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biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
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Submit VCell 7.4.0.83 #594

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 (11.2 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_91b780a2-24dd-40ba-91d3-826362371e338067955890817984533 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, 89 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 (12.2 s)
Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths Exception: ``` 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_bf8c12f7-a230-471e-88ee-2244a5ac6a135843678423738469763 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, 78 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, 37 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 (9.5 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_f0b3dbfa-ae63-46f1-b9bc-39cb5605a25f543790807933927800 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/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 (5s) ```
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (12.2 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_177e551e-404a-465e-8111-e2006b72196e5831610128220106605 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, 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/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, 44 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 (9.1 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Exception: ``` [Errno 2] No such file or directory: '/tmp/tmpp0lfaiam/docker_image/docker_image.SingularityImageExecutesSimulationsSuccessfully/1/outputs/archive.omex' ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (10.6 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_58806073-acdb-4eca-913d-28fcbbb11e226427527003170545709 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, 170 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 (6s) ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (13.7 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_62d75629-313e-42f4-9bb2-6c2802fbe57e2255449693040911466 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 facto ...
biosimulators-daemon commented 1 year ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (3.0 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 (4.4 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 (0.9 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.7 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 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 (9.6 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_fbb1d91e-4dd5-4088-a832-1b1612a3b0c08378838929256135070 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 (5s) ```
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (9.7 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``) and inherit the changes of the model. Reason for skip: ``` 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_a25269cf-6b5b-4c4b-80cb-8073c1916ba0235307430571244067 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 (5s) ```
sedml.SimulatorProducesLinear3DPlots (0.4 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 (0.4 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 (0.4 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 (16.8 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_8ecb2006-b98c-4f2e-af09-3ecfde6c57802860822381197224344 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_cd910850-a394-4be4-b2a2-0b5c1d4af9c16842759187936931251 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, 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.SimulatorSupportsComputeModelChanges (20.8 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_c8f0473c-bf87-4fc2-9c9f-f82857e1a37b1702401397835577262 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, 80 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) 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_103b7ecb-71a6-405b-8df5-1fef39919b565463018479050724468 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, 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 (6s) ```
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (9.4 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_7e92c373-8702-45e0-9222-f76e83f571b48775460108380989088 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, 76 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, 38 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 (5s) ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (9.6 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/tmpp0lfaiam/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_d5bc2ec7-bf81-49e9-b84d-e9204ebdfc2d180614611100563904 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, 92 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, 41 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-SNAPSH ...
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/3492097683). 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/3492097683).
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 (10.5 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_7ad7434b-1753-4d1e-8c2f-5d87946377083855363313367629589 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, 70 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 (13.1 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_6b6df371-3773-44e0-9d49-d998eefbf4838478614466727701930 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, 102 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, 43 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 (9.9 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_3d38c0e5-7270-4868-be43-15a6e2ad78481726590669542836245 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, 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/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 (12.7 s)
Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files. Exception: ``` The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.83' 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_de0f286c-0ac7-4a22-814b-04b28ee062c48866636289132785164 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, 43 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 (9.1 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Exception: ``` [Errno 2] No such file or directory: '/tmp/tmphq16yc0z/docker_image/docker_image.SingularityImageExecutesSimulationsSuccessfully/1/outputs/archive.omex' ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (9.8 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Exception: ``` 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_6324b129-5436-4731-bd8e-ebfc001f870d3537985809316198799 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, 169 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 (6s) ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (12.9 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000086`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000086) Exception: ``` 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_249c5372-6577-4e52-b8f7-bb3f604e9a4c1923978350425838605 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 (2.3 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 (3.9 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 (0.7 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.3 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 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 (9.6 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_922da454-c43b-4b42-9382-79a58a3c427b2423897522915742229 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, 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.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (9.9 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_56d9b31a-e375-432c-9d52-ee84c6f7c14d2049522888298136827 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, 85 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 (0.4 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 (0.4 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 (0.4 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 (16.2 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_4bbe6807-d034-4940-b866-324398d638867036259580486392068 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_1b2beb09-f474-4db2-b075-12b48cb6ef037415786103505730941 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, 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 (7s) ```
sedml.SimulatorSupportsComputeModelChanges (20.1 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_ba306475-e774-4e1d-bab8-afb88cb03aab3845077977439152476 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, 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) 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_85eca659-bf41-478a-af82-0f74210f39347356463776083046302 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, 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 (6s) ```
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (9.1 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_11a7a0b5-452e-45e0-b72e-06bf9e5518888984880637367078993 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, 87 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, 40 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 (5s) ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (9.1 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/tmphq16yc0z/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_6dda0427-e927-452a-8a88-4c10f388cf978624061620523048502 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, 82 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, 45 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-SNAP ...
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/3498924864). 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/3498924864).
