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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 7.4.0.30 #533

Closed vcdaemon closed 2 years ago

vcdaemon commented 2 years ago

id: vcell version: 7.4.0.30 specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.4.0.30/biosimulators.json specificationsPatch: version: 7.4.0.30 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.30 digest: "sha256:d3bd85f29ef35f92bf950260322f2da4a8d2842c15c45580f1cb62d0af95f5e0" validateImage: true commitSimulator: true

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, validating your Docker image, and committing your simulator to the BioSimulators registry.

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

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

biosimulators-daemon commented 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

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (2.8 s)
Test that SED documents in nested directories can be executed Exception: ``` Simulator did not generate the following expected reports - `subdir/BIOMD0000000912_sim.sedml/report` ``` Log: ``` Jan 21, 2022 7:38:12 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_ca921e60-abaf-43e1-9c63-09f781f48f901569311278353573772 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_ca921e60-abaf-43e1-9c63-09f781f48f901569311278353573772/subdir/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (2.4 s)
Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths Exception: ``` Simulator did not generate the following expected reports - `subdir/BIOMD0000000912_sim.sedml/report` - `subdir__copy/BIOMD0000000912_sim.sedml/report` ``` Log: ``` Jan 21, 2022 7:38:15 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_602f7460-3aa0-49a5-888d-1855939dfabe7660060467303194227 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 2 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_602f7460-3aa0-49a5-888d-1855939dfabe7660060467303194227/subdir/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 2 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 2 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_602f7460-3aa0-49a5-888d-1855939dfabe7660060467303194227/subdir__copy/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (2.1 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file. Exception: ``` Simulator did not generate the following expected reports - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` Jan 21, 2022 7:38:17 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_8149e6c8-44e9-42cb-9d01-0ca184d20dec4081210019567871132 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_8149e6c8-44e9-42cb-9d01-0ca184d20dec4081210019567871132/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (2.4 s)
Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files. Exception: ``` Simulator did not generate the following expected reports - `BIOMD0000000912_sim.sedml/report` - `BIOMD0000000912_sim__copy.sedml/report` ``` Log: ``` Jan 21, 2022 7:38:19 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_2809344b-7d50-4455-ba0c-c417a5cba8c89065077639331956783 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 2 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_2809344b-7d50-4455-ba0c-c417a5cba8c89065077639331956783/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 2 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 2 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim__copy.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_2809344b-7d50-4455-ba0c-c417a5cba8c89065077639331956783/BIOMD0000000912_sim__copy.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim__copy.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim__copy.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
docker_image.SingularityImageExecutesSimulationsSuccessfully (14.6 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Exception: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (2.1 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: ``` No reports were generated ``` Log: ``` Jan 21, 2022 7:39:45 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_6156ee96-d8a3-43d0-ad43-641461a289928338319309252518051 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 1 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_6156ee96-d8a3-43d0-ad43-641461a289928338319309252518051/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (2.2 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000086`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000086) Exception: ``` No reports were generated ``` Log: ``` Jan 21, 2022 7:39:47 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_eec71269-c4ae-4b9f-b6c6-86a85ec6e6992422170663983700527 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 4 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation_1.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_eec71269-c4ae-4b9f-b6c6-86a85ec6e6992422170663983700527/simulation_1.sedml failed with error: Failed to create file /tmp/out/temp/simulation_simulation_1.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_simulation_1.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (2.3 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: ``` No reports were generated ``` Log: ``` Jan 21, 2022 7:39:50 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_f853a49e-456a-4ea2-abd1-f2963e8f362f7511736238080476470 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 4 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation_1.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_f853a49e-456a-4ea2-abd1-f2963e8f362f7511736238080476470/simulation_1.sedml failed with error: Failed to create file /tmp/out/temp/simulation_simulation_1.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_simulation_1.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (2.1 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: ``` No reports were generated ``` Log: ``` Jan 21, 2022 7:39:52 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Elowitz-Nature-2000-Repressilator.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_a0b55f63-e91e-4d1c-88c8-c7cd0999a1504103892920850188045 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 1 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_a0b55f63-e91e-4d1c-88c8-c7cd0999a1504103892920850188045/simulation.sedml failed with error: Failed to create file /tmp/out/temp/simulation_simulation.