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biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
MIT License
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Submit VCell 7.4.0.49 #583

Closed vcdaemon closed 2 years ago

vcdaemon commented 2 years ago

id: vcell version: 7.4.0.49 specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.4.0.49/biosimulators.json specificationsPatch: version: 7.4.0.49 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49 digest: "sha256:77b54d81ed53508052e7eda09feb51c710d57758334a132bba70f4e762e54148" validateImage: true commitSimulator: true

biosimulators-daemon commented 2 years ago

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

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

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

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

biosimulators-daemon commented 2 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 years ago

Summary of tests

biosimulators-daemon commented 2 years ago

Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (2.0 s)
Test that SED documents in nested directories can be executed Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:01 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (1.9 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:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:03 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (1.9 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:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:05 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (1.9 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:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:07 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
docker_image.SingularityImageExecutesSimulationsSuccessfully (2.9 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Exception: ``` The Docker image could not be successfully executed as a Singularity image: Jul 13, 2022 3:20:51 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. 15:20:51 [main] WARN cbit.vcell.resource.PropertyLoader - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (2.0 s)
Test that simulator logs the execution of COMBINE/OMEX archives Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:22:17 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (2.0 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:22:19 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (2.0 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:22:21 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (2.2 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:22:24 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (1.9 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:22:26 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (1.9 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000086`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000086) Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:22:28 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (1.9 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:22:29 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (1.9 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:22:31 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (1.9 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:22:37 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (1.9 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:22:33 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (1.9 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:22:35 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength (1.8 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9000`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9000) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:22:39 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
results_report.SimulatorGeneratesReportsOfSimulationResults (2.0 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:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:22:15 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorProducesLinear2DPlots (1.9 s)
Test that a simulator produces linear 2D plots Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:13 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorProducesLogarithmic2DPlots (1.9 s)
Test that a simulator produces logarithmic 2D plots Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:15 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorProducesMultiplePlots (2.0 s)
Test that a simulator produces multiple plots Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:17 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsAlgorithmParameters (1.9 s)
Test that a simulator supports setting the values of parameters of algorithms Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:23 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports (1.9 s)
Test that a simulator supports the core elements of SED: models, simulations, tasks, data generators for individual variables, and reports Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:37 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsMultipleReportsPerSedDocument (1.9 s)
Test that a simulator supports multiple reports per SED document Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:39 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsMultipleTasksPerSedDocument (1.9 s)
Test that a simulator supports multiple tasks per SED document Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:41 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (2.1 s)
Test that a simulator supports time courses with non-zero output start times Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:22:13 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
biosimulators-daemon commented 2 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.9 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports. Warnings: ``` The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports. The command-line interface does not describe the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be described in the inline help for its command-line interface. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
cli.CliDisplaysHelpInline (2.3 s)
Test that a command-line interface provides inline help. Warnings: ``` Command-line interface should support the `-h` option for displaying help inline. The command-line interface displayed the following when executed with `-h`: usage: VCell [-h | -v] [-q] -i -o [-t ] [-c] [-vcml | -sbml] [-hasDataOnly] [-makeLogsOnly] [-nonSpatialOnly] [-keepTempFiles] [-exactMatchOnly] [-forceLogFiles] BioSimulators-compliant command-line interface to the VCell simulation program . optional arguments: -c,--convert Converts OMEX Archives to either sbml or vcml format, attempting sbml first then vcml unless otherwise specificed by flags. Requires -i and -o flags. -exactMatchOnly Run the model solver only if it's an exact kisao match. -forceLogFiles Generates log files ordinarily run only for batch execution -h,--help show this help message and exit -hasDataOnly Export the sims that have been previously run and have results on the VCell server. -i,--input Path to OMEX/COMBINE Archive which contains one or more SED-ML encoded simulation experiments, or VCML file -keepTempFiles Keep simulation results for debugging. -makeLogsOnly Rather than creating the omex files, just make the logs. -nonSpatialOnly Export only non-spatial simulations. -o,--outputDir Directory to save outputs or the converted OMEX Archive from VCML file -q,--quiet Suppress all console output [NOT CURRENTLY IMPLIMENTED] -sbml Specifies conversion of OMEX Archive to sbml format. -t,--timeout Specifices a timeout duration. -v,--version Show program's version number and exit -vcml Specifies conversion of OMEX Archive to vcml format. ``` ``` Command-line interface should support the `--help` option for displaying help inline. The command-line interface displayed the following when executed with `--help`: usage: VCell [-h | -v] [-q] -i -o [-t ] [-c] [-vcml | -sbml] [-hasDataOnly] [-makeLogsOnly] [-nonSpatialOnly] [-keepTempFiles] [-exactMatchOnly] [-forceLogFiles] BioSimulators-compliant command-line interface to the VCell simulation program . optional arguments: -c,--convert Converts OMEX Archives to either sbml or vcml format, attempting sbml first then vcml unless otherwise specificed by flags. Requires -i and -o flags. -exactMatchOnly Run the model solver only if it's an exact kisao match. -forceLogFiles Generates log files ordinarily run only for batch execution -h,--help show this help message and exit -hasDataOnly Export the sims that have been previously run and have results on the VCell server. -i,--input Path to OMEX/COMBINE Archive which contains one or more SED-ML encoded simulation experiments, or VCML file -keepTempFiles Keep simulation results for debugging. -makeLogsOnly Rather than creating the omex files, just make the logs. -nonSpatialOnly Export only non-spatial simulations. -o,--outputDir Directory to save outputs or the converted OMEX Archive from VCML file -q,--quiet Suppress all console output [NOT CURRENTLY IMPLIMENTED] -sbml Specifies conversion of OMEX Archive to sbml format. -t,--timeout Specifices a timeout duration. -v,--version Show program's version number and exit -vcml Specifies conversion of OMEX Archive to vcml format. ``` Log: None
docker_image.DeclaresSupportedEnvironmentVariables (0.8 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.7 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 2 years ago

