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biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
MIT License
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Submit VCell 7.4.0.60 #587

Closed vcdaemon closed 2 years ago

vcdaemon commented 2 years ago

id: vcell version: 7.4.0.60 specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.4.0.60/biosimulators.json specificationsPatch: version: 7.4.0.60 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.60 digest: "sha256:9b8cff9c323695170fa05a46fd311b2e94d5cfd1d87a66ad0c3d6327323ea884" validateImage: true commitSimulator: false

biosimulators-daemon commented 2 years ago

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

The BioSimulators validator bot is validating the specifications of your simulator, 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 2 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 years ago

Summary of tests

biosimulators-daemon commented 2 years ago

Failures

docker_image.SingularityImageExecutesSimulationsSuccessfully (12.6 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Exception: ``` only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (10.1 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Exception: ``` Report BIOMD0000000912_sim.sedml/report could not be read ``` Log: ``` INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:53:52 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_64dfe4dc-03e9-42b5-81cd-310e4a7ec5cf2709631756120280104 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@65cc8228 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 170 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels. INFO (ExecuteImpl.java:306) - Generating outputs... INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_1_bottom_left` while CSV generation. INFO (RunUtils.java:233) - Generating report `report`. INFO (RunUtils.java:233) - Generating report `__plot__Figure_1_bottom_left`. INFO (ExecuteImpl.java:325) - Generating HDF5 file... INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_1_bottom_left` while generating idNamePlotsMap. INFO (ExecuteImpl.java:338) - Generating Plots... WARN (CLIPythonManager.java:65) - Using old style python invocation! INFO (ExecuteImpl.java:370) - Archiving result files INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`. INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl.java:374) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl.java:382) - Omex Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex processing completed (6s) ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (13.1 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000086`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000086) Exception: ``` Report simulation_1.sedml/report could not be read ``` Log: ``` INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:54:03 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_92b5bedf-70d3-4b89-9d55-3e295446ffae1233199362820172722 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:190) - Processing SED-ML: simulation_1.sedml INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : simulation_1.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter.java:3233) - model 'Ciliberto2003_Morphogenesis' doesn't have a spatial geometry INFO (SEDMLImporter.java:188) - Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000086' matched to RungeKuttaFehlberg INFO (RowColumnResultSet.java:544) - rowCount=13762 INFO (RowColumnResultSet.java:572) - scale[0] = 139.9749483060956 INFO (RowColumnResultSet.java:572) - scale[1] = 0.10337204038188977 INFO (RowColumnResultSet.java:572) - scale[2] = 0.18451723700540568 INFO (RowColumnResultSet.java:572) - scale[3] = 1.248823182479924 INFO (RowColumnResultSet.java:572) - scale[4] = 0.0866281958361408 INFO (RowColumnResultSet.java:572) - scale[5] = 0.2487316750047834 INFO (RowColumnResultSet.java:572) - scale[6] = 0.957165622333867 INFO (RowColumnResultSet.java:572) - scale[7] = 0.5222071967202937 INFO (RowColumnResultSet.java:572) - scale[8] = 1.6250612922233858 INFO (RowColumnResultSet.java:572) - scale[9] = 1.163399212713716 INFO (RowColumnResultSet.java:572) - scale[10] = 0.9944445913091504 INFO (RowColumnResultSet.java:572) - scale[11] = 0.1689497310030451 INFO (RowColumnResultSet.java:572) - scale[12] = 0.02826956834397453 INFO (RowColumnResultSet.java:572) - scale[13] = 0.0032627104470246394 INFO (RowColumnResultSet.java:572) - scale[14] = 0.013335866633246523 INFO (RowColumnResultSet.java:572) - scale[15] = 0.8080848330089925 INFO (RowColumnResultSet.java:572) - scale[16] = 0.932880719855319 INFO (RowColumnResultSet.java:572) - scale[17] = 0.9725777981904435 INFO (RowColumnResultSet.java:572) - scale[18] = 0.9307398276790282 INFO (RowColumnResultSet.java:572) - scale[19] = 0.813079283325805 INFO (RowColumnResultSet.java:572) - scale[20] = 1.0 INFO (RowColumnResultSet.java:572) - scale[21] = 1.0 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.01, size=8424 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.02, size=4232 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.03, size=2129 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.04, size=1074 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.05, size=552 final tolerance=0.1 final threshold=0.060000000000000005, 552 remaining (keepAtMost=1000) INFO (SolverHandler.java:200) - Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg_simulation_1.sedml_Ciliberto2003_Morphogenesis' Task 'simulation 1'. INFO (SolverHandler.java:207) - Running simulation task_1, 990 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels. INFO (ExecuteImpl.java:306) - Generating outputs... INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_3a` while CSV generation. INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_3b` while CSV generation. INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_3c` while CSV generation. INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_3d` while CSV generation. INFO (RunUtils.java:233) - Generating report `report`. INFO (RunUtils.java:233) - Generating report `__plot__Figure_3a`. INFO (RunUtils.java:233) - Generating report `__plot__Figure_3b`. INFO (RunUtils.java:233) - Generating report `__plot__Figure_3c`. INFO (RunUtils.java:233) - Generating report `__plot__Figure_3d`. INFO (ExecuteImpl.java:325) - Generating HDF5 file... INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_3a` while generating idNamePlotsMap. INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_3b` while generating