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biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
MIT License
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Submit VCell 7.4.0.83 #592

Closed vcdaemon closed 1 year ago

vcdaemon commented 1 year ago

id: vcell version: 7.4.0.83 specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.4.0.83/biosimulators.json specificationsPatch: version: 7.4.0.83 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.83 digest: "sha256:97aefabde448182987feefb7c36a795bdf64d2de4c845f490045f9a0654e1fa2" validateImage: true commitSimulator: true

biosimulators-daemon commented 1 year ago

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

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

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

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

biosimulators-daemon commented 1 year ago

The specifications of your simulator is valid!

biosimulators-daemon commented 1 year ago

Summary of tests

biosimulators-daemon commented 1 year ago

Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (13.1 s)
Test that SED documents in nested directories can be executed Exception: ``` Simulator did not generate the following expected reports - `subdir/BIOMD0000000912_sim.sedml/report` ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute INFO (CLIStandalone:34) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.83 INFO (BiosimulationsCommand:106) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:83) - Preparing output directory... ERROR (CLIUtils:27) - Failed to delete the file: /tmp/out INFO (ExecuteImpl:175) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:927) - TempPath Created: /tmp/vcell_temp_db8a2b18-3f85-4778-98f8-a296e6eb2f595348687373953705829 INFO (ExecuteImpl:208) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:224) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:259) - Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) INFO (ExecuteImpl:264) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:268) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:280) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:319) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter:3337) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:157) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@68c87fc3 INFO (SolverHandler:391) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:437) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:449) - Running simulation Caravagna2010, 90 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:557) - Ran 1 simulation jobs for 1 biomodels. INFO (ExecuteImpl:359) - Generating outputs... INFO (ExecuteImpl:364) - Generating CSV file... INFO (RunUtils:237) - Generating report `report`. INFO (RunUtils:428) - created csv file for report report: /tmp/out/subdir/BIOMD0000000912_sim.sedml/report.csv INFO (ExecuteImpl:381) - Generating Plots... WARN (CLIPythonManager:65) - Using old style python invocation! INFO (ExecuteImpl:389) - Generating HDF5 file... INFO (RunUtils:477) - Generating report `report`. INFO (RunUtils:706) - Generating report `report`. INFO (NativeLib:29) - Loading jhdf5 writing to file /tmp/out/subdir/BIOMD0000000912_sim.sedml/reports.h5 INFO (ExecuteImpl:455) - Archiving result files ERROR (RunUtils:897) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils:901) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl:460) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl:468) - Omex archive.omex processing completed (6s) ```
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (13.7 s)
Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.83' 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 INFO (CLIStandalone:34) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.83 INFO (BiosimulationsCommand:106) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:83) - Preparing output directory... ERROR (CLIUtils:27) - Failed to delete the file: /tmp/out INFO (ExecuteImpl:175) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:927) - TempPath Created: /tmp/vcell_temp_5c9f40a1-220f-412e-84ad-0e2e5a94eabf1863375774234364329 INFO (ExecuteImpl:208) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:224) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:259) - Found 2 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) INFO (ExecuteImpl:264) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:268) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:280) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:319) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter:3337) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:157) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@15ac59c2 INFO (SolverHandler:391) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:437) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:449) - Running simulation Caravagna2010, 75 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:557) - Ran 1 simulation jobs for 1 biomodels. INFO (ExecuteImpl:359) - Generating outputs... INFO (ExecuteImpl:364) - Generating CSV file... INFO (RunUtils:237) - Generating report `report`. INFO (RunUtils:428) - created csv file for report report: /tmp/out/subdir/BIOMD0000000912_sim.sedml/report.csv INFO (ExecuteImpl:381) - Generating Plots... WARN (CLIPythonManager:65) - Using old style python invocation! INFO (ExecuteImpl:389) - Generating HDF5 file... INFO (RunUtils:477) - Generating report `report`. INFO (RunUtils:706) - Generating report `report`. INFO (NativeLib:29) - Loading jhdf5 writing to file /tmp/out/subdir/BIOMD0000000912_sim.sedml/reports.h5 INFO (ExecuteImpl:455) - Archiving result files ERROR (RunUtils:897) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils:901) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl:460) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl:208) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:224) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:259) - Found 2 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 2 report(s), 0 plot2D(s), and 0 plot3D(s) INFO (ExecuteImpl:264) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:268) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:280) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:319) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter:3337) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:157) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@67fc2aad INFO (SolverHandler:391) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:437) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:449) - Running simulation Caravagna2010, 51 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:557) - Ran 1 simulation jobs for 1 biomodels. INFO (ExecuteImpl:359) - Generating outputs... INFO (ExecuteImpl:364) - Generating CSV file... INFO (RunUtils:237) - Generating report `report`. INFO (RunUtils:428) - created csv file for report report: /tmp/out/subdir__copy/BIOMD0000000912_sim.sedml/report.csv INFO (ExecuteImpl:381) - Generating Plots... WARN (CLIPythonManager:65) - Using old style python invocation! INFO (ExecuteImpl:389) - Generating HDF5 file... INFO (RunUtils:477) - Generating report `report`. INFO (RunUtils:706) - Generating report `report`. writing to file /tmp/out/subdir__copy/BIOMD0000000912_sim.sedml/reports.h5 ERROR (BiosimulationsCommand:120) - /tmp/out/reports.h5 java.nio.file.FileAlreadyExistsException: /tmp/out/reports.h5 at sun.nio.fs.UnixCopyFile.move(UnixCopyFile.java:429) ~[?:1.8.0_342] at sun.nio.fs.UnixFileSystemProvider.move(UnixFileSystemProvider.java:262) ~[?:1.8.0_342] at java.nio.file.Files.move(Files.java:1395) ~[?:1.8.0_342] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:451) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:87) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:96) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:109) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:38) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ```
