search

biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
MIT License
13 stars 0 forks source link

Submit VCell 7.4.0.21 #420

Closed vcdaemon closed 3 years ago

vcdaemon commented 3 years ago

id: vcell version: 7.4.0.21 specificationsUrl: https://raw.githubusercontent.com/virtualcell/vcell/7.4.0.21/biosimulators.json specificationsPatch: version: 7.4.0.21 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.21 validateImage: true commitSimulator: true

Changelog

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 validation/submission of your simulator failed.

- 'url'

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly 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.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

moraru commented 3 years ago

Failed in biosimulators_utils routine before actually testing the simulator

https://github.com/biosimulators/Biosimulators/runs/3646372208?check_suite_focus=true

jonrkarr commented 3 years ago

The message body above was not correctly formatted. url must be a property of image. @moraru this likely needs to be corrected in your submission action.

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

Failures

sedml.SimulatorProducesLinear2DPlots (12.6 s)

Test that a simulator produces linear 2D plots

Exception:

  Simulator did not record the following data generators:
    - `data_gen_E`
    - `data_gen_I`
    - `data_gen_T`
    - `data_gen_time`

Log:

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

  Sep 20, 2021 12:36:23 AM java.util.prefs.FileSystemPreferences$1 run

  INFO: Created user preferences directory.

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

  TempPath Created: /tmp/vcell_temp_3e7533da-a04e-42cf-8f85-e797bb7d67cf2236823500470505317

  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), 0  report(s),  1 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@51fadaff, name=time, getId()=data_gen_time]

  DataGenerator [math=org.jmathml.ASTRootNode@401f7633, name=T, getId()=data_gen_T]

  DataGenerator [math=org.jmathml.ASTRootNode@31ff43be, name=E, getId()=data_gen_E]

  DataGenerator [math=org.jmathml.ASTRootNode@5b6ec132, name=I, getId()=data_gen_I]

  Plot2D [listOfCurves=[Curve [id=curve_0, logX=false, logY=false, name=null, xDataReference=data_gen_time, yDataReference=data_gen_time], Curve [id=curve_1, logX=false, logY=false, name=null, xDataReference=data_gen_T, yDataReference=data_gen_T], Curve [id=curve_2, logX=false, logY=false, name=null, xDataReference=data_gen_E, yDataReference=data_gen_E], Curve [id=curve_3, logX=false, logY=false, name=null, xDataReference=data_gen_I, yDataReference=data_gen_I]], name=null]

  org.jlibsedml.Report@903fe012

  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/temp1301353016527913898.xml

  /tmp/out/BIOMD0000000912_sim.sedml

  false

  cbit.vcell.solver.ode.CVodeSolverStandalone@718607eb

  Finished: SOLVER_FINISHED:completed

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

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

  Ignoring unsupported output `plot_0` while CSV generation.

  Generating report `__plot__plot_0`.

  HDF conversion successful

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  Archiving resultant PDF files to `plots.zip`.

  Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorProducesLogarithmic2DPlots (13.0 s)

Test that a simulator produces logarithmic 2D plots

Exception:

  Simulator did not record the following data generators:
    - `data_gen_E`
    - `data_gen_I`
    - `data_gen_T`
    - `data_gen_time`

Log:

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

  Sep 20, 2021 12:36:36 AM java.util.prefs.FileSystemPreferences$1 run

  INFO: Created user preferences directory.

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

  TempPath Created: /tmp/vcell_temp_418f5954-fd21-4680-b37b-f91d17065b625197795256953095257

  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), 0  report(s),  1 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@51fadaff, name=time, getId()=data_gen_time]

  DataGenerator [math=org.jmathml.ASTRootNode@401f7633, name=T, getId()=data_gen_T]

  DataGenerator [math=org.jmathml.ASTRootNode@31ff43be, name=E, getId()=data_gen_E]

  DataGenerator [math=org.jmathml.ASTRootNode@5b6ec132, name=I, getId()=data_gen_I]

