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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 7.4.0.23 #440

Closed vcdaemon closed 3 years ago

vcdaemon commented 3 years ago

id: vcell version: 7.4.0.23 specificationsUrl: https://raw.githubusercontent.com/virtualcell/vcell/7.4.0.23/biosimulators.json specificationsPatch: version: 7.4.0.23 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.23 validateImage: true commitSimulator: true

biosimulators-daemon commented 3 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 3 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 3 years ago

Summary of tests

biosimulators-daemon commented 3 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.5 s)

Test that the inline help for a command-line interface describes the environment variables that the simulator supports.

Warnings:

  The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

  The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
    - 'ALGORITHM_SUBSTITUTION_POLICY'
    - 'BUNDLE_OUTPUTS'
    - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
    - 'COLLECT_SED_DOCUMENT_RESULTS'
    - 'DEBUG'
    - 'H5_REPORTS_PATH'
    - 'KEEP_INDIVIDUAL_OUTPUTS'
    - 'LOG_PATH'
    - 'OMEX_METADATA_INPUT_FORMAT'
    - 'OMEX_METADATA_OUTPUT_FORMAT'
    - 'OMEX_METADATA_SCHEMA'
    - 'PLOTS_PATH'
    - 'REPORTS_PATH'
    - 'REPORT_FORMATS'
    - 'SAVE_PLOT_DATA'
    - 'VALIDATE_IMAGES'
    - 'VALIDATE_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:

cli.CliDisplaysHelpInline (2.9 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:

cli.CliDisplaysVersionInformationInline (2.4 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:

docker_image.DeclaresSupportedEnvironmentVariables (0.3 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_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:

docker_image.HasBioContainersLabels (0.3 s)

Test that a Docker image has BioContainers labels with metadata about the image

Warnings:

  The Docker image should have the following BioContainers labels:
    extra.identifiers.biotools

Log:

docker_image.HasOciLabels (0.2 s)

Test that a Docker image has Open Container Initiative (OCI) labels with metadata about the image

Warnings:

  The Docker image should have the following Open Container Initiative (OCI) labels:
    org.opencontainers.image.created
    org.opencontainers.image.revision

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (18.8 s)

Required model formats and simulation algorithms for SED tasks:

biosimulators-daemon commented 3 years ago

Skips

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (14.5 s)

Test that simulator logs the execution of COMBINE/OMEX archives

Reason for skip:

  The execution status report produced by the simulator is not valid:

    load() missing 1 required positional argument: 'Loader'

Log:

  Oct 14, 2021 3:34:57 AM java.util.prefs.FileSystemPreferences$1 run

  INFO: Created user preferences directory.

  VCell CLI input archive /tmp/in/archive.omex

  -----------------------------------------------------------------------------------------------------

  TempPath Created: /tmp/vcell_temp_c084048e-4989-4742-8213-97cf6f59fe157472210901806582979

  Python 3.8.10

  utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

  cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

  cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

  statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

  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: SED-ML file BIOMD0000000912_sim.sedml

  -----------------------------------------------------------------------------------------------------

  name:  BIOMD0000000912_sim

  SED-ML version level not supported, import may fail

  SED-ML version level not supported, import may fail

  Unsupported version, import may fail

  Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

  UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

  Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

  DataGenerator [math=org.jmathml.ASTRootNode@2c78d320, name=time, getId()=data_gen_time]

  DataGenerator [math=org.jmathml.ASTRootNode@132e0cc, name=T, getId()=data_gen_T]

  DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=E, getId()=data_gen_E]

  DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=I, getId()=data_gen_I]

  org.jlibsedml.Report@c84c5553

  SED-ML version level not supported, import may fail

  SED-ML version level not supported, import may fail

  Unsupported version, import may fail

  Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

  SBML Import: no assignment rules.

  SBML Import: no assignment rules.

  LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

  - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. 

  User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

  Succesful model import: SBML file /tmp/temp8086111508179903275.xml

  /tmp/out/BIOMD0000000912_sim.sedml

  false

  cbit.vcell.solver.ode.CVodeSolverStandalone@757f675c

  Finished: SOLVER_FINISHED:completed

  Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

  Running simulation BIOMD0000000912_task_Caravagna2010, 103 ms

  -----------------------------------------------------------------------------------------------------

  Ran 1 simulations for 1 biomodels.

  Generating report `report`.

  report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv

  HDF conversion successful

  No PDF files found, skipping archiving `plots.zip` files

  Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (14.4 s)

Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives

Reason for skip:

  The execution status report produced by the simulator is not valid:

    load() missing 1 required positional argument: 'Loader'

Log:

  Oct 14, 2021 3:35:11 AM java.util.prefs.FileSystemPreferences$1 run

  INFO: Created user preferences directory.

  VCell CLI input archive /tmp/in/archive.omex

  -----------------------------------------------------------------------------------------------------

  TempPath Created: /tmp/vcell_temp_4470a289-68e9-4b26-a023-fed2723d7d743717328942117994241

  Python 3.8.10

  utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

  cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

  cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

  statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

  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: SED-ML file BIOMD0000000912_sim.sedml

  -----------------------------------------------------------------------------------------------------

  name:  BIOMD0000000912_sim

  SED-ML version level not supported, import may fail

  SED-ML version level not supported, import may fail

  Unsupported version, import may fail

  Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

  UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

  Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

  DataGenerator [math=org.jmathml.ASTRootNode@2c78d320, name=time, getId()=data_gen_time]

  DataGenerator [math=org.jmathml.ASTRootNode@132e0cc, name=T, getId()=data_gen_T]

  DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=E, getId()=data_gen_E]

  DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=I, getId()=data_gen_I]

  org.jlibsedml.Report@c84c5553

  SED-ML version level not supported, import may fail

  SED-ML version level not supported, import may fail

  Unsupported version, import may fail

  Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

  SBML Import: no assignment rules.