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (10.2 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file. Exception: ``` Simulator did not generate the following expected reports - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute INFO (CLIStandalone:34) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.83 INFO (BiosimulationsCommand:106) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:83) - Preparing output directory... ERROR (CLIUtils:27) - Failed to delete the file: /tmp/out INFO (ExecuteImpl:175) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:927) - TempPath Created: /tmp/vcell_temp_efb8b8ce-6cfb-46a0-b741-1930825bd87b841749670217924995 INFO (ExecuteImpl:208) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:224) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:259) - Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) INFO (ExecuteImpl:264) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:268) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:280) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:319) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter:3337) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:157) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@68c87fc3 INFO (SolverHandler:391) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:437) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:449) - Running simulation Caravagna2010, 74 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:557) - Ran 1 simulation jobs for 1 biomodels. INFO (ExecuteImpl:359) - Generating outputs... INFO (ExecuteImpl:364) - Generating CSV file... INFO (RunUtils:237) - Generating report `report`. INFO (RunUtils:428) - created csv file for report report: /tmp/out/BIOMD0000000912_sim.sedml/report.csv INFO (ExecuteImpl:381) - Generating Plots... WARN (CLIPythonManager:65) - Using old style python invocation! INFO (ExecuteImpl:389) - Generating HDF5 file... INFO (RunUtils:477) - Generating report `report`. INFO (RunUtils:706) - Generating report `report`. INFO (NativeLib:29) - Loading jhdf5 writing to file /tmp/out/BIOMD0000000912_sim.sedml/reports.h5 INFO (ExecuteImpl:455) - Archiving result files ERROR (RunUtils:897) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils:901) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl:460) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl:468) - Omex archive.omex processing completed (6s) ```
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (13.5 s)
Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files. Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.83' 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 INFO (CLIStandalone:34) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.83 INFO (BiosimulationsCommand:106) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:83) - Preparing output directory... ERROR (CLIUtils:27) - Failed to delete the file: /tmp/out INFO (ExecuteImpl:175) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:927) - TempPath Created: /tmp/vcell_temp_0ba2a7b7-6604-4f59-b6e3-6f7870580df66081700237951516345 INFO (ExecuteImpl:208) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:224) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:259) - Found 2 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) INFO (ExecuteImpl:264) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:268) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:280) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:319) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter:3337) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:157) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@68c87fc3 INFO (SolverHandler:391) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:437) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:449) - Running simulation Caravagna2010, 93 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:557) - Ran 1 simulation jobs for 1 biomodels. INFO (ExecuteImpl:359) - Generating outputs... INFO (ExecuteImpl:364) - Generating CSV file... INFO (RunUtils:237) - Generating report `report`. INFO (RunUtils:428) - created csv file for report report: /tmp/out/BIOMD0000000912_sim.sedml/report.csv INFO (ExecuteImpl:381) - Generating Plots... WARN (CLIPythonManager:65) - Using old style python invocation! INFO (ExecuteImpl:389) - Generating HDF5 file... INFO (RunUtils:477) - Generating report `report`. INFO (RunUtils:706) - Generating report `report`. INFO (NativeLib:29) - Loading jhdf5 writing to file /tmp/out/BIOMD0000000912_sim.sedml/reports.h5 INFO (ExecuteImpl:455) - Archiving result files ERROR (RunUtils:897) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils:901) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl:460) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl:208) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:224) - Processing SED-ML: BIOMD0000000912_sim__copy.sedml INFO (ExecuteImpl:259) - Found 2 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 2 report(s), 0 plot2D(s), and 0 plot3D(s) INFO (ExecuteImpl:264) - Successful translation of SED-ML file : BIOMD0000000912_sim__copy.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:268) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:280) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:319) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter:3337) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:157) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@153cd6bb INFO (SolverHandler:391) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:437) - Succesful execution: Model 'archive_BIOMD0000000912_sim__copy.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:449) - Running simulation Caravagna2010, 40 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:557) - Ran 1 simulation jobs for 1 biomodels. INFO (ExecuteImpl:359) - Generating outputs... INFO (ExecuteImpl:364) - Generating CSV file... INFO (RunUtils:237) - Generating report `report`. INFO (RunUtils:428) - created csv file for report report: /tmp/out/BIOMD0000000912_sim__copy.sedml/report.csv INFO (ExecuteImpl:381) - Generating Plots... WARN (CLIPythonManager:65) - Using old style python invocation! INFO (ExecuteImpl:389) - Generating HDF5 file... INFO (RunUtils:477) - Generating report `report`. INFO (RunUtils:706) - Generating report `report`. writing to file /tmp/out/BIOMD0000000912_sim__copy.sedml/reports.h5 ERROR (BiosimulationsCommand:120) - /tmp/out/reports.h5 java.nio.file.FileAlreadyExistsException: /tmp/out/reports.h5 at sun.nio.fs.UnixCopyFile.move(UnixCopyFile.java:429) ~[?:1.8.0_342] at sun.nio.fs.UnixFileSystemProvider.move(UnixFileSystemProvider.java:262) ~[?:1.8.0_342] at java.nio.file.Files.move(Files.java:1395) ~[?:1.8.0_342] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:451) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:87) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:96) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:109) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:38) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ```