  Plot2D [listOfCurves=[Curve [id=curve_0, logX=true, logY=true, name=null, xDataReference=data_gen_time, yDataReference=data_gen_time], Curve [id=curve_1, logX=true, logY=true, name=null, xDataReference=data_gen_T, yDataReference=data_gen_T], Curve [id=curve_2, logX=true, logY=true, name=null, xDataReference=data_gen_E, yDataReference=data_gen_E], Curve [id=curve_3, logX=true, logY=true, name=null, xDataReference=data_gen_I, yDataReference=data_gen_I]], name=null]

  org.jlibsedml.Report@903fe012

  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/temp1325018608088274907.xml

  /tmp/out/BIOMD0000000912_sim.sedml

  false

  cbit.vcell.solver.ode.CVodeSolverStandalone@718607eb

  Finished: SOLVER_FINISHED:completed

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

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

  Ignoring unsupported output `plot_0` while CSV generation.

  Generating report `__plot__plot_0`.

  HDF conversion successful

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  Archiving resultant PDF files to `plots.zip`.

  Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorProducesMultiplePlots (12.7 s)

Test that a simulator produces multiple plots

Exception:

  Simulator did not record the following data generators:
    - `data_gen_E`
    - `data_gen_time`

Log:

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

  Sep 20, 2021 12:36:49 AM java.util.prefs.FileSystemPreferences$1 run

  INFO: Created user preferences directory.

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

  TempPath Created: /tmp/vcell_temp_0ac830c9-4408-41ca-9aed-9dd4b68c1f618049486801628417660

  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), 0  report(s),  2 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@51fadaff, name=time, getId()=data_gen_time]

  DataGenerator [math=org.jmathml.ASTRootNode@401f7633, name=T, getId()=data_gen_T]

  DataGenerator [math=org.jmathml.ASTRootNode@31ff43be, name=E, getId()=data_gen_E]

  DataGenerator [math=org.jmathml.ASTRootNode@5b6ec132, name=I, getId()=data_gen_I]

  Plot2D [listOfCurves=[Curve [id=curve_0, logX=false, logY=false, name=null, xDataReference=data_gen_time, yDataReference=data_gen_time], Curve [id=curve_2, logX=false, logY=false, name=null, xDataReference=data_gen_E, yDataReference=data_gen_E]], name=null]

  Plot2D [listOfCurves=[Curve [id=curve_1, logX=false, logY=false, name=null, xDataReference=data_gen_T, yDataReference=data_gen_T], Curve [id=curve_3, logX=false, logY=false, name=null, xDataReference=data_gen_I, yDataReference=data_gen_I]], name=null]

  org.jlibsedml.Report@903fe012

  org.jlibsedml.Report@903fe013

  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/temp8962240215965307900.xml

  /tmp/out/BIOMD0000000912_sim.sedml

  false

  cbit.vcell.solver.ode.CVodeSolverStandalone@718607eb

  Finished: SOLVER_FINISHED:completed

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

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

  Ignoring unsupported output `plot_0` while CSV generation.

  Ignoring unsupported output `plot_1` while CSV generation.

  Generating report `__plot__plot_0`.

  Generating report `__plot__plot_1`.

  HDF conversion successful

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  Archiving resultant PDF files to `plots.zip`.

  Archiving resultant CSV files to `reports.zip`.
biosimulators-daemon commented 3 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'
    - '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:

docker_image.DeclaresSupportedEnvironmentVariables (0.7 s)

Test if a Docker image declares the environment variables that is supports

Warnings:

  Docker images for simulation tools should declare the environment variables that they support.

  The Docker image does not declare the following standard environment variables recognized by BioSimulators:
    - 'BUNDLE_OUTPUTS'
    - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
    - 'COLLECT_SED_DOCUMENT_RESULTS'
    - 'DEBUG'
    - 'H5_REPORTS_PATH'
    - 'KEEP_INDIVIDUAL_OUTPUTS'
    - 'LOG_PATH'
    - '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 (0.5 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 (0.5 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 (17.2 s)

Required model formats and simulation algorithms for SED tasks:

biosimulators-daemon commented 3 years ago

Skips

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (12.7 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://biosimulators.org/conventions/status

Log:

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

  Sep 20, 2021 12:40:29 AM java.util.prefs.FileSystemPreferences$1 run

  INFO: Created user preferences directory.