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_simulation.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (2.6 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) * 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: ``` No reports were generated ``` Log: ``` Jan 21, 2022 7:39:59 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_ec7b9f9e-71f8-477b-9aab-c5b96d64a7c75826372385348432768 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 4 model(s), 5 simulation(s), 5 task(s), 5 report(s), 5 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_ec7b9f9e-71f8-477b-9aab-c5b96d64a7c75826372385348432768/simulation.sedml failed with error: Failed to create file /tmp/out/temp/simulation_simulation.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_simulation.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (2.3 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: ``` No reports were generated ``` Log: ``` Jan 21, 2022 7:39:54 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_56790f18-62a2-4e0b-a490-8e7e702cfb146090812171915906175 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 2 model(s), 2 simulation(s), 2 task(s), 2 report(s), 3 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_56790f18-62a2-4e0b-a490-8e7e702cfb146090812171915906175/simulation.sedml failed with error: Failed to create file /tmp/out/temp/simulation_simulation.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_simulation.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (2.2 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) Exception: ``` No reports were generated ``` Log: ``` Jan 21, 2022 7:39:56 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_1ad5f554-de77-4089-8eb4-5d083d37841a2329870877220361380 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 2 model(s), 2 simulation(s), 2 task(s), 2 report(s), 2 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_1ad5f554-de77-4089-8eb4-5d083d37841a2329870877220361380/simulation.sedml failed with error: Failed to create file /tmp/out/temp/simulation_simulation.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_simulation.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
results_report.SimulatorGeneratesReportsOfSimulationResults (2.2 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file. Exception: ``` Simulator must generate reports of simulation results ``` Log: ``` Jan 21, 2022 7:39:34 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_8af4be5f-8a5f-4c59-a395-8ce7ccb4984c3433015026036117071 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_8af4be5f-8a5f-4c59-a395-8ce7ccb4984c3433015026036117071/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
sedml.SimulatorSupportsAlgorithmParameters (2.1 s)
Test that a simulator supports setting the values of parameters of algorithms Exception: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` Jan 21, 2022 7:38:39 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_d87f2241-a6d4-425f-b1b7-7d65ac4079791987635119159969883 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_d87f2241-a6d4-425f-b1b7-7d65ac4079791987635119159969883/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports (2.1 s)
Test that a simulator supports the core elements of SED: models, simulations, tasks, data generators for individual variables, and reports Exception: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` Jan 21, 2022 7:38:56 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_5946701b-9724-4896-bd03-6539e9c6341f1060725805331798267 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_5946701b-9724-4896-bd03-6539e9c6341f1060725805331798267/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
sedml.SimulatorSupportsMultipleReportsPerSedDocument (2.2 s)
Test that a simulator supports multiple reports per SED document Exception: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report_1` - `BIOMD0000000912_sim.sedml/report_2` ``` Log: ``` Jan 21, 2022 7:38:58 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_a766a4eb-52ef-4696-803f-4ae02afbc3e43748111229797105633 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 2 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_a766a4eb-52ef-4696-803f-4ae02afbc3e43748111229797105633/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
sedml.SimulatorSupportsMultipleTasksPerSedDocument (2.2 s)
Test that a simulator supports multiple tasks per SED document Exception: ``` Reports for duplicate tasks were not generated: BIOMD0000000912_sim.sedml/report BIOMD0000000912_sim.sedml/report__test_suite_copy ``` Log: ``` Jan 21, 2022 7:39:00 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_2729bb62-9b09-4fbf-99db-bc9e4d3c1a9e2987296710884375821 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 2 task(s), 2 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_2729bb62-9b09-4fbf-99db-bc9e4d3c1a9e2987296710884375821/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (2.1 s)
Test that a simulator supports time courses with non-zero output start times Exception: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpkscqhkzb/sedml/sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 21, 2022 7:39:32 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_8774012e-fb40-4748-9429-612d637587d247123382964170348 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_8774012e-fb40-4748-9429-612d637587d247123382964170348/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
biosimulators-daemon commented 2 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.4 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports. Warnings: ``` The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports. The command-line interface does not describe the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be described in the inline help for its command-line interface. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
cli.CliDisplaysHelpInline (1.9 s)
Test that a command-line interface provides inline help. Warnings: ``` Command-line interface should support the `-h` option for displaying help inline. The command-line interface displayed the following when executed with `-h`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` ``` Command-line interface should support the `--help` option for displaying help inline. The command-line interface displayed the following when executed with `--help`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` Log: None