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000030 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9012`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9012) Algorithm: [`KISAO_0000669`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000669) Reason for skip: ``` Case requires model formats format_9012 and simulation algorithms KISAO_0000669 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000088`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000088 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) Reason for skip: ``` Case requires model formats format_9001 and simulation algorithms KISAO_0000057 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9010 and simulation algorithms KISAO_0000019 ``` Log: None
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (1.9 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:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:09 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (1.9 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:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:11 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 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 (3.8 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:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:19 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more Jul 13, 2022 3:21:21 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsComputeModelChanges (3.8 s)
Test that a simulator supports compute model changes Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:25 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more Jul 13, 2022 3:21:27 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (1.9 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:29 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (1.9 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:31 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsModelAttributeChanges (4.0 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:33 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more Jul 13, 2022 3:21:35 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsRepeatedTasksWithChanges (3.8 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:43 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more Jul 13, 2022 3:21:45 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (4.0 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:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:47 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more Jul 13, 2022 3:21:49 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (2.0 s)
Test that a simulator supports repeated tasks over functional ranges Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:51 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (2.1 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:53 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (2.0 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:55 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (2.0 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:57 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (2.1 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:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:21:59 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (2.0 s)
Test that a simulator supports nested repeated tasks Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:22:01 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (2.0 s)
Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their ``order`` attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes. Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:22:03 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (2.0 s)
Test that a simulator supports repeated tasks over vector ranges Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:22:05 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsSubstitutingAlgorithms (4.0 s)
Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.SAME_METHOD`. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.NONE`. Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:22:07 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more Jul 13, 2022 3:22:09 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (2.0 s)
Test that a simulator supports multiple time courses with non-zero initial times Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive: Unknown error ``` Log: ``` Jul 13, 2022 3:22:11 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. ServerID=7.3.0.16, SoftwareVersion=unknown Encountered fatal IOException while creating CLIUtils; killing VCell. java.io.IOException: Cannot run program "python": error=2, No such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989) at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149) at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521) at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more ```
biosimulators-daemon commented 2 years ago 
- 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/2664415161). 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/2664415161).
moraru commented 2 years ago

Superseded by https://github.com/biosimulators/Biosimulators/issues/587