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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 7.7.0.7 #707

Open jcschaff opened 6 hours ago

jcschaff commented 6 hours ago

id: vcell version: 7.7.0.7 specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.7.0.7/biosimulators.json specificationsPatch: version: 7.7.0.7 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7 digest: "sha256:47620241d9f45eef4bc2ae4579869dacaea1ea629520ab166cd8778afc658293" validateImage: true commitSimulator: true

biosimulators-daemon commented 6 hours ago

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

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

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

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

biosimulators-daemon commented 6 hours ago

The specifications of your simulator is valid!

biosimulators-daemon commented 6 hours ago

Summary of tests

biosimulators-daemon commented 6 hours ago

Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (6.0 s)
Test that SED documents in nested directories can be executed Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_6c08b14f-c79a-436a-b701-1eb050ffc74814460595282573942265 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{} | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more ```
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (6.0 s)
Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_ac6d685f-07e5-4c9d-ae6d-d4068b8778726995872997310686966 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{} | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more ```
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (6.0 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file. Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_540bbcac-3ccf-42a9-b9a2-ebd87f6a38e311678898603710670896 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{} | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more ```
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (6.0 s)
Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files. Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_2494aaff-299a-420c-a621-465afa046ada3992512678325046624 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{} | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more ```
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (6.0 s)
Test that simulator logs the execution of COMBINE/OMEX archives Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_be88e133-7bff-47a8-a659-91e867c923f817212834272546219466 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{} | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (5.9 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_d1db1e22-6fdd-4944-9e9c-284273f273981138305137471505004 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{} | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (5.9 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_3374f42e-3c30-4c95-83f8-89399b15f19916650803482323609533 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{} | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (5.9 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_ce648b54-3b65-4b65-85d2-13f97842dbcf15920455319487380012 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{} | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (5.9 s)
Required model formats and simulation algorithms for SED tasks: * 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:7.7.0.7' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_e1c0dff8-5536-4604-8c69-479a9702373313131275715174480900 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex []{} | Root(root) | OMEX_EXECUTE(Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (6.1 s)
Required model formats and simulation algorithms for SED tasks: * 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:7.7.0.7' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_793609b7-f5fe-4c42-a270-1868f056bd075322912117424875926 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex []{} | Root(root) | OMEX_EXECUTE(Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (6.0 s)
Required model formats and simulation algorithms for SED tasks: * 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:7.7.0.7' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_9ad2b029-98c1-4b68-bac5-1c2370a537ae15621726241964701802 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex []{} | Root(root) | OMEX_EXECUTE(Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (5.8 s)
Required model formats and simulation algorithms for SED tasks: * 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:7.7.0.7' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/Elowitz-Nature-2000-Repressilator.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate pl ...
biosimulators-daemon commented 6 hours ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.7 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports. Warnings: ``` The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports. The command-line interface does not describe the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be described in the inline help for its command-line interface. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
cli.CliDisplaysHelpInline (4.2 s)
Test that a command-line interface provides inline help. Warnings: ``` Command-line interfaces should display basic help when no arguments are provided. The command-line interface displayed the following when no argument was provided: docker: Command recieved::<> <> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} ERROR (BiosimulationsCommand:118) - Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null []{} java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null at org.vcell.cli.CLIRecorder.(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:53) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ``` ``` Command-line interface should support the `-h` option for displaying help inline. The command-line interface displayed the following when executed with `-h`: docker: Command recieved::<-h> <-h> Default case selected VCell shall execute 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: CLIStandalone biosimulations [-dhqv] [-i=] [-o=] BioSimulators-compliant command-line interface to the vcell simulation program . -d, --debug full application debug mode -h, --help show this help message and exit -i, --archive= Path to a COMBINE/OMEX archive file which contains one or more SED-ML-encoded simulation experiments -o, --out-dir= Directory to save outputs -q, --quiet suppress all console output -v, --version show program's version number and exit ``` ``` Command-line interface should support the `--help` option for displaying help inline. The command-line interface displayed the following when executed with `--help`: docker: Command recieved::<--help> <--help> Default case selected VCell shall execute 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: CLIStandalone biosimulations [-dhqv] [-i=] [-o=] BioSimulators-compliant command-line interface to the vcell simulation program . -d, --debug full application debug mode -h, --help show this help message and exit -i, --archive= Path to a COMBINE/OMEX archive file which contains one or more SED-ML-encoded simulation experiments -o, --out-dir= Directory to save outputs -q, --quiet suppress all console output -v, --version show program's version number and exit ``` Log: None
docker_image.DeclaresSupportedEnvironmentVariables (0.3 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.3 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 6 hours 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/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 (6.0 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``). Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_897b9540-783b-423d-89d0-e99d5a0969b42590833688905727990 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{} | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more ```
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (5.9 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``) and inherit the changes of the model. Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_58d032d9-b66f-4493-afd9-a2cf9421a45711357371195743966648 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{} | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more ```
sedml.SimulatorProducesLinear3DPlots (0.3 s)
Test that a simulator produces linear 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (0.3 s)
Test that a simulator produces logarithmic 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (11.9 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_7aa7ea53-5e0a-4a74-92cf-7d378845ae9a7823832000886853925 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{} | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_177f7599-0c83-4e19-940d-01537d12af8a3641130053861013962 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{} | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more ```
sedml.SimulatorSupportsComputeModelChanges (12.0 s)
Test that a simulator supports compute model changes Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_2de80205-ecda-418d-833f-5c673cb14d0f1021106735253169347 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{} | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_650d55c2-b570-43b8-8c6f-e4022f6dfd885262109790751499754 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{} | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more ```
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (5.9 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_80677158-90d3-4c09-9ed0-3ac9767814b115304312591928566782 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{} | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (5.9 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_e2f928be-b0d8-4693-9033-1abd749645d317050529008376326207 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{} | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more ```
sedml.SimulatorSupportsModelAttributeChanges (12.1 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.7.0.7' could not execute the archive: Unknown error ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_539ea365-bb04-4546-8a0d-4df85845e5a38695807706606524269 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{} | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.nio.file.ReadOnlyFileSystemException at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?] at jdk.zipfs@17.0.13/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?] at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?] at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?] at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?] at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?] at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.OmexHandler.(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 14 more docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:95) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:134) - Preparing output directory... []{} INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_86828b63-717e-44b5-b3ed-0a14037cb3395688182611506956163 []{} ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{} | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message ERROR (BiosimulationsCommand:118) - null, error for archive /tmp/in/archive.omex []{} java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli ...
biosimulators-daemon commented 6 hours 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/11729180129). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/11729180129).