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 (10.0 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_3c97a577-7ab0-4591-a7ad-96eab9c5b60a50808395899883598 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@6d9fb2d1 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, 79 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 (5s) ```
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (11.8 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_b8724aca-547e-4357-9569-2a0f555aac6f5508038047146145897 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@3d98d138 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, 78 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@472698d 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, 36 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 (9.2 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_24d545d5-760e-4795-89c9-ba3fa0c7d56f661581568073508808 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@6d9fb2d1 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 (5s) ```
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (11.5 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_2b2084c2-e628-495f-bd9a-0b61058847f41509519111855398735 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@6d9fb2d1 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, 78 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@52d6cd34 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, 48 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 (6.3 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Exception: ``` [Errno 2] No such file or directory: '/tmp/tmp0m97m2uc/docker_image/docker_image.SingularityImageExecutesSimulationsSuccessfully/1/outputs/archive.omex' ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (9.6 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_050e6e0e-a181-4873-b3cf-b167014395b33566598731086694489 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@7144655b 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, 164 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 (6s) ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (12.4 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_cf3c31fb-62f9-4f8f-832c-69497dc01cd51051961209750913114 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 factor wa ...
biosimulators-daemon commented 1 year ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (2.5 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports. Warnings: ``` The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports. The command-line interface does not describe the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be described in the inline help for its command-line interface. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
cli.CliDisplaysHelpInline (4.1 s)
Test that a command-line interface provides inline help. Warnings: ``` Command-line interfaces should display basic help when no arguments are provided. The command-line interface displayed the following when no argument was provided: docker: Command recieved::<> <> Default case selected VCell shall execute 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 (0.8 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.6 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 (9.1 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_7df6cf85-688a-4071-9db7-cafbd591a8516901513135307990489 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@7906578e(archive_BIOMD0000000912_sim.sedml___source__) with model from BioModel@51c929ae(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@62566842 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, 66 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 (5s) ```
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (9.1 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_d93f4302-3220-4076-b969-648ec022216f401097116757199236 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@1bbae752(archive_BIOMD0000000912_sim.sedml___source__) with model from BioModel@3abd581e(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@58b67519 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, 69 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 (5s) ```
sedml.SimulatorProducesLinear3DPlots (0.4 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 (0.4 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 (0.4 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 (15.9 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_5822c6be-4d56-4a6c-ba13-9da1e0845437280804147847391019 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_7d25000f-be81-46b8-8214-651fdc46dd323974105272897254411 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@7a7cc52c 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, 73 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.SimulatorSupportsComputeModelChanges (19.3 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_1a366c04-762a-4011-9bea-d291ab5bbe368835520215923402466 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@1b4ae4e0 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, 67 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) 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_e3ba1acc-05c1-4a59-9ba8-b25633f0552a705549208902359376 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@64968732 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/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.SimulatorSupportsDataGeneratorsWithDifferentShapes (9.1 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_1f19ad97-96fc-4b12-842d-4b9a20bfd1a71876883900813741059 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@540a903b 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, 62 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@6eb82908 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, 44 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 (5s) ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (8.9 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/tmp0m97m2uc/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_533427e6-0da9-4e9e-90cd-5c7c286d58838869699327118501492 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@7ce9e05a 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, 77 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@50194e8d 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, 41 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-SNAP ...
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/3577002474). 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/3577002474).
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 (9.3 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_4f767fc6-9862-4b47-8a74-61ce2eaf125c4455874870584126886 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@6d9fb2d1 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, 67 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 (5s) ```
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (11.3 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_cb4818de-1463-4972-b2aa-4a0f08f42de94782996638630280539 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@3d98d138 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/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@472698d 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, 38 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 (8.7 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_858f48d1-9755-4935-876e-b768ca4b674f8824158195884411175 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@6d9fb2d1 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, 77 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 (5s) ```
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (11.1 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_981efbc6-8904-4a3b-a424-4f9c81bdf8f2864537685734825291 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@6d9fb2d1 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, 71 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@52d6cd34 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, 50 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 (8.7 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Exception: ``` [Errno 2] No such file or directory: '/tmp/tmpx4ym3fkw/docker_image/docker_image.SingularityImageExecutesSimulationsSuccessfully/1/outputs/archive.omex' ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (9.3 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_a9218725-5b35-4a28-8593-928d9337fd377994252599382936811 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@7144655b 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, 156 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 (6s) ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (12.2 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_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_8548ab4b-f227-4a4a-96f1-9016ba463bff4329526509422268009 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 factor w ...