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

  TempPath Created: /tmp/vcell_temp_b7aa71ec-4154-4365-83d3-e041d298775c5255591662087110991

  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@51fadaff, name=time, getId()=data_gen_time]

  DataGenerator [math=org.jmathml.ASTRootNode@401f7633, name=T, getId()=data_gen_T]

  DataGenerator [math=org.jmathml.ASTRootNode@31ff43be, name=E, getId()=data_gen_E]

  DataGenerator [math=org.jmathml.ASTRootNode@5b6ec132, 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/temp6618229381665354769.xml

  /tmp/out/BIOMD0000000912_sim.sedml

  false

  cbit.vcell.solver.ode.CVodeSolverStandalone@718607eb

  Finished: SOLVER_FINISHED:completed

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

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

  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 (12.4 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://biosimulators.org/conventions/status

Log:

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

  Sep 20, 2021 12:40:41 AM java.util.prefs.FileSystemPreferences$1 run

  INFO: Created user preferences directory.

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

  TempPath Created: /tmp/vcell_temp_9365d3ad-5482-43a6-a450-c8c48d7e8cfd1746586725181652175

  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@51fadaff, name=time, getId()=data_gen_time]

  DataGenerator [math=org.jmathml.ASTRootNode@401f7633, name=T, getId()=data_gen_T]

  DataGenerator [math=org.jmathml.ASTRootNode@31ff43be, name=E, getId()=data_gen_E]

  DataGenerator [math=org.jmathml.ASTRootNode@5b6ec132, 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/temp7646726206615836797.xml

  /tmp/out/BIOMD0000000912_sim.sedml

  false

  cbit.vcell.solver.ode.CVodeSolverStandalone@718607eb

  Finished: SOLVER_FINISHED:completed

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

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

  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 (12.2 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://biosimulators.org/conventions/status

Log:

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

  Sep 20, 2021 12:40:54 AM java.util.prefs.FileSystemPreferences$1 run

  INFO: Created user preferences directory.

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

  TempPath Created: /tmp/vcell_temp_cfa719e2-31c6-46b6-bb94-9b1e05c3cb841884098742132424969

  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@51fadaff, name=time, getId()=data_gen_time]

  DataGenerator [math=org.jmathml.ASTRootNode@401f7633, name=T, getId()=data_gen_T]

  DataGenerator [math=org.jmathml.ASTRootNode@31ff43be, name=E, getId()=data_gen_E]

  DataGenerator [math=org.jmathml.ASTRootNode@5b6ec132, 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/temp2837987993907001345.xml

  /tmp/out/BIOMD0000000912_sim.sedml

  false

  cbit.vcell.solver.ode.CVodeSolverStandalone@718607eb

  Finished: SOLVER_FINISHED:completed

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

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

  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 (12.4 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://biosimulators.org/conventions/status

Log:

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

  Sep 20, 2021 12:41:06 AM java.util.prefs.FileSystemPreferences$1 run

  INFO: Created user preferences directory.

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

  TempPath Created: /tmp/vcell_temp_981bb94b-9d3f-44fa-9041-e65bd1548c0d5267586446267955969

  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@51fadaff, name=time, getId()=data_gen_time]

  DataGenerator [math=org.jmathml.ASTRootNode@401f7633, name=T, getId()=data_gen_T]

  DataGenerator [math=org.jmathml.ASTRootNode@31ff43be, name=E, getId()=data_gen_E]

  DataGenerator [math=org.jmathml.ASTRootNode@5b6ec132, 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/temp7307031436694370362.xml

  /tmp/out/BIOMD0000000912_sim.sedml

  false

  cbit.vcell.solver.ode.CVodeSolverStandalone@718607eb

  Finished: SOLVER_FINISHED:completed

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

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

  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 
- 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/1251830701). 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/1251830701).
jonrkarr commented 3 years ago

@moraru the GitHub action looks correct. When creating issues by hand, the YAML needs to be formatted correctly.

