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biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
MIT License
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Submit VCell 7.5.0.26 #610

Closed vcdaemon closed 1 year ago

vcdaemon commented 1 year ago

id: vcell version: 7.5.0.26 specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.5.0.26/biosimulators.json specificationsPatch: version: 7.5.0.26 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.5.0.26 digest: "sha256:be818344ee6f2b955afcb9d0a3f81a36221d3bd4243ee2434e71e4d3e667d53f" validateImage: true commitSimulator: false

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, and validating your Docker image. You have chosen not to submit your simulator to the BioSimulators registry.

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

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

biosimulators-daemon commented 1 year ago

The specifications of your simulator is valid!

biosimulators-daemon commented 1 year ago

Summary of tests

biosimulators-daemon commented 1 year ago

Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (13.6 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:38) - Starting Vcell... []{} INFO (PropertyLoader:576) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{} INFO (PropertyLoader:582) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.26 []{} INFO (BiosimulationsCommand:98) - Beginning execution []{} INFO (CLIPythonManager:115) - Initializing Python... []{} INFO (CLIPythonManager:135) - Python initialization success! []{} INFO (ExecuteImpl:77) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} INFO (ExecutionJob:85) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej []{} INFO (RunUtils:527) - TempPath Created: /tmp/vcell_temp_d0457c2e-60a8-480f-a85d-6c1f7fe206178413457804116322842 []{} INFO (SedmlJob:97) - 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 (SedmlJob:108) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:144) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:149) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:153) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:165) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:227) - 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 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:180) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:416) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@1a2909ae []{} INFO (SolverHandler:417) - Status: Finished: SOLVER_FINISHED:completed []{} INFO (SolverHandler:463) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. []{} INFO (SolverHandler:475) - Running simulation Caravagna2010, 68 ms []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:583) - Ran 1 simulation jobs for 1 biomodels. []{} INFO (SedmlJob:260) - Generating outputs... []{} INFO (SedmlJob:310) - Generating CSV file... []{} INFO (RunUtils:240) - Generating report `report`. []{} INFO (RunUtils:431) - created csv file for report report: /tmp/out/subdir/BIOMD0000000912_sim.sedml/report.csv []{} INFO (SedmlJob:328) - Generating Plots... []{} WARN (CLIPythonManager:77) - Using old style python invocation! []{} WARN (CLIPythonManager:248) - Temp out file didn't delete properly []{} WARN (CLIPythonManager:249) - Temp error file didn't delete properly []{} INFO (SedmlJob:339) - Generating HDF5 file... []{} INFO (SedmlJob:296) - Archiving result files []{} ERROR (RunUtils:497) - No PDF files found, skipping archiving `plots.zip` files []{} INFO (RunUtils:501) - Archiving resultant CSV files to `reports.zip`. []{} INFO (SedmlJob:303) - SED-ML : BIOMD0000000912_sim.sedml successfully completed []{} INFO (ExecutionJob:141) - Processing of SedML succeeded. org.vcell.cli.run.SedmlStatistics@3414a8c3 []{} INFO (NativeLib:29) - Loading jhdf5 []{} INFO (Hdf5Writer:40) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:92) - HDF5 file successfully written to. []{} INFO (ExecutionJob:171) - Omex archive.omex processing completed (6s) []{} ```
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (16.1 s)
Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths Exception: ``` Simulator did not generate the following expected reports - `subdir/BIOMD0000000912_sim.sedml/report` - `subdir__copy/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:38) - Starting Vcell... []{} INFO (PropertyLoader:576) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{} INFO (PropertyLoader:582) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.26 []{} INFO (BiosimulationsCommand:98) - Beginning execution []{} INFO (CLIPythonManager:115) - Initializing Python... []{} INFO (CLIPythonManager:135) - Python initialization success! []{} INFO (ExecuteImpl:77) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} INFO (ExecutionJob:85) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej []{} INFO (RunUtils:527) - TempPath Created: /tmp/vcell_temp_9f8594d2-fac4-445f-a391-a0810787b0bd6259399968183148832 []{} INFO (SedmlJob:97) - 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 (SedmlJob:108) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:144) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:149) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:153) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:165) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:227) - 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 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:180) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:416) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@1894593a []{} INFO (SolverHandler:417) - Status: Finished: SOLVER_FINISHED:completed []{} INFO (SolverHandler:463) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. []{} INFO (SolverHandler:475) - Running simulation Caravagna2010, 85 ms []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:583) - Ran 1 simulation jobs for 1 biomodels. []{} INFO (SedmlJob:260) - Generating outputs... []{} INFO (SedmlJob:310) - Generating CSV file... []{} INFO (RunUtils:240) - Generating report `report`. []{} INFO (RunUtils:431) - created csv file for report report: /tmp/out/subdir/BIOMD0000000912_sim.sedml/report.csv []{} INFO (SedmlJob:328) - Generating Plots... []{} WARN (CLIPythonManager:77) - Using old style python invocation! []{} WARN (CLIPythonManager:248) - Temp out file didn't delete properly []{} WARN (CLIPythonManager:249) - Temp error file didn't delete properly []{} INFO (SedmlJob:339) - Generating HDF5 file... []{} INFO (SedmlJob:296) - Archiving result files []{} ERROR (RunUtils:497) - No PDF files found, skipping archiving `plots.zip` files []{} INFO (RunUtils:501) - Archiving resultant CSV files to `reports.zip`. []{} INFO (SedmlJob:303) - SED-ML : BIOMD0000000912_sim.sedml successfully completed []{} INFO (ExecutionJob:141) - Processing of SedML succeeded. org.vcell.cli.run.SedmlStatistics@6ed16657 []{} INFO (SedmlJob:97) - 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 (SedmlJob:108) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:144) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:149) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:153) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:165) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:227) - 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 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:180) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:416) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@ae73c80 []{} INFO (SolverHandler:417) - Status: Finished: SOLVER_FINISHED:completed []{} INFO (SolverHandler:463) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. []{} INFO (SolverHandler:475) - Running simulation Caravagna2010, 50 ms []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:583) - Ran 1 simulation jobs for 1 biomodels. []{} INFO (SedmlJob:260) - Generating outputs... []{} INFO (SedmlJob:310) - Generating CSV file... []{} INFO (RunUtils:240) - Generating report `report`. []{} INFO (RunUtils:431) - created csv file for report report: /tmp/out/subdir__copy/BIOMD0000000912_sim.sedml/report.csv []{} INFO (SedmlJob:328) - Generating Plots... []{} WARN (CLIPythonManager:77) - Using old style python invocation! []{} WARN (CLIPythonManager:248) - Temp out file didn't delete properly []{} WARN (CLIPythonManager:249) - Temp error file didn't delete properly []{} INFO (SedmlJob:339) - Generating HDF5 file... []{} INFO (SedmlJob:296) - Archiving result files []{} ERROR (RunUtils:497) - No PDF files found, skipping archiving `plots.zip` files []{} INFO (RunUtils:501) - Archiving resultant CSV files to `reports.zip`. []{} INFO (SedmlJob:303) - SED-ML : BIOMD0000000912_sim.sedml successfully completed []{} INFO (ExecutionJob:141) - Processing of SedML succeeded. org.vcell.cli.run.SedmlStatistics@22f4f8f2 []{} INFO (NativeLib:29) - Loading jhdf5 []{} INFO (Hdf5Writer:40) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:92) - HDF5 file successfully written to. []{} INFO (ExecutionJob:171) - Omex archive.omex processing completed (9s) []{} ```