cli.CliDisplaysVersionInformationInline (1.5 s)
Test that a command-line interface provides version information inline. Warnings: ``` Command-line interface should support the `-v` option for displaying version information inline. The command-line interface displayed the following when executed with `-v`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` ``` Command-line interface should support the `--version` option for displaying version information inline. The command-line interface displayed the following when executed with `--version`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` Log: None
docker_image.DeclaresSupportedEnvironmentVariables (0.4 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.3 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (2.1 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) Warnings: ``` Plots were not produced: BIOMD0000000912_sim.sedml/Figure_1_bottom_left ``` Log: ``` Jan 21, 2022 7:39:45 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_6156ee96-d8a3-43d0-ad43-641461a289928338319309252518051 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 1 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_6156ee96-d8a3-43d0-ad43-641461a289928338319309252518051/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (2.2 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000086`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000086) Warnings: ``` Plots were not produced: simulation_1.sedml/Figure_3a simulation_1.sedml/Figure_3b simulation_1.sedml/Figure_3c simulation_1.sedml/Figure_3d ``` Log: ``` Jan 21, 2022 7:39:47 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_eec71269-c4ae-4b9f-b6c6-86a85ec6e6992422170663983700527 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 4 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation_1.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_eec71269-c4ae-4b9f-b6c6-86a85ec6e6992422170663983700527/simulation_1.sedml failed with error: Failed to create file /tmp/out/temp/simulation_simulation_1.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_simulation_1.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (2.3 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) Warnings: ``` Plots were not produced: simulation_1.sedml/Figure_3a simulation_1.sedml/Figure_3b simulation_1.sedml/Figure_3c simulation_1.sedml/Figure_3d ``` Log: ``` Jan 21, 2022 7:39:50 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_f853a49e-456a-4ea2-abd1-f2963e8f362f7511736238080476470 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 4 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation_1.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_f853a49e-456a-4ea2-abd1-f2963e8f362f7511736238080476470/simulation_1.sedml failed with error: Failed to create file /tmp/out/temp/simulation_simulation_1.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_simulation_1.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (2.1 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) Warnings: ``` Plots were not produced: simulation.sedml/Figure_1c ``` Log: ``` Jan 21, 2022 7:39:52 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Elowitz-Nature-2000-Repressilator.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_a0b55f63-e91e-4d1c-88c8-c7cd0999a1504103892920850188045 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 1 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_a0b55f63-e91e-4d1c-88c8-c7cd0999a1504103892920850188045/simulation.sedml failed with error: Failed to create file /tmp/out/temp/simulation_simulation.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_simulation.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (2.6 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) * 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) Warnings: ``` Plots were not produced: simulation.sedml/plot2d_Euler_small_step_size simulation.sedml/plot2d_Fig_1_c simulation.sedml/plot2d_Fig_1a simulation.sedml/plot2d_low_delta_R_det simulation.sedml/plot2d_low_delta_R_stoch ``` Log: ``` Jan 21, 2022 7:39:59 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_ec7b9f9e-71f8-477b-9aab-c5b96d64a7c75826372385348432768 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 4 model(s), 5 simulation(s), 5 task(s), 5 report(s), 5 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_ec7b9f9e-71f8-477b-9aab-c5b96d64a7c75826372385348432768/simulation.sedml failed with error: Failed to create file /tmp/out/temp/simulation_simulation.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_simulation.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (2.3 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) Warnings: ``` Plots were not produced: simulation.sedml/Figure_2ab simulation.sedml/plot2d_Fig_1a simulation.sedml/plot2d_low_delta_R_det ``` Log: ``` Jan 21, 2022 7:39:54 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_56790f18-62a2-4e0b-a490-8e7e702cfb146090812171915906175 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 2 model(s), 2 simulation(s), 2 task(s), 2 report(s), 3 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_56790f18-62a2-4e0b-a490-8e7e702cfb146090812171915906175/simulation.sedml failed with error: Failed to create file /tmp/out/temp/simulation_simulation.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_simulation.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (2.2 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) Warnings: ``` Plots were not produced: simulation.sedml/plot2d_Fig_1_c simulation.sedml/plot2d_low_delta_R_stoch ``` Log: ``` Jan 21, 2022 7:39:56 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_1ad5f554-de77-4089-8eb4-5d083d37841a2329870877220361380 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 2 model(s), 2 simulation(s), 2 task(s), 2 report(s), 2 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_1ad5f554-de77-4089-8eb4-5d083d37841a2329870877220361380/simulation.sedml failed with error: Failed to create file /tmp/out/temp/simulation_simulation.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_simulation.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
biosimulators-daemon commented 2 years ago