idNamePlotsMap. INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_3c` while generating idNamePlotsMap. INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_3d` while generating idNamePlotsMap. INFO (ExecuteImpl.java:338) - Generating Plots... WARN (CLIPythonManager.java:65) - Using old style python invocation! INFO (ExecuteImpl.java:370) - Archiving result files INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`. INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl.java:374) - SED-ML : simulation_1.sedml successfully completed INFO (ExecuteImpl.java:382) - Omex Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex processing completed (9s) ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (12.3 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Exception: ``` Report simulation_1.sedml/report could not be read ``` Log: ``` INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:54:16 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_6f51806e-d6e6-4a65-9f01-5c45bf80cf128031127589343496412 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:190) - Processing SED-ML: simulation_1.sedml INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : simulation_1.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter.java:3233) - model 'Ciliberto2003_Morphogenesis' doesn't have a spatial geometry INFO (SEDMLImporter.java:188) - Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@5eb2172 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous_simulation_1.sedml_Ciliberto2003_Morphogenesis' Task 'simulation 1'. INFO (SolverHandler.java:207) - Running simulation task_1, 180 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels. INFO (ExecuteImpl.java:306) - Generating outputs... INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_3a` while CSV generation. INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_3b` while CSV generation. INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_3c` while CSV generation. INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_3d` while CSV generation. INFO (RunUtils.java:233) - Generating report `report`. INFO (RunUtils.java:233) - Generating report `__plot__Figure_3a`. INFO (RunUtils.java:233) - Generating report `__plot__Figure_3b`. INFO (RunUtils.java:233) - Generating report `__plot__Figure_3c`. INFO (RunUtils.java:233) - Generating report `__plot__Figure_3d`. INFO (ExecuteImpl.java:325) - Generating HDF5 file... INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_3a` while generating idNamePlotsMap. INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_3b` while generating idNamePlotsMap. INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_3c` while generating idNamePlotsMap. INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_3d` while generating idNamePlotsMap. INFO (ExecuteImpl.java:338) - Generating Plots... WARN (CLIPythonManager.java:65) - Using old style python invocation! INFO (ExecuteImpl.java:370) - Archiving result files INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`. INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl.java:374) - SED-ML : simulation_1.sedml successfully completed INFO (ExecuteImpl.java:382) - Omex Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex processing completed (8s) ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (9.7 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Exception: ``` Report simulation.sedml/report could not be read ``` Log: ``` INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:54:28 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/Elowitz-Nature-2000-Repressilator.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_265a2283-00ca-464f-9143-6392e2d1d46f2924184681532741438 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:190) - Processing SED-ML: simulation.sedml INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter.java:3233) - model 'BIOMD0000000012' doesn't have a spatial geometry INFO (SEDMLImporter.java:188) - Task (id='task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@6124287a INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'Elowitz-Nature-2000-Repressilator_simulation.sedml_model' Task 'task'. INFO (SolverHandler.java:207) - Running simulation task, 131 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels. INFO (ExecuteImpl.java:306) - Generating outputs... INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_1c` while CSV generation. INFO (RunUtils.java:233) - Generating report `report`. INFO (RunUtils.java:233) - Generating report `__plot__Figure_1c`. INFO (ExecuteImpl.java:325) - Generating HDF5 file... INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_1c` while generating idNamePlotsMap. INFO (ExecuteImpl.java:338) - Generating Plots... WARN (CLIPythonManager.java:65) - Using old style python invocation! INFO (ExecuteImpl.java:370) - Archiving result files INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`. INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl.java:374) - SED-ML : simulation.sedml successfully completed INFO (ExecuteImpl.java:382) - Omex Elowitz-Nature-2000-Repressilator.omex processing completed (6s) ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (24.0 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) * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) Exception: ``` Report simulation.sedml/report_Fig_1a could not be read Report simulation.sedml/report_low_delta_R_det could not be read Report simulation.sedml/report_Euler_small_step_size could not be read Report simulation.sedml/report_Fig_1_c could not be read Report simulation.sedml/report_low_delta_R_stoch could not be read ``` Log: ``` INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:55:05 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_85842ed6-7aa3-4dd7-a74e-7b9461afa96f3293380909276017486 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:190) - Processing SED-ML: simulation.sedml INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter.java:3233) - model '__example_biosim_vilar_ODE_deterministic' doesn't have a spatial geometry WARN (AbstractNameScope.java:276) - AbstractNameScope.getRelativeScopePrefix() scopes 'cell_mapping' and 'PrmA_scs' are unrelated ERROR (SBMLImporter.java:2740) - failed to set expression for SBML object species [ id="PrmA" boundaryCondition="false" compartment="cell" constant="false" hasOnlySubstanceUnits="true" substanceUnits="molecules"] on vcell object cbit.vcell.mapping.SpeciesContextSpec$SpeciesContextSpecParameter@773bd77b: = 'Expression@b9f2 '0.0'' [molecules.um-3], "initial