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (12.9 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:38) - Starting Vcell... []{} INFO (PropertyLoader:576) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{} INFO (PropertyLoader:582) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.26 []{} INFO (BiosimulationsCommand:98) - Beginning execution []{} INFO (CLIPythonManager:115) - Initializing Python... []{} INFO (CLIPythonManager:135) - Python initialization success! []{} INFO (ExecuteImpl:77) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} INFO (ExecutionJob:85) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej []{} INFO (RunUtils:527) - TempPath Created: /tmp/vcell_temp_2c8b0cb0-510d-4679-b2e7-d773196785ce4894344050074412439 []{} INFO (SedmlJob:97) - 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 (SedmlJob:108) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:144) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:149) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:153) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:165) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:227) - 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 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:180) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:416) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@1a2909ae []{} INFO (SolverHandler:417) - Status: Finished: SOLVER_FINISHED:completed []{} INFO (SolverHandler:463) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. []{} INFO (SolverHandler:475) - Running simulation Caravagna2010, 68 ms []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:583) - Ran 1 simulation jobs for 1 biomodels. []{} INFO (SedmlJob:260) - Generating outputs... []{} INFO (SedmlJob:310) - Generating CSV file... []{} INFO (RunUtils:240) - Generating report `report`. []{} INFO (RunUtils:431) - created csv file for report report: /tmp/out/BIOMD0000000912_sim.sedml/report.csv []{} INFO (SedmlJob:328) - Generating Plots... []{} WARN (CLIPythonManager:77) - Using old style python invocation! []{} WARN (CLIPythonManager:248) - Temp out file didn't delete properly []{} WARN (CLIPythonManager:249) - Temp error file didn't delete properly []{} INFO (SedmlJob:339) - Generating HDF5 file... []{} INFO (SedmlJob:296) - Archiving result files []{} ERROR (RunUtils:497) - No PDF files found, skipping archiving `plots.zip` files []{} INFO (RunUtils:501) - Archiving resultant CSV files to `reports.zip`. []{} INFO (SedmlJob:303) - SED-ML : BIOMD0000000912_sim.sedml successfully completed []{} INFO (ExecutionJob:141) - Processing of SedML succeeded. org.vcell.cli.run.SedmlStatistics@2241f05b []{} INFO (NativeLib:29) - Loading jhdf5 []{} INFO (Hdf5Writer:40) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:92) - HDF5 file successfully written to. []{} INFO (ExecutionJob:171) - Omex archive.omex processing completed (6s) []{} ```
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (16.0 s)
Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files. Exception: ``` Simulator did not generate the following expected reports - `BIOMD0000000912_sim.sedml/report` - `BIOMD0000000912_sim__copy.sedml/report` ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute INFO (CLIStandalone:38) - Starting Vcell... []{} INFO (PropertyLoader:576) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{} INFO (PropertyLoader:582) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.26 []{} INFO (BiosimulationsCommand:98) - Beginning execution []{} INFO (CLIPythonManager:115) - Initializing Python... []{} INFO (CLIPythonManager:135) - Python initialization success! []{} INFO (ExecuteImpl:77) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} INFO (ExecutionJob:85) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej []{} INFO (RunUtils:527) - TempPath Created: /tmp/vcell_temp_aae4dbc0-8454-4d17-b849-caad422500f77768850888697280540 []{} INFO (SedmlJob:97) - 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 (SedmlJob:108) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:144) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:149) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:153) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:165) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:227) - 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 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:180) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:416) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@1a2909ae []{} INFO (SolverHandler:417) - Status: Finished: SOLVER_FINISHED:completed []{} INFO (SolverHandler:463) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. []{} INFO (SolverHandler:475) - Running simulation Caravagna2010, 69 ms []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:583) - Ran 1 simulation jobs for 1 biomodels. []{} INFO (SedmlJob:260) - Generating outputs... []{} INFO (SedmlJob:310) - Generating CSV file... []{} INFO (RunUtils:240) - Generating report `report`. []{} INFO (RunUtils:431) - created csv file for report report: /tmp/out/BIOMD0000000912_sim.sedml/report.csv []{} INFO (SedmlJob:328) - Generating Plots... []{} WARN (CLIPythonManager:77) - Using old style python invocation! []{} WARN (CLIPythonManager:248) - Temp out file didn't delete properly []{} WARN (CLIPythonManager:249) - Temp error file didn't delete properly []{} INFO (SedmlJob:339) - Generating HDF5 file... []{} INFO (SedmlJob:296) - Archiving result files []{} ERROR (RunUtils:497) - No PDF files found, skipping archiving `plots.zip` files []{} INFO (RunUtils:501) - Archiving resultant CSV files to `reports.zip`. []{} INFO (SedmlJob:303) - SED-ML : BIOMD0000000912_sim.sedml successfully completed []{} INFO (ExecutionJob:141) - Processing of SedML succeeded. org.vcell.cli.run.SedmlStatistics@2241f05b []{} INFO (SedmlJob:97) - 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 (SedmlJob:108) - Processing SED-ML: BIOMD0000000912_sim__copy.sedml []{} INFO (SedmlJob:144) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:149) - Successful translation of SED-ML file : BIOMD0000000912_sim__copy.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:153) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:165) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:227) - 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 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:180) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:416) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@47ac613b []{} INFO (SolverHandler:417) - Status: Finished: SOLVER_FINISHED:completed []{} INFO (SolverHandler:463) - Succesful execution: Model 'archive_BIOMD0000000912_sim__copy.sedml_BIOMD0000000912' Task 'Caravagna2010'. []{} INFO (SolverHandler:475) - Running simulation Caravagna2010, 53 ms []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:583) - Ran 1 simulation jobs for 1 biomodels. []{} INFO (SedmlJob:260) - Generating outputs... []{} INFO (SedmlJob:310) - Generating CSV file... []{} INFO (RunUtils:240) - Generating report `report`. []{} INFO (RunUtils:431) - created csv file for report report: /tmp/out/BIOMD0000000912_sim__copy.sedml/report.csv []{} INFO (SedmlJob:328) - Generating Plots... []{} WARN (CLIPythonManager:77) - Using old style python invocation! []{} WARN (CLIPythonManager:248) - Temp out file didn't delete properly []{} WARN (CLIPythonManager:249) - Temp error file didn't delete properly []{} INFO (SedmlJob:339) - Generating HDF5 file... []{} INFO (SedmlJob:296) - Archiving result files []{} ERROR (RunUtils:497) - No PDF files found, skipping archiving `plots.zip` files []{} INFO (RunUtils:501) - Archiving resultant CSV files to `reports.zip`. []{} INFO (SedmlJob:303) - SED-ML : BIOMD0000000912_sim__copy.sedml successfully completed []{} INFO (ExecutionJob:141) - Processing of SedML succeeded. org.vcell.cli.run.SedmlStatistics@60d6fdd4 []{} INFO (NativeLib:29) - Loading jhdf5 []{} INFO (Hdf5Writer:40) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:92) - HDF5 file successfully written to. []{} INFO (ExecutionJob:171) - Omex archive.omex processing completed (9s) []{} ```