docker_image.SingularityImageExecutesSimulationsSuccessfully (9.9 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Exception: ``` [Errno 2] No such file or directory: '/tmp/tmp71wbq9hv/docker_image/docker_image.SingularityImageExecutesSimulationsSuccessfully/1/outputs/archive.omex' ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (11.2 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: ``` unhashable type: 'numpy.ndarray' ``` 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 INFO (CLIStandalone:34) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.83 INFO (BiosimulationsCommand:106) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:83) - Preparing output directory... ERROR (CLIUtils:27) - Failed to delete the file: /tmp/out INFO (ExecuteImpl:175) - Executing OMEX archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:927) - TempPath Created: /tmp/vcell_temp_09513117-2bf1-4bbe-9d93-e04a55dcffe61879472198997660106 INFO (ExecuteImpl:208) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:224) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:259) - Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 1 plot2D(s), and 0 plot3D(s) INFO (ExecuteImpl:264) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:268) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:280) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:319) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter:3337) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:157) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@345cf395 INFO (SolverHandler:391) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:437) - Succesful execution: Model 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:449) - Running simulation Caravagna2010, 160 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:557) - Ran 1 simulation jobs for 1 biomodels. INFO (ExecuteImpl:359) - Generating outputs... INFO (ExecuteImpl:364) - Generating CSV file... INFO (RunUtils:231) - Ignoring unsupported output `Figure_1_bottom_left` while CSV generation. INFO (RunUtils:237) - Generating report `report`. INFO (RunUtils:428) - created csv file for report report: /tmp/out/BIOMD0000000912_sim.sedml/report.csv INFO (RunUtils:237) - Generating report `__plot__Figure_1_bottom_left`. INFO (RunUtils:428) - created csv file for report __plot__Figure_1_bottom_left: /tmp/out/BIOMD0000000912_sim.sedml/__plot__Figure_1_bottom_left.csv INFO (ExecuteImpl:381) - Generating Plots... WARN (CLIPythonManager:65) - Using old style python invocation! INFO (ExecuteImpl:389) - Generating HDF5 file... INFO (RunUtils:472) - Ignoring unsupported output `Figure_1_bottom_left` while CSV generation. INFO (RunUtils:477) - Generating report `report`. INFO (RunUtils:477) - Generating report `__plot__Figure_1_bottom_left`. INFO (RunUtils:699) - Ignoring unsupported output `Figure_1_bottom_left` during HDF5 generation. INFO (RunUtils:706) - Generating report `report`. INFO (RunUtils:706) - Generating report `__plot__Figure_1_bottom_left`. INFO (NativeLib:29) - Loading jhdf5 writing to file /tmp/out/BIOMD0000000912_sim.sedml/reports.h5 INFO (ExecuteImpl:455) - Archiving result files INFO (RunUtils:901) - Archiving resultant PDF files to `plots.zip`. INFO (RunUtils:901) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl:460) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl:468) - Omex Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex processing completed (7s) ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (15.0 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_0000086`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000086) Exception: ``` unhashable type: 'numpy.ndarray' ``` 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 INFO (CLIStandalone:34) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.83 INFO (BiosimulationsCommand:106) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:83) - Preparing output directory... ERROR (CLIUtils:27) - Failed to delete the file: /tmp/out INFO (ExecuteImpl:175) - Executing OMEX archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:927) - TempPath Created: /tmp/vcell_temp_21d8a552-7cf4-4e64-aab2-b6c830d8a19f6933533503322290030 INFO (ExecuteImpl:208) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:224) - Processing SED-ML: simulation_1.sedml INFO (ExecuteImpl:259) - Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 4 plot2D(s), and 0 plot3D(s) INFO (ExecuteImpl:264) - Successful translation of SED-ML file : simulation_1.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:268) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:280) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:319) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter:3337) - model 'Ciliberto2003_Morphogenesis' doesn't have a spatial geometry cbit.vcell.parser.ExpressionException: linear factor was null, lumped reaction R1 could not be transformed to distributed at cbit.vcell.model.DistributedKinetics.toDistributedKinetics(DistributedKinetics.java:204) at org.vcell.sbml.vcell.SBMLImporter.getBioModel(SBMLImporter.java:1784) at org.vcell.sedml.SEDMLImporter.importModel(SEDMLImporter.java:767) at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:719) at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:126) at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:591) at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:297) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:321) at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:87) at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:96) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:109) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:38) WARN (SBMLImporter:1786) - failed to transform lumped reaction R1 to distributed: failed to create distributed Kinetics for reaction: "R1": linear factor was null, lumped reaction R1 could not be transformed to distributed java.lang.RuntimeException: failed to create distributed Kinetics for reaction: "R1": linear factor was null, lumped reaction R1 could not be transformed to distributed at cbit.vcell.model.DistributedKinetics.toDistributedKinetics(DistributedKinetics.java:243) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sbml.vcell.SBMLImporter.getBioModel(SBMLImporter.java:1784) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.importModel(SEDMLImporter.java:767) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:719) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:126) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:591) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:297) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:321) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:87) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:109) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:38) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] cbit.vcell.parser.ExpressionException: linear factor was null, lumped reaction R2 could not be transformed to distributed at cbit.vcell.model.DistributedKinetics.toDistributedKinetics(DistributedKinetics.java:204) at org.vcell.sbml.vcell.SBMLImporter.getBioModel(SBMLImporter.java:1784) at org.vcell.sedml.SEDMLImporter.importModel(SEDMLImporter.java:767) at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:719) at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:126) at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:591) at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:297) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:321) at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:87) at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:96) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:109) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:38) WARN (SBMLImporter:1786) - failed to transform lumped reaction R2 to distributed: failed to create distributed Kinetics for reaction: "R2": linear factor was null, lumped reaction R2 could not be transformed to distributed java.lang.RuntimeException: failed to create distributed Kinetics for reaction: "R2": linear factor was null, lumped reaction R2 could not be transformed to distributed at cbit.vcell.model.DistributedKinetics.toDistributedKinetics(DistributedKinetics.java:243) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sbml.vcell.SBMLImporter.getBioModel(SBMLImporter.java:1784) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.importModel(SEDMLImporter.java:767) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:719) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:126) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:591) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:297) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:321) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:87) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:109) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:38) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] cbit.vcell.parser.ExpressionException: linear factor was null, lumped reaction R3 could not be transformed to distributed at cbit.vcell.model.DistributedKinetics.toDistributedKinetics(DistributedKinetics.java:204) at org.vcell.sbml.vcell.SBMLImporter.getBioModel(SBMLImporter.java:1784) at org.vcell.sedml.SEDMLImporter.importModel(SEDMLImporter.java:767) at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:719) at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:126) at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:591) at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:297) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:321) at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:87) at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:96) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:109) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:38) WARN (SBMLImporter:1786) - failed to transform lumped reaction R3 to distributed: failed to create distributed Kinetics for reaction: "R3": linear factor was null, lumped reaction R3 could not be transformed to distributed java.lang.RuntimeException: failed to create distributed Kinetics for reaction: "R3": linear factor was null, lumped reaction R3 could not be transformed to distributed at cbit.vcell.model.DistributedKinetics.toDistributedKinetics(DistributedKinetics.java:243) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sbml.vcell.SBMLImporter.getBioModel(SBMLImporter.java:1784) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.importModel(SEDMLImporter.java:767) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:719) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:126) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:591) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:297) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:321) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:87) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:109) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:38) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] cbit.vcell.parser.ExpressionException: linear factor was null, lumped reaction R4 could not be transformed to distributed at cbit.vcell.model.DistributedKinetics.toDistributedKinetics(DistributedKinetics.java:204) at org.vcell.sbml.vcell.SBMLImporter.getBioModel(SBMLImporter.java:1784) at org.vcell.sedml.SEDMLImporter.importModel(SEDMLImporter.java:767) at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:719) at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:126) at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:591) at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:297) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:321) at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:87) at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:96) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:109) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:38) WARN (SBMLImporter:1786) - failed to transform lumped reaction R4 to distributed: failed to create distributed Kinetics for reaction: "R4": linear factor was null, lumped reaction R4 could not be transformed to distributed java.lang.RuntimeException: failed to create distributed Kinetics for reaction: "R4": linear factor was null, lumped reaction R4 could not be transformed to distributed at cbit.vcell.model.DistributedKinetics.toDistributedKinetics(DistributedKinetics.java:243) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sbml.vcell.SBMLImporter.getBioModel(SBMLImporter.java:1784) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.importModel(SEDMLImporter.java:767) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:719) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:126) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:591) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:297) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:321) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:87) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:109) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:38) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] cbit.vcell.parser.ExpressionException: linear factor was null, lumped reaction R5 could not be transformed to distributed at cbit.vcell.model.DistributedKinetics.toDistributedKinetics(DistributedKinetics.java:204) at org.vcell.sbml.vcell.SBMLImporter.getBioModel(SBMLImporter.java:1784) at org.vcell.sedml.SEDMLImporter.importModel(SEDMLImporter.java:767) at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:719) at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:126) at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:591) at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:297) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:321) at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:87) at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:96) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:109) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:38) WARN (SBMLImporter:1786) - failed to transform lumped reaction R5 to distributed: failed to create distributed Kinetics for reaction: "R5": linear factor was null, lumped reaction R5 could not be transformed to distributed java.lang.RuntimeException: failed to create distributed Kinetics for reaction: "R5": linear factor was null, lumped reaction R5 could not be transformed to distributed at cbit.vcell.model.DistributedKinetics.toDistributedKinetics(DistributedKinetics.java:243) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sbml.vcell.SBMLImporter.getBioModel(SBMLImporter.java:1784) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.importModel(SEDMLImporter.java:767) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:719) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:126) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:591) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:297) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:321) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:87) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:109) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:38) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] cbit.vcell.parser.ExpressionException: linear factor was null, lumped reaction R6 could not be transformed to distributed at cbit.vcell.model.DistributedKinetics.toDistributedKinetics(DistributedKinetics.java:204) at org.vcell.sbml.vcell.SBMLImporter.getBioModel(SBMLImporter.java:1784) at org.vcell.sedml.SEDMLImporter.importModel(SEDMLImporter.java:767) at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:719) at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:126) at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:591) at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:297) at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:321) at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:87) at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:96) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:109) at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at picocli.CommandLine.execute(CommandLine.java:2078) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:38) WARN (SBMLImporter:1786) - failed to transform lumped reaction R6 to distributed: failed to create distributed Kinetics for reaction: "R6": linear factor was null, lumped reaction R6 could not be transformed to distributed java.lang.RuntimeException: failed to create distributed Kinetics for reaction: "R6": linear fact ...