concentration for PrmA" WARN (AbstractNameScope.java:276) - AbstractNameScope.getRelativeScopePrefix() scopes 'cell_mapping' and 'PrmR_scs' are unrelated ERROR (SBMLImporter.java:2740) - failed to set expression for SBML object species [ id="PrmR" boundaryCondition="false" compartment="cell" constant="false" hasOnlySubstanceUnits="true" substanceUnits="molecules"] on vcell object cbit.vcell.mapping.SpeciesContextSpec$SpeciesContextSpecParameter@6b580b88: = 'Expression@b9f2 '0.0'' [molecules.um-3], "initial concentration for PrmR" ERROR (SBMLImporter.java:1756) - SKIPPING translation back to vcell unit system ... testing only WARN (DiffEquMathMapping.java:1483) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique INFO (SBMLImporter.java:3233) - model '__example_biosim_vilar_ODE_stochastic' doesn't have a spatial geometry ERROR (SBMLImporter.java:1756) - SKIPPING translation back to vcell unit system ... testing only WARN (DiffEquMathMapping.java:1483) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique INFO (SEDMLImporter.java:188) - Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (SEDMLImporter.java:188) - Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (SEDMLImporter.java:188) - Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler INFO (SEDMLImporter.java:188) - Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson INFO (SEDMLImporter.java:188) - Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@2a03d65c INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_deterministic' Task 'tsk_0_0'. INFO (SolverHandler.java:207) - Running simulation tsk_0_0, 169 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@588307f7 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_deterministic' Task 'tsk_0_1'. INFO (SolverHandler.java:207) - Running simulation tsk_0_1, 45 ms ----------------------------------------------------------------------------------------------------- INFO (RowColumnResultSet.java:544) - rowCount=200001 INFO (RowColumnResultSet.java:572) - scale[0] = 199.998 INFO (RowColumnResultSet.java:572) - scale[1] = 1.0 INFO (RowColumnResultSet.java:572) - scale[2] = 1.0 INFO (RowColumnResultSet.java:572) - scale[3] = 1.0 INFO (RowColumnResultSet.java:572) - scale[4] = 1.0 INFO (RowColumnResultSet.java:572) - scale[5] = 1.0 INFO (RowColumnResultSet.java:572) - scale[6] = 1.0 INFO (RowColumnResultSet.java:572) - scale[7] = 1.0 INFO (RowColumnResultSet.java:572) - scale[8] = 1.0 INFO (RowColumnResultSet.java:572) - scale[9] = 1.0 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.01, size=100001 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.02, size=50001 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.03, size=25001 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.04, size=12501 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.05, size=6251 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.060000000000000005, size=3126 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.07, size=1564 INFO (RowColumnResultSet.java:608) - TOLERANCE=0.1, threshold=0.08, size=783 final tolerance=0.1 final threshold=0.09, 783 remaining (keepAtMost=1000) INFO (SolverHandler.java:200) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_deterministic' Task 'tsk_0_3'. INFO (SolverHandler.java:207) - Running simulation tsk_0_3, 697 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.stoch.GibsonSolver@763cf5b9 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_stochastic' Task 'tsk_1_0'. INFO (SolverHandler.java:207) - Running simulation tsk_1_0, 234 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.stoch.GibsonSolver@2f508f3c INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_simulation.sedml_ODE_stochastic' Task 'tsk_1_1'. INFO (SolverHandler.java:207) - Running simulation tsk_1_1, 164 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:282) - Ran 5 simulations for 2 biomodels. INFO (ExecuteImpl.java:306) - Generating outputs... INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_Fig_1a` while CSV generation. INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation. INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation. INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation. INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation. INFO (RunUtils.java:233) - Generating report `report_Fig_1a`. INFO (RunUtils.java:233) - Generating report `report_low_delta_R_det`. INFO (RunUtils.java:233) - Generating report `report_Euler_small_step_size`. INFO (RunUtils.java:233) - Generating report `report_Fig_1_c`. INFO (RunUtils.java:233) - Generating report `report_low_delta_R_stoch`. INFO (RunUtils.java:233) - Generating report `__plot__plot2d_Fig_1a`. INFO (RunUtils.java:233) - Generating report `__plot__plot2d_low_delta_R_det`. INFO (RunUtils.java:233) - Generating report `__plot__plot2d_Euler_small_step_size`. INFO (RunUtils.java:233) - Generating report `__plot__plot2d_Fig_1_c`. INFO (RunUtils.java:233) - Generating report `__plot__plot2d_low_delta_R_stoch`. INFO (ExecuteImpl.java:325) - Generating HDF5 file... INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_Fig_1a` while generating idNamePlotsMap. INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_low_delta_R_det` while generating idNamePlotsMap. INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_Euler_small_step_size` while generating idNamePlotsMap. INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_Fig_1_c` while generating idNamePlotsMap. INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_low_delta_R_stoch` while generating idNamePlotsMap. INFO (ExecuteImpl.java:338) - Generating Plots... WARN (CLIPythonManager.java:65) - Using old style python invocation! INFO (ExecuteImpl.java:370) - Archiving result files INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`. INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl.java:374) - SED-ML : simulation.sedml successfully completed INFO (ExecuteImpl.java:382) - Omex Vilar-PNAS-2002-minimal-circardian-clock.omex processing completed (20s) ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (12.9 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Exception: ``` Report simulation.sedml/report_Fig_1a could not be read Report simulation.sedml/report_low_delta_R_det could not be read ``` Log: ``` INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:54:38 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_5a210c3d-f54d-47c0-a3b5-9dd664b59f186370883313959451802 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:190) - Processing SED-ML: simulation.sedml INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter.java:3233) - model '__example_biosim_vilar_ODE_deterministic' doesn't have a spatial geometry WARN (AbstractNameScope.java:276) - AbstractNameScope.getRelativeScopePrefix() scopes 'cell_mapping' and 'PrmA_scs' are unrelated ERROR (SBMLImporter.java:2740) - failed to set expression for SBML object species [ id="PrmA" boundaryCondition="false" compartment="cell" constant="false" hasOnlySubstanceUnits="true" substanceUnits="molecules"] on vcell object cbit.vcell.mapping.SpeciesContextSpec$SpeciesContextSpecParameter@7b22ec89: = 'Expression@b9f2 '0.0'' [molecules.um-3], "initial concentration for PrmA" WARN (AbstractNameScope.java:276) - AbstractNameScope.getRelativeScopePrefix() scopes 'cell_mapping' and 'PrmR_scs' are unrelated ERROR (SBMLImporter.java:2740) - failed to set expression for SBML object species [ id="PrmR" boundaryCondition="false" compartment="cell" constant="false" hasOnlySubstanceUnits="true" substanceUnits="molecules"] on vcell object cbit.vcell.mapping.SpeciesContextSpec$SpeciesContextSpecParameter@790132f7: = 'Expression@b9f2 '0.0'' [molecules.um-3], "initial concentration for PrmR" ERROR (SBMLImporter.java:1756) - SKIPPING translation back to vcell unit system ... testing only WARN (DiffEquMathMapping.java:1483) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique INFO (SEDMLImporter.java:188) - Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (SEDMLImporter.java:188) - Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@4c27d39d INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous_simulation.sedml_ODE_deterministic' Task 'tsk_0_0'. INFO (SolverHandler.java:207) - Running simulation tsk_0_0, 106 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@3adbe50f INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous_simulation.sedml_ODE_deterministic' Task 'tsk_0_1'. INFO (SolverHandler.java:207) - Running simulation tsk_0_1, 45 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:282) - Ran 2 simulations for 1 biomodels. INFO (ExecuteImpl.java:306) - Generating outputs... INFO (RunUtils.java:231) - Ignoring unsupported output `Figure_2ab` while CSV generation. INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_Fig_1a` while CSV generation. INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation. INFO (RunUtils.java:233) - Generating report `report_Fig_1a`. INFO (RunUtils.java:233) - Generating report `report_low_delta_R_det`. INFO (RunUtils.java:233) - Generating report `__plot__Figure_2ab`. INFO (RunUtils.java:233) - Generating report `__plot__plot2d_Fig_1a`. INFO (RunUtils.java:233) - Generating report `__plot__plot2d_low_delta_R_det`. INFO (ExecuteImpl.java:325) - Generating HDF5 file... INFO (RunUtils.java:387) - Ignoring unsupported output `Figure_2ab` while generating idNamePlotsMap. INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_Fig_1a` while generating idNamePlotsMap. INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_low_delta_R_det` while generating idNamePlotsMap. INFO (ExecuteImpl.java:338) - Generating Plots... WARN (CLIPythonManager.java:65) - Using old style python invocation! INFO (ExecuteImpl.java:370) - Archiving result files INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`. INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl.java:374) - SED-ML : simulation.sedml successfully completed INFO (ExecuteImpl.java:382) - Omex Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex processing completed (9s) ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (13.7 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) Exception: ``` Report simulation.sedml/report_Fig_1_c could not be read Report simulation.sedml/report_low_delta_R_stoch could not be read ``` Log: ``` INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:54:51 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_f0440068-78b9-4042-9ab0-2932eb5a9db83976787186033063842 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:190) - Processing SED-ML: simulation.sedml INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter.java:3233) - model '__example_biosim_vilar_ODE_stochastic' doesn't have a spatial geometry ERROR (SBMLImporter.java:1756) - SKIPPING translation back to vcell unit system ... testing only WARN (DiffEquMathMapping.java:1483) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique INFO (SEDMLImporter.java:188) - Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson INFO (SEDMLImporter.java:188) - Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.stoch.GibsonSolver@14bf57b2 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM_simulation.sedml_ODE_stochastic' Task 'tsk_1_0'. INFO (SolverHandler.java:207) - Running simulation tsk_1_0, 379 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.stoch.GibsonSolver@bc4d5e1 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM_simulation.sedml_ODE_stochastic' Task 'tsk_1_1'. INFO (SolverHandler.java:207) - Running simulation tsk_1_1, 159 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:282) - Ran 2 simulations for 1 biomodels. INFO (ExecuteImpl.java:306) - Generating outputs... INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation. INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation. INFO (RunUtils.java:233) - Generating report `report_Fig_1_c`. INFO (RunUtils.java:233) - Generating report `report_low_delta_R_stoch`. INFO (RunUtils.java:233) - Generating report `__plot__plot2d_Fig_1_c`. INFO (RunUtils.java:233) - Generating report `__plot__plot2d_low_delta_R_stoch`. INFO (ExecuteImpl.java:325) - Generating HDF5 file... INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_Fig_1_c` while generating idNamePlotsMap. INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_low_delta_R_stoch` while generating idNamePlotsMap. INFO (ExecuteImpl.java:338) - Generating Plots... WARN (CLIPythonManager.java:65) - Using old style python invocation! INFO (ExecuteImpl.java:370) - Archiving result files INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`. INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl.java:374) - SED-ML : simulation.sedml successfully completed INFO (ExecuteImpl.java:382) - Omex Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex processing completed (10s) ```