docker_image.SingularityImageExecutesSimulationsSuccessfully (9.0 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Exception: ``` [Errno 2] No such file or directory: '/tmp/tmp509cfdjo/docker_image/docker_image.SingularityImageExecutesSimulationsSuccessfully/1/outputs/archive.omex' ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (14.1 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: ``` b'SedPlot2D' ``` 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:38) - Starting Vcell... []{} INFO (PropertyLoader:576) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{} INFO (PropertyLoader:582) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.26 []{} INFO (BiosimulationsCommand:98) - Beginning execution []{} INFO (CLIPythonManager:115) - Initializing Python... []{} INFO (CLIPythonManager:135) - Python initialization success! []{} INFO (ExecuteImpl:77) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} INFO (ExecutionJob:85) - Executing OMEX archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej []{} INFO (RunUtils:527) - TempPath Created: /tmp/vcell_temp_93f9ac2a-3586-4483-bd71-6e91f546c53a6380986141120637057 []{} INFO (SedmlJob:97) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:108) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:144) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 1 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:149) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:153) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:165) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:227) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:180) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:416) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@608bc8f8 []{} INFO (SolverHandler:417) - Status: Finished: SOLVER_FINISHED:completed []{} INFO (SolverHandler:463) - Succesful execution: Model 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. []{} INFO (SolverHandler:475) - Running simulation Caravagna2010, 174 ms []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:583) - Ran 1 simulation jobs for 1 biomodels. []{} INFO (SedmlJob:260) - Generating outputs... []{} INFO (SedmlJob:310) - Generating CSV file... []{} INFO (RunUtils:234) - Ignoring unsupported output `Figure_1_bottom_left` while CSV generation. []{} INFO (RunUtils:240) - Generating report `report`. []{} INFO (RunUtils:431) - created csv file for report report: /tmp/out/BIOMD0000000912_sim.sedml/report.csv []{} INFO (RunUtils:240) - Generating report `__plot__Figure_1_bottom_left`. []{} INFO (RunUtils:431) - created csv file for report __plot__Figure_1_bottom_left: /tmp/out/BIOMD0000000912_sim.sedml/__plot__Figure_1_bottom_left.csv []{} INFO (SedmlJob:328) - Generating Plots... []{} WARN (CLIPythonManager:77) - Using old style python invocation! []{} WARN (CLIPythonManager:248) - Temp out file didn't delete properly []{} WARN (CLIPythonManager:249) - Temp error file didn't delete properly []{} INFO (SedmlJob:339) - Generating HDF5 file... []{} INFO (NonspatialResultsConverter:208) - Ignoring unsupported output `Figure_1_bottom_left` while CSV generation. []{} INFO (SpatialResultsConverter:131) - Ignoring unsupported output `Figure_1_bottom_left` while CSV generation. []{} INFO (SedmlJob:296) - Archiving result files []{} INFO (RunUtils:501) - Archiving resultant PDF files to `plots.zip`. []{} INFO (RunUtils:501) - Archiving resultant CSV files to `reports.zip`. []{} INFO (SedmlJob:303) - SED-ML : BIOMD0000000912_sim.sedml successfully completed []{} INFO (ExecutionJob:141) - Processing of SedML succeeded. org.vcell.cli.run.SedmlStatistics@51a6cc2a []{} INFO (NativeLib:29) - Loading jhdf5 []{} INFO (Hdf5Writer:40) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:92) - HDF5 file successfully written to. []{} INFO (ExecutionJob:171) - 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 (17.4 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: ``` b'SedPlot2D' ``` 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:38) - Starting Vcell... []{} INFO (PropertyLoader:576) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{} INFO (PropertyLoader:582) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.26 []{} INFO (BiosimulationsCommand:98) - Beginning execution []{} INFO (CLIPythonManager:115) - Initializing Python... []{} INFO (CLIPythonManager:135) - Python initialization success! []{} INFO (ExecuteImpl:77) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} INFO (ExecutionJob:85) - Executing OMEX archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej []{} INFO (RunUtils:527) - TempPath Created: /tmp/vcell_temp_d691074a-3881-447f-952d-f3ba5262a3897647353073674411334 []{} INFO (SedmlJob:97) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:108) - Processing SED-ML: simulation_1.sedml []{} INFO (SedmlJob:144) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 4 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:149) - Successful translation of SED-ML file : simulation_1.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:153) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:165) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:227) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SBMLImporter:2833) - failed to transform lumped reaction R1 to distributed: linear factor was null, lumped reaction R1 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R2 to distributed: linear factor was null, lumped reaction R2 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R3 to distributed: linear factor was null, lumped reaction R3 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R4 to distributed: linear factor was null, lumped reaction R4 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R5 to distributed: linear factor was null, lumped reaction R5 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R6 to distributed: linear factor was null, lumped reaction R6 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R7 to distributed: linear factor was null, lumped reaction R7 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R8 to distributed: linear factor was null, lumped reaction R8 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R9 to distributed: linear factor was null, lumped reaction R9 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R10 to distributed: linear factor was null, lumped reaction R10 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R11 to distributed: linear factor was null, lumped reaction R11 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R12 to distributed: linear factor was null, lumped reaction R12 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R13 to distributed: linear factor was null, lumped reaction R13 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R14 to distributed: linear factor was null, lumped reaction R14 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R15 to distributed: linear factor was null, lumped reaction R15 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R16 to distributed: linear factor was null, lumped reaction R16 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R18 to distributed: linear factor was null, lumped reaction R18 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R19 to distributed: linear factor was null, lumped reaction R19 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R20 to distributed: linear factor was null, lumped reaction R20 