biosimulators-daemon commented 1 year ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (3.4 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports. Warnings: ``` The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports. The command-line interface does not describe the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be described in the inline help for its command-line interface. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
cli.CliDisplaysHelpInline (4.9 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 INFO (CLIStandalone:34) - Starting Vcell... ERROR (BiosimulationsCommand:120) - null java.lang.NullPointerException: null at org.vcell.cli.CLIRecorder.(CLIRecorder.java:43) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:39) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:35) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:46) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:38) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ``` ``` Command-line interface should support the `-h` option for displaying help inline. The command-line interface displayed the following when executed with `-h`: docker: Command recieved::<-h> <-h> Default case selected VCell shall execute INFO (CLIStandalone:34) - 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 INFO (CLIStandalone:34) - 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 (1.0 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.6 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 1 year 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 (11.0 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``). Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute INFO (CLIStandalone:34) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.83 INFO (BiosimulationsCommand:106) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:83) - Preparing output directory... ERROR (CLIUtils:27) - Failed to delete the file: /tmp/out INFO (ExecuteImpl:175) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:927) - TempPath Created: /tmp/vcell_temp_b23076b4-04f8-4986-b711-d1b854e56cb3543971418853501600 INFO (ExecuteImpl:208) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:224) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:259) - Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) INFO (ExecuteImpl:264) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:268) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:280) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:319) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter:3337) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry INFO (SBMLImporter:3337) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:157) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE ----comparing model from----BioModel@5ee34b1b(archive_BIOMD0000000912_sim.sedml___source__) with model from BioModel@3228d990(archive_BIOMD0000000912_sim.sedml_BIOMD0000000912) true INFO (XmlBase:4549) - RbmModelContainer is missing. INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@15f2eda3 INFO (SolverHandler:391) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:437) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:449) - Running simulation Caravagna2010, 81 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:557) - Ran 1 simulation jobs for 1 biomodels. INFO (ExecuteImpl:359) - Generating outputs... INFO (ExecuteImpl:364) - Generating CSV file... INFO (RunUtils:237) - Generating report `report`. INFO (RunUtils:428) - created csv file for report report: /tmp/out/BIOMD0000000912_sim.sedml/report.csv INFO (ExecuteImpl:381) - Generating Plots... WARN (CLIPythonManager:65) - Using old style python invocation! INFO (ExecuteImpl:389) - Generating HDF5 file... INFO (RunUtils:477) - Generating report `report`. INFO (RunUtils:706) - Generating report `report`. INFO (NativeLib:29) - Loading jhdf5 writing to file /tmp/out/BIOMD0000000912_sim.sedml/reports.h5 INFO (ExecuteImpl:455) - Archiving result files ERROR (RunUtils:897) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils:901) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl:460) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl:468) - Omex archive.omex processing completed (6s) ```
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (10.9 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: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute INFO (CLIStandalone:34) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.83 INFO (BiosimulationsCommand:106) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:83) - Preparing output directory... ERROR (CLIUtils:27) - Failed to delete the file: /tmp/out INFO (ExecuteImpl:175) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:927) - TempPath Created: /tmp/vcell_temp_c7223613-f68c-4f9d-9836-4e00c2cab5667163709115173768106 INFO (ExecuteImpl:208) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:224) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:259) - Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) INFO (ExecuteImpl:264) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:268) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:280) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:319) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter:3337) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry INFO (SBMLImporter:3337) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:157) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE ----comparing model from----BioModel@1bcf67e8(archive_BIOMD0000000912_sim.sedml___source__) with model from BioModel@33c2bd(archive_BIOMD0000000912_sim.sedml_BIOMD0000000912) true INFO (XmlBase:4549) - RbmModelContainer is missing. INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@65ec8b24 INFO (SolverHandler:391) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:437) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:449) - Running simulation Caravagna2010, 87 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:557) - Ran 1 simulation jobs for 1 biomodels. INFO (ExecuteImpl:359) - Generating outputs... INFO (ExecuteImpl:364) - Generating CSV file... INFO (RunUtils:237) - Generating report `report`. INFO (RunUtils:428) - created csv file for report report: /tmp/out/BIOMD0000000912_sim.sedml/report.csv INFO (ExecuteImpl:381) - Generating Plots... WARN (CLIPythonManager:65) - Using old style python invocation! INFO (ExecuteImpl:389) - Generating HDF5 file... INFO (RunUtils:477) - Generating report `report`. INFO (RunUtils:706) - Generating report `report`. INFO (NativeLib:29) - Loading jhdf5 writing to file /tmp/out/BIOMD0000000912_sim.sedml/reports.h5 INFO (ExecuteImpl:455) - Archiving result files ERROR (RunUtils:897) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils:901) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl:460) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl:468) - Omex archive.omex processing completed (6s) ```
sedml.SimulatorProducesLinear3DPlots (0.5 s)