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

Failures

sedml.SimulatorProducesLinear2DPlots (12.5 s)

Test that a simulator produces linear 2D plots

Exception:

  Simulator did not record the following data generators:
    - `data_gen_E`
    - `data_gen_I`
    - `data_gen_T`
    - `data_gen_time`

Log:

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

  Sep 20, 2021 4:08:32 PM java.util.prefs.FileSystemPreferences$1 run

  INFO: Created user preferences directory.

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

  TempPath Created: /tmp/vcell_temp_94d4e678-580f-4c0c-ba7a-46b9037583ff5427738682535092877

  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), 0  report(s),  1 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@401f7633, name=time, getId()=data_gen_time]

  DataGenerator [math=org.jmathml.ASTRootNode@31ff43be, name=T, getId()=data_gen_T]

  DataGenerator [math=org.jmathml.ASTRootNode@5b6ec132, name=E, getId()=data_gen_E]

  DataGenerator [math=org.jmathml.ASTRootNode@5c44c582, name=I, getId()=data_gen_I]

  Plot2D [listOfCurves=[Curve [id=curve_0, logX=false, logY=false, name=null, xDataReference=data_gen_time, yDataReference=data_gen_time], Curve [id=curve_1, logX=false, logY=false, name=null, xDataReference=data_gen_T, yDataReference=data_gen_T], Curve [id=curve_2, logX=false, logY=false, name=null, xDataReference=data_gen_E, yDataReference=data_gen_E], Curve [id=curve_3, logX=false, logY=false, name=null, xDataReference=data_gen_I, yDataReference=data_gen_I]], name=null]

  org.jlibsedml.Report@903fe012

  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/temp9113570874236514709.xml

  /tmp/out/BIOMD0000000912_sim.sedml

  false

  cbit.vcell.solver.ode.CVodeSolverStandalone@27f3b6d6

  Finished: SOLVER_FINISHED:completed

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

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

  Ignoring unsupported output `plot_0` while CSV generation.

  Generating report `__plot__plot_0`.

  HDF conversion successful

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  Archiving resultant PDF files to `plots.zip`.

  Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorProducesLogarithmic2DPlots (12.5 s)

Test that a simulator produces logarithmic 2D plots

Exception:

  Simulator did not record the following data generators:
    - `data_gen_E`
    - `data_gen_I`
    - `data_gen_T`
    - `data_gen_time`

Log:

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

  Sep 20, 2021 4:08:45 PM java.util.prefs.FileSystemPreferences$1 run

  INFO: Created user preferences directory.

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

  TempPath Created: /tmp/vcell_temp_0543698d-e2b6-49b3-8c56-f001700cc1c1689276177924590365

  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), 0  report(s),  1 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@401f7633, name=time, getId()=data_gen_time]

  DataGenerator [math=org.jmathml.ASTRootNode@31ff43be, name=T, getId()=data_gen_T]

  DataGenerator [math=org.jmathml.ASTRootNode@5b6ec132, name=E, getId()=data_gen_E]

  DataGenerator [math=org.jmathml.ASTRootNode@5c44c582, name=I, getId()=data_gen_I]

  Plot2D [listOfCurves=[Curve [id=curve_0, logX=true, logY=true, name=null, xDataReference=data_gen_time, yDataReference=data_gen_time], Curve [id=curve_1, logX=true, logY=true, name=null, xDataReference=data_gen_T, yDataReference=data_gen_T], Curve [id=curve_2, logX=true, logY=true, name=null, xDataReference=data_gen_E, yDataReference=data_gen_E], Curve [id=curve_3, logX=true, logY=true, name=null, xDataReference=data_gen_I, yDataReference=data_gen_I]], name=null]

  org.jlibsedml.Report@903fe012

  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/temp487651342420418791.xml

  /tmp/out/BIOMD0000000912_sim.sedml

  false

  cbit.vcell.solver.ode.CVodeSolverStandalone@27f3b6d6

  Finished: SOLVER_FINISHED:completed

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

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

  Ignoring unsupported output `plot_0` while CSV generation.