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R21 to distributed: linear factor was null, lumped reaction R21 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R22 to distributed: linear factor was null, lumped reaction R22 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R23 to distributed: linear factor was null, lumped reaction R23 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R24 to distributed: linear factor was null, lumped reaction R24 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R25 to distributed: linear factor was null, lumped reaction R25 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R26 to distributed: linear factor was null, lumped reaction R26 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R27 to distributed: linear factor was null, lumped reaction R27 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R28 to distributed: linear factor was null, lumped reaction R28 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R29 to distributed: linear factor was null, lumped reaction R29 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R30 to distributed: linear factor was null, lumped reaction R30 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R31 to distributed: linear factor was null, lumped reaction R31 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R32 to distributed: linear factor was null, lumped reaction R32 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R33 to distributed: linear factor was null, lumped reaction R33 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R34 to distributed: linear factor was null, lumped reaction R34 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R35 to distributed: linear factor was null, lumped reaction R35 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R36 to distributed: linear factor was null, lumped reaction R36 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R37 to distributed: linear factor was null, lumped reaction R37 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R38 to distributed: linear factor was null, lumped reaction R38 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R39 to distributed: linear factor was null, lumped reaction R39 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R40 to distributed: linear factor was null, lumped reaction R40 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R41 to distributed: linear factor was null, lumped reaction R41 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R42 to distributed: linear factor was null, lumped reaction R42 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R43 to distributed: linear factor was null, lumped reaction R43 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R44 to distributed: linear factor was null, lumped reaction R44 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R45 to distributed: linear factor was null, lumped reaction R45 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R46 to distributed: linear factor was null, lumped reaction R46 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R47 to distributed: linear factor was null, lumped reaction R47 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R48 to distributed: linear factor was null, lumped reaction R48 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R49 to distributed: linear factor was null, lumped reaction R49 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R50 to distributed: linear factor was null, lumped reaction R50 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R51 to distributed: linear factor was null, lumped reaction R51 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R52 to distributed: linear factor was null, lumped reaction R52 could not be transformed to distributed []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:180) - Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000086' matched to RungeKuttaFehlberg []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (RowColumnResultSet:534) - rowCount=13762 []{} INFO (RowColumnResultSet:562) - scale[0] = 139.9749483060956 []{} INFO (RowColumnResultSet:562) - scale[1] = 0.10337204038188977 []{} INFO (RowColumnResultSet:562) - scale[2] = 0.18451723700540568 []{} INFO (RowColumnResultSet:562) - scale[3] = 1.248823182479924 []{} INFO (RowColumnResultSet:562) - scale[4] = 0.0866281958361408 []{} INFO (RowColumnResultSet:562) - scale[5] = 0.2487316750047834 []{} INFO (RowColumnResultSet:562) - scale[6] = 0.957165622333867 []{} INFO (RowColumnResultSet:562) - scale[7] = 0.5222071967202937 []{} INFO (RowColumnResultSet:562) - scale[8] = 1.6250612922233858 []{} INFO (RowColumnResultSet:562) - scale[9] = 1.163399212713716 []{} INFO (RowColumnResultSet:562) - scale[10] = 0.9944445913091504 []{} INFO (RowColumnResultSet:562) - scale[11] = 0.1689497310030451 []{} INFO (RowColumnResultSet:562) - scale[12] = 0.02826956834397453 []{} INFO (RowColumnResultSet:562) - scale[13] = 0.0032627104470246394 []{} INFO (RowColumnResultSet:562) - scale[14] = 0.013335866633246523 []{} INFO (RowColumnResultSet:562) - scale[15] = 0.8080848330089925 []{} INFO (RowColumnResultSet:562) - scale[16] = 0.932880719855319 []{} INFO (RowColumnResultSet:562) - scale[17] = 0.9725777981904435 []{} INFO (RowColumnResultSet:562) - scale[18] = 0.9307398276790282 []{} INFO (RowColumnResultSet:562) - scale[19] = 0.813079283325805 []{} INFO (RowColumnResultSet:562) - scale[20] = 1.0 []{} INFO (RowColumnResultSet:562) - scale[21] = 1.0 []{} INFO (RowColumnResultSet:598) - TOLERANCE=0.1, threshold=0.01, size=8424 []{} INFO (RowColumnResultSet:598) - TOLERANCE=0.1, threshold=0.02, size=4232 []{} INFO (RowColumnResultSet:598) - TOLERANCE=0.1, threshold=0.03, size=2129 []{} INFO (RowColumnResultSet:598) - TOLERANCE=0.1, threshold=0.04, size=1074 []{} INFO (RowColumnResultSet:598) - TOLERANCE=0.1, threshold=0.05, size=552 []{} INFO (SolverHandler:463) - Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg_simulation_1.sedml_Ciliberto2003_Morphogenesis' Task 'simulation 1'. []{} INFO (SolverHandler:475) - Running simulation simulation 1, 916 ms []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:583) - Ran 1 simulation jobs for 1 biomodels. []{} INFO (SedmlJob:260) - Generating outputs... []{} INFO (SedmlJob:310) - Generating CSV file... []{} INFO (RunUtils:234) - Ignoring unsupported output `Figure_3a` while CSV generation. []{} INFO (RunUtils:234) - Ignoring unsupported output `Figure_3b` while CSV generation. []{} INFO (RunUtils:234) - Ignoring unsupported output `Figure_3c` while CSV generation. []{} INFO (RunUtils:234) - Ignoring unsupported output `Figure_3d` while CSV generation. []{} INFO (RunUtils:240) - Generating report `report`. []{} INFO (RunUtils:431) - created csv file for report report: /tmp/out/simulation_1.sedml/report.csv []{} INFO (RunUtils:240) - Generating report `__plot__Figure_3a`. []{} INFO (RunUtils:431) - created csv file for report __plot__Figure_3a: /tmp/out/simulation_1.sedml/__plot__Figure_3a.csv []{} INFO (RunUtils:240) - Generating report `__plot__Figure_3b`. []{} INFO (RunUtils:431) - created csv file for report __plot__Figure_3b: /tmp/out/simulation_1.sedml/__plot__Figure_3b.csv []{} INFO (RunUtils:240) - Generating report `__plot__Figure_3c`. []{} INFO (RunUtils:431) - created csv file for report __plot__Figure_3c: /tmp/out/simulation_1.sedml/__plot__Figure_3c.csv []{} INFO (RunUtils:240) - Generating report `__plot__Figure_3d`. []{} INFO (RunUtils:431) - created csv file for report __plot__Figure_3d: /tmp/out/simulation_1.sedml/__plot__Figure_3d.csv []{} INFO (SedmlJob:328) - Generating Plots... []{} WARN (CLIPythonManager:77) - Using old style python invocation! []{} WARN (CLIPythonManager:248) - Temp out file didn't delete properly []{} WARN (CLIPythonManager:249) - Temp error file didn't delete properly []{} INFO (SedmlJob:339) - Generating HDF5 file... []{} INFO (NonspatialResultsConverter:208) - Ignoring unsupported output `Figure_3a` while CSV generation. []{} INFO (NonspatialResultsConverter:208) - Ignoring unsupported output `Figure_3b` while CSV generation. []{} INFO (NonspatialResultsConverter:208) - Ignoring unsupported output `Figure_3c` while CSV generation. []{} INFO (NonspatialResultsConverter:208) - Ignoring unsupported