Test that a simulator produces linear 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (0.5 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 (0.5 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 (18.3 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute INFO (CLIStandalone:34) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.83 INFO (BiosimulationsCommand:106) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:83) - Preparing output directory... ERROR (CLIUtils:27) - Failed to delete the file: /tmp/out INFO (ExecuteImpl:175) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:927) - TempPath Created: /tmp/vcell_temp_c238d18e-37c9-404b-8ffb-909aa5cabdda6466448789538714893 INFO (ExecuteImpl:208) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:224) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:259) - Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) INFO (ExecuteImpl:264) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:268) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:280) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:319) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail ERROR (SEDMLImporter:784) - VCLoggerException occured: org.vcell.sbml.vcell.SBMLImportException: Inconsistent unit system in SBML model, cannot import into VCell. cbit.util.xml.VCLoggerException: org.vcell.sbml.vcell.SBMLImportException: Inconsistent unit system in SBML model, cannot import into VCell. at org.vcell.cli.run.SolverHandler$LocalLogger.sendMessage(SolverHandler.java:661) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sbml.vcell.SBMLImporter.getBioModel(SBMLImporter.java:1736) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.importModel(SEDMLImporter.java:767) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:719) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:126) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:591) [vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:297) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:321) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:87) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:109) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:38) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] Caused by: org.vcell.sbml.vcell.SBMLImportException: Inconsistent unit system in SBML model, cannot import into VCell. ... 21 more ERROR (SolverHandler:299) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection VCLoggerException occured: org.vcell.sbml.vcell.SBMLImportException: Inconsistent unit system in SBML model, cannot import into VCell. java.lang.RuntimeException: Unable to initialize bioModel for the given selection VCLoggerException occured: org.vcell.sbml.vcell.SBMLImportException: Inconsistent unit system in SBML model, cannot import into VCell. at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:334) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:591) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:297) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:321) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:87) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:109) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:38) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] Caused by: java.lang.RuntimeException: VCLoggerException occured: org.vcell.sbml.vcell.SBMLImportException: Inconsistent unit system in SBML model, cannot import into VCell. at org.vcell.sedml.SEDMLImporter.importModel(SEDMLImporter.java:785) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:719) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:126) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 16 more Caused by: cbit.util.xml.VCLoggerException: org.vcell.sbml.vcell.SBMLImportException: Inconsistent unit system in SBML model, cannot import into VCell. at org.vcell.cli.run.SolverHandler$LocalLogger.sendMessage(SolverHandler.java:661) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sbml.vcell.SBMLImporter.getBioModel(SBMLImporter.java:1736) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.importModel(SEDMLImporter.java:767) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:719) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:126) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 16 more Caused by: org.vcell.sbml.vcell.SBMLImportException: Inconsistent unit system in SBML model, cannot import into VCell. at org.vcell.cli.run.SolverHandler$LocalLogger.sendMessage(SolverHandler.java:661) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sbml.vcell.SBMLImporter.getBioModel(SBMLImporter.java:1736) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.importModel(SEDMLImporter.java:767) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:719) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:126) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 16 more ERROR (ExecuteImpl:327) - Unable to initialize bioModel for the given selection VCLoggerException occured: org.vcell.sbml.vcell.SBMLImportException: Inconsistent unit system in SBML model, cannot import into VCell. java.lang.RuntimeException: Unable to initialize bioModel for the given selection VCLoggerException occured: org.vcell.sbml.vcell.SBMLImportException: Inconsistent unit system in SBML model, cannot import into VCell. at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:334) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:591) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:297) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:321) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:87) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:109) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:38) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] Caused by: java.lang.RuntimeException: VCLoggerException occured: org.vcell.sbml.vcell.SBMLImportException: Inconsistent unit system in SBML model, cannot import into VCell. at org.vcell.sedml.SEDMLImporter.importModel(SEDMLImporter.java:785) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:719) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:126) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 16 more Caused by: cbit.util.xml.VCLoggerException: org.vcell.sbml.vcell.SBMLImportException: Inconsistent unit system in SBML model, cannot import into VCell. at org.vcell.cli.run.SolverHandler$LocalLogger.sendMessage(SolverHandler.java:661) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sbml.vcell.SBMLImporter.getBioModel(SBMLImporter.java:1736) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.importModel(SEDMLImporter.java:767) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:719) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:126) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 16 more Caused by: org.vcell.sbml.vcell.SBMLImportException: Inconsistent unit system in SBML model, cannot import into VCell. at org.vcell.cli.run.SolverHandler$LocalLogger.sendMessage(SolverHandler.java:661) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sbml.vcell.SBMLImporter.getBioModel(SBMLImporter.java:1736) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.importModel(SEDMLImporter.java:767) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:719) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:126) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 