published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength (10.8 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9000`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9000) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Exception: ``` Report biomodel_100596964.sedml/report_Simulation1 could not be read ``` Log: ``` INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:55:29 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_ee0a108f-636f-4015-bbce-26df76c0908c682944670831763597 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... INFO (ExecuteImpl.java:190) - Processing SED-ML: biomodel_100596964.sedml INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : biomodel_100596964.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... INFO (XmlReader.java:4580) - RbmModelContainer is missing. INFO (SEDMLImporter.java:188) - Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (SolverHandler.java:151) - Solver: cbit.vcell.solvers.CombinedSundialsSolver@5c84624f INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength_biomodel_100596964.sedml_minepsp' Task ''. INFO (SolverHandler.java:207) - Running simulation tsk_0_0, 165 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels. INFO (ExecuteImpl.java:306) - Generating outputs... INFO (RunUtils.java:231) - Ignoring unsupported output `plot2d_Simulation1` while CSV generation. INFO (RunUtils.java:233) - Generating report `report_Simulation1`. INFO (RunUtils.java:233) - Generating report `__plot__plot2d_Simulation1`. INFO (ExecuteImpl.java:325) - Generating HDF5 file... INFO (RunUtils.java:387) - Ignoring unsupported output `plot2d_Simulation1` while generating idNamePlotsMap. INFO (ExecuteImpl.java:338) - Generating Plots... WARN (CLIPythonManager.java:65) - Using old style python invocation! INFO (ExecuteImpl.java:370) - Archiving result files INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`. INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl.java:374) - SED-ML : biomodel_100596964.sedml successfully completed INFO (ExecuteImpl.java:382) - Omex Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength.omex processing completed (7s) ```
results_report.SimulatorGeneratesReportsOfSimulationResults (8.4 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file. Exception: ``` only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices ``` Log: ``` INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:53:08 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_7e41857e-7cf0-458a-965d-73a1a52660055392436976761597864 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@56de6d6b INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 78 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels. INFO (ExecuteImpl.java:306) - Generating outputs... INFO (RunUtils.java:233) - Generating report `report`. INFO (ExecuteImpl.java:325) - Generating HDF5 file... INFO (ExecuteImpl.java:338) - Generating Plots... WARN (CLIPythonManager.java:65) - Using old style python invocation! INFO (ExecuteImpl.java:370) - Archiving result files ERROR (RunUtils.java:434) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl.java:374) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (5s) ```
sedml.SimulatorProducesLinear2DPlots (9.0 s)
Test that a simulator produces linear 2D plots Exception: ``` only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices ``` Log: ``` INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:49:22 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_94b2cc5c-8fc6-47f5-8707-f54bc3d0ba815636475759970342312 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@56de6d6b INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 79 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels. INFO (ExecuteImpl.java:306) - Generating outputs... INFO (RunUtils.java:231) - Ignoring unsupported output `plot_0` while CSV generation. INFO (RunUtils.java:233) - Generating report `__plot__plot_0`. INFO (ExecuteImpl.java:325) - Generating HDF5 file... INFO (RunUtils.java:387) - Ignoring unsupported output `plot_0` while generating idNamePlotsMap. INFO (ExecuteImpl.java:338) - Generating Plots... WARN (CLIPythonManager.java:65) - Using old style python invocation! INFO (ExecuteImpl.java:370) - Archiving result files INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`. INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl.java:374) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (5s) ```
sedml.SimulatorProducesLogarithmic2DPlots (9.1 s)
Test that a simulator produces logarithmic 2D plots Exception: ``` only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices ``` Log: ``` INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:49:31 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_90d6cca9-f272-4a6a-8470-77c18a200f195614387254456221131 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@56de6d6b INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 85 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels. INFO (ExecuteImpl.java:306) - Generating outputs... INFO (RunUtils.java:231) - Ignoring unsupported output `plot_0` while CSV generation. INFO (RunUtils.java:233) - Generating report `__plot__plot_0`. INFO (ExecuteImpl.java:325) - Generating HDF5 file... INFO (RunUtils.java:387) - Ignoring unsupported output `plot_0` while generating idNamePlotsMap. INFO (ExecuteImpl.java:338) - Generating Plots... WARN (CLIPythonManager.java:65) - Using old style python invocation! INFO (ExecuteImpl.java:370) - Archiving result files INFO (RunUtils.java:438) - Archiving resultant PDF files to `plots.zip`. INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl.java:374) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (5s) ```
sedml.SimulatorProducesMultiplePlots (9.1 s)
Test that a simulator produces multiple plots Exception: ``` only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices ``` Log: ``` INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:49:40 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_538003e7-8a0a-4425-8689-7950eacb3ed36308411309292550586 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... SED-ML versio ...
biosimulators-daemon commented 2 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (2.5 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports. Warnings: ``` The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports. The command-line interface does not describe the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be described in the inline help for its command-line interface. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
cli.CliDisplaysHelpInline (4.3 s)