output `Figure_3d` while CSV generation. []{} INFO (SpatialResultsConverter:131) - Ignoring unsupported output `Figure_3a` while CSV generation. []{} INFO (SpatialResultsConverter:131) - Ignoring unsupported output `Figure_3b` while CSV generation. []{} INFO (SpatialResultsConverter:131) - Ignoring unsupported output `Figure_3c` while CSV generation. []{} INFO (SpatialResultsConverter:131) - Ignoring unsupported output `Figure_3d` while CSV generation. []{} INFO (SedmlJob:296) - Archiving result files []{} INFO (RunUtils:501) - Archiving resultant PDF files to `plots.zip`. []{} INFO (RunUtils:501) - Archiving resultant CSV files to `reports.zip`. []{} INFO (SedmlJob:303) - SED-ML : simulation_1.sedml successfully completed []{} INFO (ExecutionJob:141) - Processing of SedML succeeded. org.vcell.cli.run.SedmlStatistics@6a7db16e []{} INFO (NativeLib:29) - Loading jhdf5 []{} INFO (Hdf5Writer:40) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:92) - HDF5 file successfully written to. []{} INFO (ExecutionJob:171) - Omex Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex processing completed (11s) []{} ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (16.9 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Exception: ``` b'SedPlot2D' ``` Log: ``` docker: Command recieved::<-i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex -o /tmp/out> <-i> Default case selected VCell shall execute INFO (CLIStandalone:38) - Starting Vcell... []{} INFO (PropertyLoader:576) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{} INFO (PropertyLoader:582) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.26 []{} INFO (BiosimulationsCommand:98) - Beginning execution []{} INFO (CLIPythonManager:115) - Initializing Python... []{} INFO (CLIPythonManager:135) - Python initialization success! []{} INFO (ExecuteImpl:77) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} INFO (ExecutionJob:85) - Executing OMEX archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej []{} INFO (RunUtils:527) - TempPath Created: /tmp/vcell_temp_c77c48c7-41c2-4141-829d-5e895b60d5b78813454078805107494 []{} INFO (SedmlJob:97) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:108) - Processing SED-ML: simulation_1.sedml []{} INFO (SedmlJob:144) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 4 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:149) - Successful translation of SED-ML file : simulation_1.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:153) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:165) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:227) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SBMLImporter:2833) - failed to transform lumped reaction R1 to distributed: linear factor was null, lumped reaction R1 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R2 to distributed: linear factor was null, lumped reaction R2 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R3 to distributed: linear factor was null, lumped reaction R3 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R4 to distributed: linear factor was null, lumped reaction R4 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R5 to distributed: linear factor was null, lumped reaction R5 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R6 to distributed: linear factor was null, lumped reaction R6 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R7 to distributed: linear factor was null, lumped reaction R7 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R8 to distributed: linear factor was null, lumped reaction R8 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R9 to distributed: linear factor was null, lumped reaction R9 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R10 to distributed: linear factor was null, lumped reaction R10 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R11 to distributed: linear factor was null, lumped reaction R11 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R12 to distributed: linear factor was null, lumped reaction R12 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R13 to distributed: linear factor was null, lumped reaction R13 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R14 to distributed: linear factor was null, lumped reaction R14 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R15 to distributed: linear factor was null, lumped reaction R15 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R16 to distributed: linear factor was null, lumped reaction R16 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R18 to distributed: linear factor was null, lumped reaction R18 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R19 to distributed: linear factor was null, lumped reaction R19 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R20 to distributed: linear factor was null, lumped reaction R20 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R21 to distributed: linear factor was null, lumped reaction R21 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R22 to distributed: linear factor was null, lumped reaction R22 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R23 to distributed: linear factor was null, lumped reaction R23 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R24 to distributed: linear factor was null, lumped reaction R24 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R25 to distributed: linear factor was null, lumped reaction R25 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R26 to distributed: linear factor was null, lumped reaction R26 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R27 to distributed: linear factor was null, lumped reaction R27 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R28 to distributed: linear factor was null, lumped reaction R28 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R29 to distributed: linear factor was null, lumped reaction R29 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R30 to distributed: linear factor was null, lumped reaction R30 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R31 to distributed: linear factor was null, lumped reaction R31 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R32 to distributed: linear factor was null, lumped reaction R32 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R33 to distributed: linear factor was null, lumped reaction R33 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R34 to distributed: linear factor was null, lumped reaction R34 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R35 to distributed: linear factor was null, lumped reaction R35 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R36 to distributed: linear factor was null, lumped reaction R36 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R37 to distributed: linear factor was null, lumped reaction R37 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R38 to distributed: linear factor was null, lumped reaction R38 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R39 to distributed: linear factor was null, lumped reaction R39 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R40 to distributed: linear factor was null, lumped reaction R40 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R41 to distributed: linear factor was null, lumped reaction R41 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R42 to distributed: linear factor was null, lumped reaction R42 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R43 to distributed: linear factor was null, lumped reaction R43 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R44 to distributed: linear factor was null, lumped reaction R44 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R45 to distributed: linear factor was null, lumped reaction R45 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R46 to distributed: linear factor was null, lumped reaction R46 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R47 to distributed: linear factor was null, lumped reaction R47 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to transform lumped reaction R48 to distributed: linear factor was null, lumped reaction R48 could not be transformed to distributed []{} WARN (SBMLImporter:2833) - failed to trans ...
