SED-ML for HDF5 conversion... []{}
INFO (SedmlJob:181) - 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:256) - 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:258) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:229) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:134) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:147) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.
at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
... 18 more
Caused by: java.lang.Exception: Errors reported:
IllegalArgumentException occurred: Must be of type int!
at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
... 18 more
ERROR (SedmlJob:272) - 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:258) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:229) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:134) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:147) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.
at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
... 18 more
Caused by: java.lang.Exception: Errors reported:
IllegalArgumentException occurred: Must be of type int!
at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
... 18 more
INFO (SedmlJob:297) - Generating outputs... []{}
INFO (SedmlJob:387) - Generating HDF5 file... []{}
WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}
WARN (SpatialResultsConverter:56) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (SpatialResultsConverter:56) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (SpatialResultsConverter:56) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (SpatialResultsConverter:56) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (SpatialResultsConverter:118) - We encountered non-compatible (or non-existent) data. 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:322) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:243) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:134) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:147) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
WARN (SedmlJob:331) - Unable to initialize bioModel for the given selection
Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported:
IllegalArgumentException occurred: Must be of type int!
Failure executing the sed document. []{}
ERROR (ExecutionJob:144) - Processing of SedML has failed.
org.vcell.cli.run.SedmlStatistics@2daf06fc []{}
INFO (NativeLib:33) - Loading jhdf5 []{}
INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/tmp/out []{}
INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{}
INFO (ExecutionJob:172) - Omex archive.omex processing completed (3s) []{}
ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{}
| Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error:
docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>
<-i>
Default case selected
VCell shall execute <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:92) - Beginning execution []{}
INFO (CLIPythonManager:116) - Initializing Python... []{}
INFO (CLIPythonManager:136) - Python initialization success! []{}
INFO (ExecuteImpl:126) - Preparing output directory... []{}
ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}
ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}
INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{}
-----------------------------------------------------------------------------------------------------
INFO (NativeLib:33) - Loading combinej []{}
INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_b99debad-4e0e-4815-9426-0d14908bec60376377118815953317 []{}
INFO (SedmlJob:109) - 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:124) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}
INFO (SedmlJob:160) - 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:165) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}
-----------------------------------------------------------------------------------------------------
INFO (SedmlJob:169) - Creating pseudo SED-ML for HDF5 conversion... []{}
INFO (SedmlJob:181) - 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:256) - 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:258) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:229) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:134) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:147) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import
at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
... 18 more
ERROR (SedmlJob:272) - 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:258) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:229) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:134) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:147) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import
at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
... 18 more
INFO (SedmlJob:297) - Generating outputs... []{}
INFO (SedmlJob:387) - Generating HDF5 file... []{}
WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (NonspatialResultsConverter:72) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (NonspatialResultsConverter:159) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}
WARN (SpatialResultsConverter:56) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (SpatialResultsConverter:56) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (SpatialResultsConverter:56) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (SpatialResultsConverter:56) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}
WARN (SpatialResultsConverter:118) - We encountered non-compatible (or non-existent) data. 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:322) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:243) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:134) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:147) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
at picocli.CommandLine$RunLast.handle(Comma ...
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