Test that a command-line interface provides inline help. Warnings: ``` Command-line interfaces should display basic help when no arguments are provided. The command-line interface displayed the following when no argument was provided: INFO (CLIStandalone.java:29) - Starting Vcell... ERROR (BiosimulationsCommand.java:119) - null java.lang.NullPointerException: null at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:60) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [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:32) [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`: INFO (CLIStandalone.java:29) - 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`: INFO (CLIStandalone.java:29) - Starting Vcell... Usage: CLIStandalone biosimulations [-dhqv] [-i=] [-o=] BioSimulators-compliant command-line interface to the vcell simulation program . -d, --debug full application debug mode -h, --help show this help message and exit -i, --archive= Path to a COMBINE/OMEX archive file which contains one or more SED-ML-encoded simulation experiments -o, --out-dir= Directory to save outputs -q, --quiet suppress all console output -v, --version show program's version number and exit ``` Log: None
docker_image.DeclaresSupportedEnvironmentVariables (0.7 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.5 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
biosimulators-daemon commented 2 years ago

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000030 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9012`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9012) Algorithm: [`KISAO_0000669`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000669) Reason for skip: ``` Case requires model formats format_9012 and simulation algorithms KISAO_0000669 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000088`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000088 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) Reason for skip: ``` Case requires model formats format_9001 and simulation algorithms KISAO_0000057 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9010 and simulation algorithms KISAO_0000019 ``` Log: None
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (6.6 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: ``` INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:49:08 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_a20baed6-9a8f-41b5-b755-272df97e3eb54691195488345918356 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE ERROR (SolverHandler.java:87) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection null java.lang.RuntimeException: Unable to initialize bioModel for the given selection null at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:338) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:580) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:85) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:272) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [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:32) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] Caused by: java.util.ConcurrentModificationException at java.util.ArrayList$Itr.checkForComodification(ArrayList.java:911) ~[?:1.8.0_342] at java.util.ArrayList$Itr.next(ArrayList.java:861) ~[?:1.8.0_342] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:331) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 14 more ERROR (ExecuteImpl.java:279) - Unable to initialize bioModel for the given selection null java.lang.RuntimeException: Unable to initialize bioModel for the given selection null at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:338) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:580) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:85) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:272) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [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:32) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] Caused by: java.util.ConcurrentModificationException at java.util.ArrayList$Itr.checkForComodification(ArrayList.java:911) ~[?:1.8.0_342] at java.util.ArrayList$Itr.next(ArrayList.java:861) ~[?:1.8.0_342] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:331) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 14 more INFO (ExecuteImpl.java:306) - Generating outputs... INFO (RunUtils.java:233) - Generating report `report`. ERROR (RunUtils.java:374) - Encountered exception: null java.lang.NullPointerException: null at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:302) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:307) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [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:32) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl.java:325) - Generating HDF5 file... ERROR (ExecuteImpl.java:342) - Failed to generate the HDF5 output file. java.lang.RuntimeException: Failed to generate the HDF5 output file. at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:333) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [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:32) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (3s) ERROR (ExecuteImpl.java:392) - All sedml documents in this archive failed to execute ```
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (6.6 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: ``` INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:49:15 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_575f1a5c-61e9-4469-b75c-f1142ec336c35112620803683021966 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE ERROR (SolverHandler.java:87) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection null java.lang.RuntimeException: Unable to initialize bioModel for the given selection null at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:338) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:580) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:85) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:272) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [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:32) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] Caused by: java.util.ConcurrentModificationException at java.util.ArrayList$Itr.checkForComodification(ArrayList.java:911) ~[?:1.8.0_342] at java.util.ArrayList$Itr.next(ArrayList.java:861) ~[?:1.8.0_342] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:331) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 14 more ERROR (ExecuteImpl.java:279) - Unable to initialize bioModel for the given selection null java.lang.RuntimeException: Unable to initialize bioModel for the given selection null at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:338) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at cbit.vcell.xml.XmlHelper.importSEDML(XmlHelper.java:580) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:85) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:272) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [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:32) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] Caused by: java.util.ConcurrentModificationException at java.util.ArrayList$Itr.checkForComodification(ArrayList.java:911) ~[?:1.8.0_342] at java.util.ArrayList$Itr.next(ArrayList.java:861) ~[?:1.8.0_342] at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:331) ~[vcell-core-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] ... 