16 more INFO (ExecuteImpl:359) - Generating outputs... ERROR (ExecuteImpl:441) - Failure executing the sed document. java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:439) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:87) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:109) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:20) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:38) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl:468) - Omex archive.omex processing completed (2s) ERROR (ExecuteImpl:478) - At least one document in this archive failed to execute docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute INFO (CLIStandalone:34) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.83 INFO (BiosimulationsCommand:106) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:83) - Preparing output directory... ERROR (CLIUtils:27) - Failed to delete the file: /tmp/out INFO (ExecuteImpl:175) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:927) - TempPath Created: /tmp/vcell_temp_6e02f45d-a362-4f78-98c5-0bd3df3b7bd8755381467856711104 INFO (ExecuteImpl:208) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:224) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:259) - Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) INFO (ExecuteImpl:264) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:268) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:280) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:319) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter:3337) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:157) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@3e15bb06 INFO (SolverHandler:391) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:437) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:449) - Running simulation Caravagna2010, 84 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:557) - Ran 1 simulation jobs for 1 biomodels. INFO (ExecuteImpl:359) - Generating outputs... INFO (ExecuteImpl:364) - Generating CSV file... INFO (RunUtils:237) - Generating report `report`. INFO (RunUtils:428) - created csv file for report report: /tmp/out/BIOMD0000000912_sim.sedml/report.csv INFO (ExecuteImpl:381) - Generating Plots... WARN (CLIPythonManager:65) - Using old style python invocation! INFO (ExecuteImpl:389) - Generating HDF5 file... INFO (RunUtils:477) - Generating report `report`. INFO (RunUtils:706) - Generating report `report`. INFO (NativeLib:29) - Loading jhdf5 writing to file /tmp/out/BIOMD0000000912_sim.sedml/reports.h5 INFO (ExecuteImpl:455) - Archiving result files ERROR (RunUtils:897) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils:901) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl:460) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl:468) - Omex archive.omex processing completed (7s) ```
sedml.SimulatorSupportsComputeModelChanges (24.0 s)
Test that a simulator supports compute model changes Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute INFO (CLIStandalone:34) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.83 INFO (BiosimulationsCommand:106) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:83) - Preparing output directory... ERROR (CLIUtils:27) - Failed to delete the file: /tmp/out INFO (ExecuteImpl:175) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:927) - TempPath Created: /tmp/vcell_temp_9ce0634a-1a19-44e1-a721-0f0d89b2a1d28610356167700992038 INFO (ExecuteImpl:208) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:224) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:259) - Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) INFO (ExecuteImpl:264) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:268) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:280) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:319) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter:3337) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:157) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE ERROR (SEDMLImporter:511) - couldn't find SBase with sid=null in SBMLSymbolMapping WARN (SEDMLImporter:736) - could not map changeAttribute for ID null to a VCell Constant INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@7e00ed0f INFO (SolverHandler:391) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:437) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:449) - Running simulation Caravagna2010, 84 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:557) - Ran 1 simulation jobs for 1 biomodels. INFO (ExecuteImpl:359) - Generating outputs... INFO (ExecuteImpl:364) - Generating CSV file... INFO (RunUtils:237) - Generating report `report`. INFO (RunUtils:428) - created csv file for report report: /tmp/out/BIOMD0000000912_sim.sedml/report.csv INFO (ExecuteImpl:381) - Generating Plots... WARN (CLIPythonManager:65) - Using old style python invocation! INFO (ExecuteImpl:389) - Generating HDF5 file... INFO (RunUtils:477) - Generating report `report`. INFO (RunUtils:706) - Generating report `report`. INFO (NativeLib:29) - Loading jhdf5 writing to file /tmp/out/BIOMD0000000912_sim.sedml/reports.h5 INFO (ExecuteImpl:455) - Archiving result files ERROR (RunUtils:897) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils:901) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl:460) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl:468) - Omex archive.omex processing completed (7s) docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute INFO (CLIStandalone:34) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.83 INFO (BiosimulationsCommand:106) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:83) - Preparing output directory... ERROR (CLIUtils:27) - Failed to delete the file: /tmp/out INFO (ExecuteImpl:175) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:927) - TempPath Created: /tmp/vcell_temp_6cd2f86c-40b5-42d4-999a-7ba7a7b95a82964197734518405173 INFO (ExecuteImpl:208) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:224) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:259) - Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) INFO (ExecuteImpl:264) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:268) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:280) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:319) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter:3337) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:157) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE ERROR (SEDMLImporter:511) - couldn't find SBase with sid=null in SBMLSymbolMapping WARN (SEDMLImporter:736) - could not map changeAttribute for ID null to a VCell Constant INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@46c3a14d INFO (SolverHandler:391) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:437) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:449) - Running simulation Caravagna2010, 76 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:557) - Ran 1 simulation jobs for 1 biomodels. INFO (ExecuteImpl:359) - Generating outputs... INFO (ExecuteImpl:364) - Generating CSV file... INFO (RunUtils:237) - Generating report `report`. INFO (RunUtils:428) - created csv file for report report: /tmp/out/BIOMD0000000912_sim.sedml/report.csv INFO (ExecuteImpl:381) - Generating Plots... WARN (CLIPythonManager:65) - Using old style python invocation! INFO (ExecuteImpl:389) - Generating HDF5 file... INFO (RunUtils:477) - Generating report `report`. INFO (RunUtils:706) - Generating report `report`. INFO (NativeLib:29) - Loading jhdf5 writing to file /tmp/out/BIOMD0000000912_sim.sedml/reports.h5 INFO (ExecuteImpl:455) - Archiving result files ERROR (RunUtils:897) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils:901) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl:460) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl:468) - Omex archive.omex processing completed (7s) ```