Skips

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (2.1 s)
Test that simulator logs the execution of COMBINE/OMEX archives Reason for skip: ``` The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status. More information: https://docs.biosimulations.org/concepts/conventions/simulation-run-logs/ ``` Log: ``` Jan 21, 2022 7:39:36 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_173be7d7-23a9-4577-a294-f19a69a596681831177035587572660 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_173be7d7-23a9-4577-a294-f19a69a596681831177035587572660/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (2.2 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives Reason for skip: ``` The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status. More information: https://docs.biosimulations.org/concepts/conventions/simulation-run-logs/ ``` Log: ``` Jan 21, 2022 7:39:38 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_9e9890ac-af6e-4e7e-830c-d9e2beaa38b87360643728082723322 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_9e9890ac-af6e-4e7e-830c-d9e2beaa38b87360643728082723322/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (2.1 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives Reason for skip: ``` The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status. More information: https://docs.biosimulations.org/concepts/conventions/simulation-run-logs/ ``` Log: ``` Jan 21, 2022 7:39:41 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_b9ec1e3f-e45c-414c-aeb7-1aa9164cf7966617558390434748918 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_b9ec1e3f-e45c-414c-aeb7-1aa9164cf7966617558390434748918/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (2.2 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives Reason for skip: ``` The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status. More information: https://docs.biosimulations.org/concepts/conventions/simulation-run-logs/ ``` Log: ``` Jan 21, 2022 7:39:43 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_040cec3b-4e09-4158-954d-87176d17b4638267262554226899578 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_040cec3b-4e09-4158-954d-87176d17b4638267262554226899578/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
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 (2.2 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: ``` Jan 21, 2022 7:38:22 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_d59770af-b310-4dc7-b959-d2bf3db100ee5916728358733200856 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_d59770af-b310-4dc7-b959-d2bf3db100ee5916728358733200856/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (2.1 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``) and inherit the changes of the model. Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` Jan 21, 2022 7:38:24 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_844793ff-6f5d-473b-b0f2-4a4a9328a8456642201137020888799 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_844793ff-6f5d-473b-b0f2-4a4a9328a8456642201137020888799/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
sedml.SimulatorProducesLinear2DPlots (2.2 s)
Test that a simulator produces linear 2D plots Reason for skip: ``` Simulator did not produce plots ``` Log: ``` Jan 21, 2022 7:38:26 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_bcdc2bef-add2-4a55-b870-9c3d936653046362173697740524978 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 0 report(s), 1 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_bcdc2bef-add2-4a55-b870-9c3d936653046362173697740524978/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
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.SimulatorProducesLogarithmic2DPlots (2.1 s)
Test that a simulator produces logarithmic 2D plots Reason for skip: ``` Simulator did not produce plots ``` Log: ``` Jan 21, 2022 7:38:29 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_2ed7911b-821f-49c4-9482-7298c26689da2539530082061103465 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 0 report(s), 1 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_2ed7911b-821f-49c4-9482-7298c26689da2539530082061103465/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
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.SimulatorProducesMultiplePlots (2.2 s)
Test that a simulator produces multiple plots Reason for skip: ``` Simulator did not produce plots ``` Log: ``` Jan 21, 2022 7:38:31 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_733f274b-8d8a-4b4a-972e-0b757d9b43c54723851001774596303 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 0 report(s), 2 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_733f274b-8d8a-4b4a-972e-0b757d9b43c54723851001774596303/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
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 (5.0 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` Jan 21, 2022 7:38:34 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_2757f0ea-b55c-43e4-bca7-5404b411b3581582570726899891491 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_2757f0ea-b55c-43e4-bca7-5404b411b3581582570726899891491/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML Jan 21, 2022 7:38:36 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_f37ab054-dbb4-422c-a08b-ae563a5e6f7a4305759566234714146 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_f37ab054-dbb4-422c-a08b-ae563a5e6f7a4305759566234714146/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
sedml.SimulatorSupportsComputeModelChanges (5.5 s)
Test that a simulator supports compute model changes Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` Jan 21, 2022 7:38:41 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_8026d17c-e776-48aa-a05d-36d8d79b4b953383025663776280396 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_8026d17c-e776-48aa-a05d-36d8d79b4b953383025663776280396/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML Jan 21, 2022 7:38:44 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_336fa971-f069-4e49-b87b-3dd967668e2b7614957436095996621 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_336fa971-f069-4e49-b87b-3dd967668e2b7614957436095996621/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (2.2 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/tmpkscqhkzb/sedml/sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 21, 2022 7:38:46 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_c1adbfcd-a4d6-4305-b1e6-7c4a100b4eba8433331964094325173 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_c1adbfcd-a4d6-4305-b1e6-7c4a100b4eba8433331964094325173/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (2.3 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpkscqhkzb/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Jan 21, 2022 7:38:49 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_eae9e227-f418-4465-89a6-a2ea32dfcd875314937031264062731 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d and 3D python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML SED-ML processing for /tmp/vcell_temp_eae9e227-f418-4465-89a6-a2ea32dfcd875314937031264062731/BIOMD0000000912_sim.sedml failed with error: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml java.lang.RuntimeException: Failed to create file /tmp/out/temp/simulation_BIOMD0000000912_sim.sedml at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:335) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:144) python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating sedml document status YAML python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory All sedml documents in this archive failed to execute python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed updating task status YAML ```
sedml.SimulatorSupportsModelAttributeChanges (4.7 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` Jan 21, 2022 7:38:51 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_9eaceb54-f917-4c36-b94e-cffdc4b4b17b1396717065225034812 Python 3.8.10 utilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py': [Errno 2] No such file or directory Failed generating status YAML SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- python3: can't open file 'c:/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py': [Errno 2] No such file or directory Failed generating SED-ML for plot2d ...
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/1730428673). 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/1730428673).
moraru commented 2 years ago

wrong branch merged in this build