  SBML Import: no assignment rules.

  LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

  - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. 

  User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

  Succesful model import: SBML file /tmp/temp7016211203109970443.xml

  /tmp/out/BIOMD0000000912_sim.sedml

  false

  cbit.vcell.solver.ode.CVodeSolverStandalone@757f675c

  Finished: SOLVER_FINISHED:completed

  Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

  Running simulation BIOMD0000000912_task_Caravagna2010, 111 ms

  -----------------------------------------------------------------------------------------------------

  Ran 1 simulations for 1 biomodels.

  Generating report `report`.

  report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv

  HDF conversion successful

  No PDF files found, skipping archiving `plots.zip` files

  Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (14.7 s)

Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives

Reason for skip:

  The execution status report produced by the simulator is not valid:

    load() missing 1 required positional argument: 'Loader'

Log:

  Oct 14, 2021 3:35:26 AM java.util.prefs.FileSystemPreferences$1 run

  INFO: Created user preferences directory.

  VCell CLI input archive /tmp/in/archive.omex

  -----------------------------------------------------------------------------------------------------

  TempPath Created: /tmp/vcell_temp_d1299a33-2486-4196-837c-ab1237b62a251014813867579097538

  Python 3.8.10

  utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

  cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

  cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

  statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

  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: SED-ML file BIOMD0000000912_sim.sedml

  -----------------------------------------------------------------------------------------------------

  name:  BIOMD0000000912_sim

  SED-ML version level not supported, import may fail

  SED-ML version level not supported, import may fail

  Unsupported version, import may fail

  Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

  UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

  Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

  DataGenerator [math=org.jmathml.ASTRootNode@2c78d320, name=time, getId()=data_gen_time]

  DataGenerator [math=org.jmathml.ASTRootNode@132e0cc, name=T, getId()=data_gen_T]

  DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=E, getId()=data_gen_E]

  DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=I, getId()=data_gen_I]

  org.jlibsedml.Report@c84c5553

  SED-ML version level not supported, import may fail

  SED-ML version level not supported, import may fail

  Unsupported version, import may fail

  Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

  SBML Import: no assignment rules.

  SBML Import: no assignment rules.

  LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

  - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. 

  User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

  Succesful model import: SBML file /tmp/temp6528206683117526591.xml

  /tmp/out/BIOMD0000000912_sim.sedml

  false

  cbit.vcell.solver.ode.CVodeSolverStandalone@757f675c

  Finished: SOLVER_FINISHED:completed

  Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

  Running simulation BIOMD0000000912_task_Caravagna2010, 102 ms

  -----------------------------------------------------------------------------------------------------

  Ran 1 simulations for 1 biomodels.

  Generating report `report`.

  report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv

  HDF conversion successful

  No PDF files found, skipping archiving `plots.zip` files

  Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (14.7 s)

Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives

Reason for skip:

  The execution status report produced by the simulator is not valid:

    load() missing 1 required positional argument: 'Loader'

Log:

  Oct 14, 2021 3:35:41 AM java.util.prefs.FileSystemPreferences$1 run

  INFO: Created user preferences directory.

  VCell CLI input archive /tmp/in/archive.omex

  -----------------------------------------------------------------------------------------------------

  TempPath Created: /tmp/vcell_temp_61b04b24-0306-4b96-a0c2-8399c10367a61755933335631185923

  Python 3.8.10

  utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

  cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

  cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

  statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

  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: SED-ML file BIOMD0000000912_sim.sedml

  -----------------------------------------------------------------------------------------------------

  name:  BIOMD0000000912_sim

  SED-ML version level not supported, import may fail

  SED-ML version level not supported, import may fail

  Unsupported version, import may fail

  Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

  UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

  Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

  DataGenerator [math=org.jmathml.ASTRootNode@2c78d320, name=time, getId()=data_gen_time]

  DataGenerator [math=org.jmathml.ASTRootNode@132e0cc, name=T, getId()=data_gen_T]

  DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=E, getId()=data_gen_E]

  DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=I, getId()=data_gen_I]

  org.jlibsedml.Report@c84c5553

  SED-ML version level not supported, import may fail

  SED-ML version level not supported, import may fail

  Unsupported version, import may fail

  Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

  SBML Import: no assignment rules.

  SBML Import: no assignment rules.

  LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

  - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. 

  User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

  Succesful model import: SBML file /tmp/temp1447154212714301329.xml

  /tmp/out/BIOMD0000000912_sim.sedml

  false

  cbit.vcell.solver.ode.CVodeSolverStandalone@2617f816

  Finished: SOLVER_FINISHED:completed

  Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

  Running simulation BIOMD0000000912_task_Caravagna2010, 105 ms

  -----------------------------------------------------------------------------------------------------

  Ran 1 simulations for 1 biomodels.

  Generating report `report`.

  report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv

  HDF conversion successful

  No PDF files found, skipping archiving `plots.zip` files

  Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

Required model formats and simulation algorithms for SED tasks:

biosimulators-daemon commented 3 years ago

The image for your simulator is valid!

biosimulators-daemon commented 3 years ago

A member of the BioSimulators team will review your submission and publish your image before final committment to the registry.