biosimulators-daemon commented 1 year ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.9 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports. Warnings: ``` The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports. The command-line interface does not describe the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be described in the inline help for its command-line interface. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
cli.CliDisplaysHelpInline (3.8 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 (0.4 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.3 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 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 (8.6 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_94e5349d-4099-42ed-a4a7-33cabb83b8877004116630517954114 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@7906578e(archive_BIOMD0000000912_sim.sedml___source__) with model from BioModel@51c929ae(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@62566842 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, 78 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 (5s) ```
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (8.8 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_19020a50-0a64-4a87-8866-bbef6e41db0d1904797394060868025 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@1bbae752(archive_BIOMD0000000912_sim.sedml___source__) with model from BioModel@3abd581e(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@58b67519 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, 67 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 (5s) ```
sedml.SimulatorProducesLinear3DPlots (0.4 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 (0.4 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 (0.4 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 (14.9 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_66a9a729-50c2-4016-a7a6-1ebba0275cab4160538329558069400 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_98372281-d580-4807-bce6-f28ef65d7bf13174012015947690468 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@7a7cc52c 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, 80 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.SimulatorSupportsComputeModelChanges (18.6 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_600b9094-c4e7-4ad6-9a6c-b0a33a8ae47f2583998838627388189 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@1b4ae4e0 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, 69 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) 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_87913626-b3d5-4a8b-8b17-7d4f97ab78733300943098965093978 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@64968732 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, 71 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.SimulatorSupportsDataGeneratorsWithDifferentShapes (8.5 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_fa9f8ef7-fab2-4960-9082-e8a714b201485031792232666597320 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@540a903b 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, 78 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@6eb82908 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, 42 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 (5s) ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (8.5 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/tmpx4ym3fkw/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_86b1ae64-a63d-40a6-aa02-204b60dbdad46365294041289432961 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@7ce9e05a 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:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@50194e8d 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, 34 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-S ...
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/3577275581). 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/3577275581).
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 (12.9 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_2fa30876-079b-43d4-afb4-3996f3d6b091238841364809138101 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@6d9fb2d1 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, 97 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 (7s) ```
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (13.8 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_e0b4e70f-7c79-48a1-bbe6-49659907c18f60282548445280190 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@3d98d138 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, 92 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@472698d 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, 55 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 (11.4 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_0cc5a905-8574-4343-916d-39b0c994e8695390108305484424988 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@6d9fb2d1 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, 88 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 (15.8 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_6e39006c-968c-43ed-8cd2-3f26c31095128449003660620059342 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@6d9fb2d1 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, 100 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@52d6cd34 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, 46 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 (9.5 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Exception: ``` [Errno 2] No such file or directory: '/tmp/tmpmr38vp6z/docker_image/docker_image.SingularityImageExecutesSimulationsSuccessfully/1/outputs/archive.omex' ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (12.5 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_4cb6565e-9941-47ad-8b94-805a58a314857473471086424086048 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@7144655b 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, 177 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 (17.5 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_9f4d5342-bd75-47a0-a9da-d77d4c2689881744734595278594530 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 factor ...
biosimulators-daemon commented 1 year ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (3.1 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 (5.2 s)
Test that a command-line interface provides inline help. Warnings: ``` Command-line interfaces should display basic help when no arguments are provided. The command-line interface displayed the following when no argument was provided: docker: Command recieved::<> <> Default case selected VCell shall execute 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 (12.4 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_dc9ef04f-e64e-40da-a4a8-6a54e9bcef8b5738171857323384285 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@7906578e(archive_BIOMD0000000912_sim.sedml___source__) with model from BioModel@51c929ae(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@62566842 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, 104 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.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (11.6 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_bbc147e2-1bca-45ea-a8c9-edb4965d7b0d5617489574872971788 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@1bbae752(archive_BIOMD0000000912_sim.sedml___source__) with model from BioModel@3abd581e(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@58b67519 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, 97 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 (20.8 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_da299b92-f923-4b87-9b0b-216e1f82f2ba7272219647519986886 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_25d7d222-85da-4f78-bfc7-ed544f619f3d3972884717184076831 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@7a7cc52c 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, 97 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 (25.3 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_d53d6967-305a-4b49-b1a2-31b47d6ac3097622826522086233645 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@1b4ae4e0 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, 109 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_6cb4ca69-1e5c-4a39-a12c-4be742cb938f2997765302376629106 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@64968732 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, 94 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 (8s) ```
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (11.8 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_fc3dac05-d8e4-4934-acdb-7345ea11bfee8625250230498727972 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@540a903b 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, 100 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@6eb82908 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__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 (7s) ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (11.8 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/tmpmr38vp6z/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_d56dcd24-e67a-4d88-a77e-41ed07c8d2437080144285956476025 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@7ce9e05a 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, 106 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@50194e8d 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, 49 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 ...
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/3577275581). 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/3577275581).