14 more INFO (ExecuteImpl.java:306) - Generating outputs... INFO (RunUtils.java:233) - Generating report `report`. ERROR (RunUtils.java:374) - Encountered exception: null java.lang.NullPointerException: null at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:302) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:307) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [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:32) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl.java:325) - Generating HDF5 file... ERROR (ExecuteImpl.java:342) - Failed to generate the HDF5 output file. java.lang.RuntimeException: Failed to generate the HDF5 output file. at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:333) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [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:32) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (3s) ERROR (ExecuteImpl.java:392) - All sedml documents in this archive failed to execute ```
sedml.SimulatorProducesLinear3DPlots (0.3 s)
Test that a simulator produces linear 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (0.3 s)
Test that a simulator produces logarithmic 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (18.2 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices ``` Log: ``` INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:49:50 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_01f5625d-7071-419c-bafb-2f12414608556488458953318021672 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@160396db INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 79 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels. INFO (ExecuteImpl.java:306) - Generating outputs... INFO (RunUtils.java:233) - Generating report `report`. INFO (ExecuteImpl.java:325) - Generating HDF5 file... INFO (ExecuteImpl.java:338) - Generating Plots... WARN (CLIPythonManager.java:65) - Using old style python invocation! INFO (ExecuteImpl.java:370) - Archiving result files ERROR (RunUtils.java:434) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl.java:374) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (5s) INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:49:58 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_f09f067d-3478-426c-a6c7-4e7fb44324495315842626461988247 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@30d25c03 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 81 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels. INFO (ExecuteImpl.java:306) - Generating outputs... INFO (RunUtils.java:233) - Generating report `report`. INFO (ExecuteImpl.java:325) - Generating HDF5 file... INFO (ExecuteImpl.java:338) - Generating Plots... WARN (CLIPythonManager.java:65) - Using old style python invocation! INFO (ExecuteImpl.java:370) - Archiving result files ERROR (RunUtils.java:434) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl.java:374) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (6s) ```
sedml.SimulatorSupportsComputeModelChanges (19.6 s)
Test that a simulator supports compute model changes Reason for skip: ``` only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices ``` Log: ``` INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:50:17 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_136a217e-9043-4284-b65f-11f4468287721289695864863136137 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE ERROR (SEDMLImporter.java:396) - couldn't find SBase with sid=null in SBMLSymbolMapping WARN (SEDMLImporter.java:526) - could not map changeAttribute for ID null to a VCell Constant INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@f4c0e4e INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 74 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels. INFO (ExecuteImpl.java:306) - Generating outputs... INFO (RunUtils.java:233) - Generating report `report`. INFO (ExecuteImpl.java:325) - Generating HDF5 file... INFO (ExecuteImpl.java:338) - Generating Plots... WARN (CLIPythonManager.java:65) - Using old style python invocation! INFO (ExecuteImpl.java:370) - Archiving result files ERROR (RunUtils.java:434) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl.java:374) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (6s) INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:50:26 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_61068138-b6bf-4c73-aa11-d361bb7885da3187943323326337214 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE ERROR (SEDMLImporter.java:396) - couldn't find SBase with sid=null in SBMLSymbolMapping WARN (SEDMLImporter.java:526) - could not map changeAttribute for ID null to a VCell Constant INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@680d4a6a INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 81 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:282) - Ran 1 simulations for 1 biomodels. INFO (ExecuteImpl.java:306) - Generating outputs... INFO (RunUtils.java:233) - Generating report `report`. INFO (ExecuteImpl.java:325) - Generating HDF5 file... INFO (ExecuteImpl.java:338) - Generating Plots... WARN (CLIPythonManager.java:65) - Using old style python invocation! INFO (ExecuteImpl.java:370) - Archiving result files ERROR (RunUtils.java:434) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl.java:374) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (6s) ```