biosimulators-daemon commented 1 year ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (2.4 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports. Warnings: ``` The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports. The command-line interface does not describe the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be described in the inline help for its command-line interface. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
cli.CliDisplaysHelpInline (4.4 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:38) - Starting Vcell... []{} ERROR (BiosimulationsCommand:112) - null []{} java.lang.NullPointerException: null at org.vcell.cli.CLIRecorder.(CLIRecorder.java:68) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:57) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:46) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:51) [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:45) [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:38) - 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:38) - 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 (0.6 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 (12.6 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:38) - Starting Vcell... []{} INFO (PropertyLoader:576) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{} INFO (PropertyLoader:582) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.26 []{} INFO (BiosimulationsCommand:98) - Beginning execution []{} INFO (CLIPythonManager:115) - Initializing Python... []{} INFO (CLIPythonManager:135) - Python initialization success! []{} INFO (ExecuteImpl:77) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} INFO (ExecutionJob:85) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej []{} INFO (RunUtils:527) - TempPath Created: /tmp/vcell_temp_23d19bce-ca5b-426c-929c-5cb46662adea8781234769098013352 []{} INFO (SedmlJob:97) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:108) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:144) - Found one SED-ML document with 2 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:149) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:153) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:165) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:227) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:180) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:416) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@45e1aa48 []{} INFO (SolverHandler:417) - Status: Finished: SOLVER_FINISHED:completed []{} INFO (SolverHandler:463) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml___source__' Task 'Caravagna2010'. []{} INFO (SolverHandler:475) - Running simulation Caravagna2010, 79 ms []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:583) - Ran 1 simulation jobs for 1 biomodels. []{} INFO (SedmlJob:260) - Generating outputs... []{} INFO (SedmlJob:310) - Generating CSV file... []{} INFO (RunUtils:240) - Generating report `report`. []{} INFO (RunUtils:431) - created csv file for report report: /tmp/out/BIOMD0000000912_sim.sedml/report.csv []{} INFO (SedmlJob:328) - Generating Plots... []{} WARN (CLIPythonManager:77) - Using old style python invocation! []{} WARN (CLIPythonManager:248) - Temp out file didn't delete properly []{} WARN (CLIPythonManager:249) - Temp error file didn't delete properly []{} INFO (SedmlJob:339) - Generating HDF5 file... []{} INFO (SedmlJob:296) - Archiving result files []{} ERROR (RunUtils:497) - No PDF files found, skipping archiving `plots.zip` files []{} INFO (RunUtils:501) - Archiving resultant CSV files to `reports.zip`. []{} INFO (SedmlJob:303) - SED-ML : BIOMD0000000912_sim.sedml successfully completed []{} INFO (ExecutionJob:141) - Processing of SedML succeeded. org.vcell.cli.run.SedmlStatistics@11a8042c []{} INFO (NativeLib:29) - Loading jhdf5 []{} INFO (Hdf5Writer:40) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:92) - HDF5 file successfully written to. []{} INFO (ExecutionJob:171) - Omex archive.omex processing completed (6s) []{} ```
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (12.6 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:38) - Starting Vcell... []{} INFO (PropertyLoader:576) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{} INFO (PropertyLoader:582) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.26 []{} INFO (BiosimulationsCommand:98) - Beginning execution []{} INFO (CLIPythonManager:115) - Initializing Python... []{} INFO (CLIPythonManager:135) - Python initialization success! []{} INFO (ExecuteImpl:77) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} INFO (ExecutionJob:85) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej []{} INFO (RunUtils:527) - TempPath Created: /tmp/vcell_temp_903edaf5-cd7b-4476-b261-e6803d3580bf6764224529378992811 []{} INFO (SedmlJob:97) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:108) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:144) - Found one SED-ML document with 2 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:149) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:153) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:165) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:227) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:180) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:416) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@615e3f51 []{} INFO (SolverHandler:417) - Status: Finished: SOLVER_FINISHED:completed []{} INFO (SolverHandler:463) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml___source__' Task 'Caravagna2010'. []{} INFO (SolverHandler:475) - Running simulation Caravagna2010, 90 ms []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:583) - Ran 1 simulation jobs for 1 biomodels. []{} INFO (SedmlJob:260) - Generating outputs... []{} INFO (SedmlJob:310) - Generating CSV file... []{} INFO (RunUtils:240) - Generating report `report`. []{} INFO (RunUtils:431) - created csv file for report report: /tmp/out/BIOMD0000000912_sim.sedml/report.csv []{} INFO (SedmlJob:328) - Generating Plots... []{} WARN (CLIPythonManager:77) - Using old style python invocation! []{} WARN (CLIPythonManager:248) - Temp out file didn't delete properly []{} WARN (CLIPythonManager:249) - Temp error file didn't delete properly []{} INFO (SedmlJob:339) - Generating HDF5 file... []{} INFO (SedmlJob:296) - Archiving result files []{} ERROR (RunUtils:497) - No PDF files found, skipping archiving `plots.zip` files []{} INFO (RunUtils:501) - Archiving resultant CSV files to `reports.zip`. []{} INFO (SedmlJob:303) - SED-ML : BIOMD0000000912_sim.sedml successfully completed []{} INFO (ExecutionJob:141) - Processing of SedML succeeded. org.vcell.cli.run.SedmlStatistics@7d2998d8 []{} INFO (NativeLib:29) - Loading jhdf5 []{} INFO (Hdf5Writer:40) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:92) - HDF5 file successfully written to. []{} INFO (ExecutionJob:171) - 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 (23.3 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:38) - Starting Vcell... []{} INFO (PropertyLoader:576) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{} INFO (PropertyLoader:582) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.26 []{} INFO (BiosimulationsCommand:98) - Beginning execution []{} INFO (CLIPythonManager:115) - Initializing Python... []{} INFO (CLIPythonManager:135) - Python initialization success! []{} INFO (ExecuteImpl:77) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} INFO (ExecutionJob:85) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej []{} INFO (RunUtils:527) - TempPath Created: /tmp/vcell_temp_d09cd7a3-7aba-44d2-86f7-9ba6b91121db6791197967863021032 []{} INFO (SedmlJob:97) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:108) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:144) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:149) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:153) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:165) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:227) - 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 (SolverHandler:325) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. []{} java.lang.RuntimeException: Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:352) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:506) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:229) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:209) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:138) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:152) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:81) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:90) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [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:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:791) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:143) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 19 more Caused by: java.lang.Exception: Errors reported: VCLoggerException occurred: org.vcell.sbml.vcell.SBMLImportException: Inconsistent unit system in SBML model, cannot import into VCell. at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:790) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:143) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 19 more ERROR (SedmlJob:240) - Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported: VCLoggerException occurred: 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 Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:352) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:506) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:323) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:229) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:209) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:138) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:152) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:81) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:90) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [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:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:791) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:143) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 19 more Caused by: java.lang.Exception: Errors reported: VCLoggerException occurred: org.vcell.sbml.vcell.SBMLImportException: Inconsistent unit system in SBML model, cannot import into VCell. at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:790) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:143) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 19 more INFO (SedmlJob:260) - Generating outputs... []{} ERROR (SedmlJob:412) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evalulateResults(SedmlJob.java:285) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:216) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:138) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:152) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:81) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:90) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:101) [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:45) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] WARN (SedmlJob:289) - Unable to initialize bioModel for the given selection Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported: VCLoggerException occurred: org.vcell.sbml.vcell.SBMLImportException: Inconsistent unit system in SBML model, cannot import into VCell. Failure executing the sed document. []{} ERROR (ExecutionJob:142) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@21ec5d87 []{} INFO (NativeLib:29) - Loading jhdf5 []{} INFO (Hdf5Writer:40) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:92) - HDF5 file successfully written to. []{} INFO (ExecutionJob:171) - Omex archive.omex processing completed (2s) []{} docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute INFO (CLIStandalone:38) - Starting Vcell... []{} INFO (PropertyLoader:576) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{} INFO (PropertyLoader:582) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.26 []{} INFO (BiosimulationsCommand:98) - Beginning execution []{} INFO (CLIPythonManager:115) - Initializing Python... []{} INFO (CLIPythonManager:135) - Python initialization success! []{} INFO (ExecuteImpl:77) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} INFO (ExecutionJob:85) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej []{} INFO (RunUtils:527) - TempPath Created: /tmp/vcell_temp_0f135fbd-0303-4fb9-a304-50908aa59d798879960869644491119 []{} INFO (SedmlJob:97) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:108) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:144) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:149) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:153) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:165) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:227) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:180) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:416) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@53abfc07 []{} INFO (SolverHandler:417) - Status: Finished: SOLVER_FINISHED:completed []{} INFO (SolverHandler:463) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. []{} INFO (SolverHandler:475) - Running simulation Caravagna2010, 64 ms []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:583) - Ran 1 simulation jobs for 1 biomodels. []{} INFO (SedmlJob:260) - Generating outputs... []{} INFO (SedmlJob:310) - Generating CSV file... []{} INFO (RunUtils:240) - Generating report `report`. []{} INFO (RunUtils:431) - created csv file for report report: /tmp/out/BIOMD0000000912_sim.sedml/report.csv []{} INFO (SedmlJob:328) - Generating Plots... []{} WARN (CLIPythonManager:77) - Using old style python invocation! []{} WARN (CLIPythonManager:248) - Temp out file didn't delete properly []{} WARN (CLIPythonManager:249) - Temp error file didn't delete properly []{} INFO (SedmlJob:339) - Generating HDF5 file... []{} INFO (SedmlJob:296) - Archiving result files []{} ERROR (RunUtils:497) - No PDF files found, skipping archiving `plots.zip` files []{} INFO (RunUtils:501) - Archiving resultant CSV files to `reports.zip`. []{} INFO (SedmlJob:303) - SED-ML : BIOMD0000000912_sim.sedml successfully completed []{} INFO (ExecutionJob:141) - Processing of SedML succeeded. org.vcell.cli.run.SedmlStatistics@534e58b6 []{} INFO (NativeLib:29) - Loading jhdf5 []{} INFO (Hdf5Writer:40) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:92) - HDF5 file successfully written to. []{} INFO (ExecutionJob:171) - Omex archive.omex processing completed (7s) []{} ```
sedml.SimulatorSupportsComputeModelChanges (27.3 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:38) - Starting Vcell... []{} INFO (PropertyLoader:576) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{} INFO (PropertyLoader:582) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.26 []{} INFO (BiosimulationsCommand:98) - Beginning execution []{} INFO (CLIPythonManager:115) - Initializing Python... []{} INFO (CLIPythonManager:135) - Python initialization success! []{} INFO (ExecuteImpl:77) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} INFO (ExecutionJob:85) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej []{} INFO (RunUtils:527) - TempPath Created: /tmp/vcell_temp_09452d25-90b6-483a-9a6b-5ffd313ca2593424914902870631317 []{} INFO (SedmlJob:97) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:108) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:144) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:149) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:153) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:165) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:227) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:180) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} ERROR (SEDMLImporter:552) - couldn't find SBase with sid=null in SBMLSymbolMapping []{} WARN (SEDMLImporter:847) - could not map changeAttribute for ID null to a VCell Constant []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:416) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@4fa9ab6 []{} INFO (SolverHandler:417) - Status: Finished: SOLVER_FINISHED:completed []{} INFO (SolverHandler:463) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. []{} INFO (SolverHandler:475) - Running simulation Caravagna2010, 68 ms []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:583) - Ran 1 simulation jobs for 1 biomodels. []{} INFO (SedmlJob:260) - Generating outputs... []{} INFO (SedmlJob:310) - Generating CSV file... []{} INFO (RunUtils:240) - Generating report `report`. []{} INFO (RunUtils:431) - created csv file for report report: /tmp/out/BIOMD0000000912_sim.sedml/report.csv []{} INFO (SedmlJob:328) - Generating Plots... []{} WARN (CLIPythonManager:77) - Using old style python invocation! []{} WARN (CLIPythonManager:248) - Temp out file didn't delete properly []{} WARN (CLIPythonManager:249) - Temp error file didn't delete properly []{} INFO (SedmlJob:339) - Generating HDF5 file... []{} INFO (SedmlJob:296) - Archiving result files []{} ERROR (RunUtils:497) - No PDF files found, skipping archiving `plots.zip` files []{} INFO (RunUtils:501) - Archiving resultant CSV files to `reports.zip`. []{} INFO (SedmlJob:303) - SED-ML : BIOMD0000000912_sim.sedml successfully completed []{} INFO (ExecutionJob:141) - Processing of SedML succeeded. org.vcell.cli.run.SedmlStatistics@435cc7f9 []{} INFO (NativeLib:29) - Loading jhdf5 []{} INFO (Hdf5Writer:40) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:92) - HDF5 file successfully written to. []{} INFO (ExecutionJob:171) - 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:38) - Starting Vcell... []{} INFO (PropertyLoader:576) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{} INFO (PropertyLoader:582) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.26 []{} INFO (BiosimulationsCommand:98) - Beginning execution []{} INFO (CLIPythonManager:115) - Initializing Python... []{} INFO (CLIPythonManager:135) - Python initialization success! []{} INFO (ExecuteImpl:77) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} INFO (ExecutionJob:85) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej []{} INFO (RunUtils:527) - TempPath Created: /tmp/vcell_temp_05d86fae-51bd-46de-9ab9-caa1bb29f783251110469110242634 []{} INFO (SedmlJob:97) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:108) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:144) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:149) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:153) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:165) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:227) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:180) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} ERROR (SEDMLImporter:552) - couldn't find SBase with sid=null in SBMLSymbolMapping []{} WARN (SEDMLImporter:847) - could not map changeAttribute for ID null to a VCell Constant []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 INFO (SolverHandler:416) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@352ed70d []{} INFO (SolverHandler:417) - Status: Finished: SOLVER_FINISHED:completed []{} INFO (SolverHandler:463) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. []{} INFO (SolverHandler:475) - Running simulation Caravagna2010, 78 ms []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:583) - Ran 1 simulation jobs for 1 biomodels. []{} INFO (SedmlJob:260) - Generating outputs... []{} INFO (SedmlJob:310) - Generating CSV file... []{} INFO (RunUtils:240) - Generating report `report`. []{} INFO (RunUtils:431) - created csv file for report report: /tmp/out/BIOMD0000000912_sim.sedml/report.csv []{} INFO (SedmlJob:328) - Generating Plots... []{} WARN (CLIPythonManager:77) - Using old style python invocation! []{} WARN (CLIPythonManager:248) - Temp out file didn't delete properly []{} WARN (CLIPythonManager:249) - Temp error file didn't delete properly []{} INFO (SedmlJob:339) - Generating HDF5 file... []{} INFO (SedmlJob:296) - Archiving result files []{} ERROR (RunUtils:497) - No PDF files found, skipping archiving `plots.zip` files []{} INFO (RunUtils:501) - Archiving resultant CSV files to `reports.zip`. []{} INFO (SedmlJob:303) - SED-ML : BIOMD0000000912_sim.sedml successfully completed []{} INFO (ExecutionJob:141) - Processing of SedML succeeded. org.vcell.cli.run.SedmlStatistics@7d78f3d5 []{} INFO (NativeLib:29) - Loading jhdf5 []{} INFO (Hdf5Writer:40) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:92) - HDF5 file successfully written to. []{} INFO (ExecutionJob:171) - Omex archive.omex processing completed (7s) []{} ```
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (12.7 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` a bytes-like object is required, not 'str' ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute INFO (CLIStandalone:38) - Starting Vcell... []{} INFO (PropertyLoader:576) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{} INFO (PropertyLoader:582) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.26 []{} INFO (BiosimulationsCommand:98) - Beginning execution []{} INFO (CLIPythonManager:115) - Initializing Python... []{} INFO (CLIPythonManager:135) - Python initialization success! []{} INFO (ExecuteImpl:77) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} INFO (ExecutionJob:85) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:29) - Loading combinej []{} INFO (RunUtils:527) - TempPath Created: /tmp/vcell_temp_2e381cfd-67e0-456b-8cad-6a2eb7087c603121170272291527332 []{} INFO (SedmlJob:97) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:108) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:144) - Found one SED-ML document with 1 model(s), 2 simulation(s), 2 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:149) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:153) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:165) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:227) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:180) - 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:180) - Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} taskToSimulationMap: 2 taskToListOfSubTasksMap: 2 taskToVariableMap: 2 topTaskToBaseTask: 2 INFO (SolverHandler:416) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@1000d54d []{} INFO (SolverHandler:417) - Status: Finished: SOLVER_FINISHED:completed []{} INFO (SolverHandler:463) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. []{} INFO (SolverHandler:475) - Running simulation Caravagna2010, 68 ms []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:416) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@1894593a []{} INFO (SolverHandler:417) - Status: Finished: SOLVER_FINISHED:completed []{} INFO (SolverHandler:463) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'. []{} INFO (SolverHandler:475) - Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 43 ms []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:583) - Ran 2 simulation jobs for 1 biomodels. []{} INFO (SedmlJob:260) - Generating outputs... []{} INFO (SedmlJob:310) - Generating CSV file... []{} INFO (RunUtils:240) - Generating report `report__copy_2`. []{} INFO (RunUtils:431) - created csv file for report report__copy_2: /tmp/out/BIOMD0000000912_sim.sedml/report__copy_2.csv []{} INFO (SedmlJob:328) - Generating Plots... []{} WARN (CLIPythonManager:77) - Using old style python invocation! []{} WARN (CLIPythonManager:248) - Temp out file didn't delete properly []{} WARN (CLIPythonManager:249) - Temp error file didn't delete properly []{} INFO (SedmlJob:339) - Generating HDF5 file... []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialResultsConverter:150) - Simulations differ across variables; need to fix data structures to accomodate? []{} WARN (NonspatialRe ...
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/4734964029). 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/4734964029).
luciansmith commented 1 year ago

The 'plots' problem is because of the test itself, which I'm in the middle of fixing.