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (10.4 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` "Can't open attribute (can't locate attribute: 'sedmlDataSetShapes')" ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute INFO (CLIStandalone:34) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.83 INFO (BiosimulationsCommand:106) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:83) - Preparing output directory... ERROR (CLIUtils:27) - Failed to delete the file: /tmp/out INFO (ExecuteImpl:175) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:927) - TempPath Created: /tmp/vcell_temp_69265bbf-96c4-4041-a0ef-cb98dc9a2b353356203236362955878 INFO (ExecuteImpl:208) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:224) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:259) - Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) INFO (ExecuteImpl:264) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:268) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:280) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:319) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter:3337) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:157) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:157) - Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 2 taskToListOfSubTasksMap: 2 taskToVariableMap: 2 topTaskToBaseTask: 2 INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@8d7b252 INFO (SolverHandler:391) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:437) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:449) - Running simulation Caravagna2010, 89 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@24361cfc INFO (SolverHandler:391) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:437) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'. INFO (SolverHandler:449) - Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 47 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:557) - Ran 2 simulation jobs for 1 biomodels. INFO (ExecuteImpl:359) - Generating outputs... INFO (ExecuteImpl:364) - Generating CSV file... INFO (RunUtils:237) - Generating report `report__copy_2`. INFO (RunUtils:428) - created csv file for report report__copy_2: /tmp/out/BIOMD0000000912_sim.sedml/report__copy_2.csv INFO (ExecuteImpl:381) - Generating Plots... WARN (CLIPythonManager:65) - Using old style python invocation! INFO (ExecuteImpl:389) - Generating HDF5 file... INFO (RunUtils:477) - Generating report `report__copy_2`. INFO (RunUtils:706) - Generating report `report__copy_2`. INFO (NativeLib:29) - Loading jhdf5 writing to file /tmp/out/BIOMD0000000912_sim.sedml/reports.h5 INFO (ExecuteImpl:455) - Archiving result files ERROR (RunUtils:897) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils:901) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl:460) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl:468) - Omex archive.omex processing completed (6s) ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (11.0 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp71wbq9hv/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute INFO (CLIStandalone:34) - Starting Vcell... INFO (PropertyLoader:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.83 INFO (BiosimulationsCommand:106) - Beginning execution INFO (CLIPythonManager:129) - Initializing Python... INFO (CLIPythonManager:149) - Python initalization success! INFO (ExecuteImpl:83) - Preparing output directory... ERROR (CLIUtils:27) - Failed to delete the file: /tmp/out INFO (ExecuteImpl:175) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej INFO (RunUtils:927) - TempPath Created: /tmp/vcell_temp_28709dfa-4075-46b3-bd3f-ed24ac78ffa18861197798844214840 INFO (ExecuteImpl:208) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:224) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl:259) - Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) INFO (ExecuteImpl:264) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl:268) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl:280) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl:319) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter:3337) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:157) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping WARN (SolverUtilities:168) - KISAO - bad format, skipping INFO (SEDMLImporter:157) - Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (XmlBase:4549) - RbmModelContainer is missing. taskToSimulationMap: 2 taskToListOfSubTasksMap: 2 taskToVariableMap: 2 topTaskToBaseTask: 2 INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@1fde4f40 INFO (SolverHandler:391) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:437) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler:449) - Running simulation Caravagna2010, 93 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@26a4551a INFO (SolverHandler:391) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler:437) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'. INFO (SolverHandler:449) - Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 48 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:557) - Ran 2 simulation jobs for 1 biomodels. INFO (ExecuteImpl:359) - Generating outputs... INFO (ExecuteImpl:364) - Generating CSV file... INFO (RunUtils:237) - Generating report `report`. INFO (RunUtils:428) - created csv file for report report: /tmp/out/BIOMD0000000912_sim.sedml/report.csv INFO (ExecuteImpl:381) - Generating Plots... WARN (CLIPythonManager:65) - Using old style python invocation! INFO (ExecuteImpl:389) - Generating HDF5 file... INFO (RunUtils:477) - Generating report `report`. INFO (RunUtils:706) - Generating report `report`. INFO (NativeLib:29) - Loading jhdf5 writing to file /tmp/out/BIOMD0000000912_sim.sedml/reports.h5 ERROR (ExecuteImpl:424) - null java.lang.ArrayIndexOutOfBoundsException: null at java.lang.System.arraycopy(Native Method) ~[?:1.8.0_342] at org.vcell.cli.run.hdf5.Hdf5Writer.writeHdf5(Hdf5Writer.java:62) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:400) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:87) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:96) [vcell-cli-0.0.1-SNA ...
biosimulators-daemon commented 1 year 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/3421927099). 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/3421927099).