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (8.8 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices ``` Log: ``` INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:50:36 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_5d1f353c-b4b1-4ad3-a1bc-89e3fe900cf930260853785705076 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@267517e4 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 81 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@f14e5bf INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'. INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task__copy_2, 46 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:282) - Ran 2 simulations for 1 biomodels. INFO (ExecuteImpl.java:306) - Generating outputs... INFO (RunUtils.java:233) - Generating report `report__copy_2`. INFO (ExecuteImpl.java:325) - Generating HDF5 file... INFO (ExecuteImpl.java:338) - Generating Plots... WARN (CLIPythonManager.java:65) - Using old style python invocation! INFO (ExecuteImpl.java:370) - Archiving result files ERROR (RunUtils.java:434) - No PDF files found, skipping archiving `plots.zip` files INFO (RunUtils.java:438) - Archiving resultant CSV files to `reports.zip`. INFO (ExecuteImpl.java:374) - SED-ML : BIOMD0000000912_sim.sedml successfully completed INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (5s) ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (6.7 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpyja84g0j/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` INFO (CLIStandalone.java:29) - Starting Vcell... INFO (PropertyLoader.java:572) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory INFO (PropertyLoader.java:578) - ServerID=7.3.0.16, SoftwareVersion=7.4.0.60 INFO (BiosimulationsCommand.java:105) - Beginning execution Aug 29, 2022 8:50:45 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. INFO (CLIPythonManager.java:128) - Initializing Python... INFO (CLIPythonManager.java:148) - Python initalization success! INFO (ExecuteImpl.java:140) - Executing OMEX archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- INFO (RunUtils.java:464) - TempPath Created: /tmp/vcell_temp_7298538f-b310-4fcf-9601-6f1b0dc8a24d8586339332424846862 INFO (ExecuteImpl.java:162) - Preparing output directory... INFO (ExecuteImpl.java:172) - Initializing SED-ML document... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:190) - Processing SED-ML: BIOMD0000000912_sim.sedml INFO (ExecuteImpl.java:214) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- INFO (ExecuteImpl.java:218) - Creating pseudo SED-ML for HDF5 conversion... INFO (ExecuteImpl.java:230) - Creating Biomodel from pseudo SED-ML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (ExecuteImpl.java:270) - Building solvers and starting simulation of all tasks... SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SBMLImporter.java:3233) - model 'Caravagna2010___Tumour_suppression_by_immune_system' doesn't have a spatial geometry INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (SEDMLImporter.java:188) - Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@7923f5b3 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task, 99 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:151) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@11841b15 INFO (SolverHandler.java:152) - Status: Finished: SOLVER_FINISHED:completed INFO (SolverHandler.java:200) - Succesful execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'. INFO (SolverHandler.java:207) - Running simulation BIOMD0000000912_task__copy_2, 43 ms ----------------------------------------------------------------------------------------------------- INFO (SolverHandler.java:282) - Ran 2 simulations for 1 biomodels. INFO (ExecuteImpl.java:306) - Generating outputs... INFO (RunUtils.java:233) - Generating report `report`. INFO (ExecuteImpl.java:325) - Generating HDF5 file... ERROR (ExecuteImpl.java:342) - Python error caught: < Traceback (most recent call last): File "", line 1, in File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/wrapper.py", line 15, in execPlotOutputSedDoc cli.exec_plot_output_sed_doc(omexFilePath, idNamePlotsMap, baseOutPath) File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 167, in exec_plot_output_sed_doc data_set_df = pd.read_csv(report_filename, header=None).T File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 581, in _read return parser.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1255, in read index, columns, col_dict = self._engine.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 225, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 805, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1960, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 14 fields in line 5, saw 24 {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv > Result: HDF conversion failed org.vcell.cli.PythonStreamException: Python error caught: < Traceback (most recent call last): File "", line 1, in File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/wrapper.py", line 15, in execPlotOutputSedDoc cli.exec_plot_output_sed_doc(omexFilePath, idNamePlotsMap, baseOutPath) File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 167, in exec_plot_output_sed_doc data_set_df = pd.read_csv(report_filename, header=None).T File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 581, in _read return parser.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1255, in read index, columns, col_dict = self._engine.read(nrows) File "/poetry/.cache/virtualenvs/vcell-cli-utils-uypFi--7-py3.9/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 225, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 805, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1960, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 14 fields in line 5, saw 24 {'report': 'null'} report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv > Result: HDF conversion failed at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:247) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.PythonCalls.execPlotOutputSedDoc(PythonCalls.java:29) ~[vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:328) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:108) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [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:32) [vcell-cli-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT] INFO (ExecuteImpl.java:382) - Omex archive.omex processing completed (3s) ERROR (ExecuteImpl.java:392) - All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsModelAttributeChanges (19.7 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices ``` Log: ``` INFO (CLISta ...
biosimulators-daemon commented 2 years ago 
- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/2951586729). 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/2951586729).
CodeByDrescher commented 2 years ago

this is a result of biosimulators/Biosimulators_test_suite#63