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 (10.6 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_27957836-3ac8-4040-89b9-ea54eacc45ef2650820120483385748 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@6d9fb2d1 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/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 (12.3 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_44346d11-636e-4273-88db-8d7bd19a71e03379538601812455127 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@3d98d138 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: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@472698d 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, 39 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 (9.5 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_516bb957-8510-4c4b-b22f-6096b74c03866724922463411599507 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@6d9fb2d1 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, 82 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 (5s) ```
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (12.5 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_109e17c7-6814-49de-9738-9ccf6534962f3583892691478390855 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@6d9fb2d1 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: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@52d6cd34 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, 38 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 (6.4 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Exception: ``` [Errno 2] No such file or directory: '/tmp/tmphdp53luc/docker_image/docker_image.SingularityImageExecutesSimulationsSuccessfully/1/outputs/archive.omex' ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (10.1 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_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_840c6ab5-7cf3-4e9f-8db6-4b1d86c5bcd96656540069758754391 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@7144655b 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, 176 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 (6s) ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (13.3 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_0ff1465a-1520-4fb8-8ecf-8ce5ebbb1fac2065330779796973214 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 facto ...
biosimulators-daemon commented 1 year ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (2.3 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 (4.3 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 (0.7 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.5 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 (9.4 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_08930598-1abb-47d4-99ce-02b438c0ad8b7685542085739057367 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@7906578e(archive_BIOMD0000000912_sim.sedml___source__) with model from BioModel@51c929ae(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@62566842 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, 70 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 (5s) ```
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (9.7 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``) and inherit the changes of the model. Reason for skip: ``` 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_2a99915b-7b27-4eac-9bd1-50b569253ec41058367103213920553 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@1bbae752(archive_BIOMD0000000912_sim.sedml___source__) with model from BioModel@3abd581e(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@58b67519 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, 77 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 (0.4 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 (0.4 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 (0.4 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 (16.2 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_0f595254-a81c-4850-9bcb-aea0fb0e77d24714904871477828876 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_01798394-158e-4e15-b215-73e5a7101a6b3807813843895001420 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@7a7cc52c 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, 82 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.SimulatorSupportsComputeModelChanges (20.2 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_34ed70b3-688e-4aa0-94be-86ce6003cf475186688678386011832 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@1b4ae4e0 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, 73 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) 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_b465eb1f-6a75-46a8-b947-6e565fe354347662671570121018512 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@64968732 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, 91 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.SimulatorSupportsDataGeneratorsWithDifferentShapes (9.3 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_a5de5b94-4b4f-48f1-b9a8-a1b56ba220a23322130765551552226 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@540a903b 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@6eb82908 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, 37 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 (5s) ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (9.3 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/tmphdp53luc/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_9f63454b-549a-421e-9df5-f854943f0af52170171020811341954 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@7ce9e05a 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:390) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@50194e8d 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`. 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-S ...
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/3696095081). 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/3696095081).
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 (12.1 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_dda44624-aaa6-4046-b62c-83b4421696551985108336808714517 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, 98 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 (13.8 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_d5e4ddb2-7fc5-4f60-865a-4501776a8ab22928015297044243829 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, 92 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, 45 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 (10.5 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_1143ca89-74c0-4e70-aa1e-f13df99051a74450510814802188279 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, 94 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 (14.2 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_fd25570c-b150-4580-b72e-ac0d7c3119392917325351994724673 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, 89 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, 45 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 (7.4 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Exception: ``` [Errno 2] No such file or directory: '/tmp/tmp1soyjajb/docker_image/docker_image.SingularityImageExecutesSimulationsSuccessfully/1/outputs/archive.omex' ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (11.7 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_0fd9c095-f855-4805-8967-c3c3ab96d4e83204463308700634107 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, 185 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 (15.1 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000086`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000086) Exception: ``` 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_4ac57183-1afb-4256-aa88-93ef76b92c802225227811426685988 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 fac ...
biosimulators-daemon commented 1 year ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (2.8 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 (4.7 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 (0.8 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.6 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 (11.1 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_27dda46f-44b8-4704-9da2-8367688967446564345162349443180 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, 89 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 (11.0 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_ff40b423-fa17-4586-9ac7-e26881e270073888851264495447785 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, 89 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 (19.3 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_6849731e-018c-4333-8614-e0b56f0f17078901216555815195810 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_6c5c4353-0d63-4a1c-9409-0d235b1b905660215702678134916 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, 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/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 (23.7 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_afbc0789-5846-4971-a1d6-1120dce109374791872292449476453 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, 82 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_013cd23f-477a-414b-bb1b-6f82d05a14a75182518486679489431 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 (10.9 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_ec6338e6-ebe7-4e5d-8b50-f94f2fd172a35037338676724844124 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, 94 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, 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__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 (11.1 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/tmp1soyjajb/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_63f8bc9d-2763-47f2-9af7-d3db568658d87896227820298538017 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, 91 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, 49 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-SN ...
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/3751532395). 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/3751532395).
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.