  Generating report `__plot__plot_0`.

  HDF conversion successful

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  Archiving resultant PDF files to `plots.zip`.

  Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorProducesMultiplePlots (17.0 s)

Test that a simulator produces multiple plots

Exception:

  Simulator did not record the following data generators:
    - `data_gen_E`
    - `data_gen_time`

Log:

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

  Sep 20, 2021 4:09:02 PM java.util.prefs.FileSystemPreferences$1 run

  INFO: Created user preferences directory.

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

  TempPath Created: /tmp/vcell_temp_7b186450-4e1b-4549-aeb5-041d679a48271588957091542727641

  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), 0  report(s),  2 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@51fadaff, name=time, getId()=data_gen_time]

  DataGenerator [math=org.jmathml.ASTRootNode@401f7633, name=T, getId()=data_gen_T]

  DataGenerator [math=org.jmathml.ASTRootNode@31ff43be, name=E, getId()=data_gen_E]

  DataGenerator [math=org.jmathml.ASTRootNode@5b6ec132, name=I, getId()=data_gen_I]

  Plot2D [listOfCurves=[Curve [id=curve_0, logX=false, logY=false, name=null, xDataReference=data_gen_time, yDataReference=data_gen_time], Curve [id=curve_2, logX=false, logY=false, name=null, xDataReference=data_gen_E, yDataReference=data_gen_E]], name=null]

  Plot2D [listOfCurves=[Curve [id=curve_1, logX=false, logY=false, name=null, xDataReference=data_gen_T, yDataReference=data_gen_T], Curve [id=curve_3, logX=false, logY=false, name=null, xDataReference=data_gen_I, yDataReference=data_gen_I]], name=null]

  org.jlibsedml.Report@903fe012

  org.jlibsedml.Report@903fe013

  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/temp7829647290610092367.xml

  /tmp/out/BIOMD0000000912_sim.sedml

  false

  cbit.vcell.solver.ode.CVodeSolverStandalone@718607eb

  Finished: SOLVER_FINISHED:completed

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

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

  Ignoring unsupported output `plot_0` while CSV generation.

  Ignoring unsupported output `plot_1` while CSV generation.

  Generating report `__plot__plot_0`.

  Generating report `__plot__plot_1`.

  HDF conversion successful

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py:409: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.

  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

    np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)

  Archiving resultant PDF files to `plots.zip`.

  Archiving resultant CSV files to `reports.zip`.
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'
    - '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:

docker_image.DeclaresSupportedEnvironmentVariables (0.7 s)

Test if a Docker image declares the environment variables that is supports

Warnings:

  Docker images for simulation tools should declare the environment variables that they support.

  The Docker image does not declare the following standard environment variables recognized by BioSimulators:
    - 'BUNDLE_OUTPUTS'
    - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
    - 'COLLECT_SED_DOCUMENT_RESULTS'
    - 'DEBUG'
    - 'H5_REPORTS_PATH'
    - 'KEEP_INDIVIDUAL_OUTPUTS'
    - 'LOG_PATH'
    - '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 (0.6 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 (0.6 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 (17.0 s)

Required model formats and simulation algorithms for SED tasks:

biosimulators-daemon commented 3 years ago

Skips

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (12.2 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://biosimulators.org/conventions/status

Log:

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

  Sep 20, 2021 4:12:42 PM java.util.prefs.FileSystemPreferences$1 run

  INFO: Created user preferences directory.

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

  TempPath Created: /tmp/vcell_temp_d77ded43-06ab-4109-b8fd-76451110f3f81754244467714079033

  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@51fadaff, name=time, getId()=data_gen_time]

  DataGenerator [math=org.jmathml.ASTRootNode@401f7633, name=T, getId()=data_gen_T]

  DataGenerator [math=org.jmathml.ASTRootNode@31ff43be, name=E, getId()=data_gen_E]

  DataGenerator [math=org.jmathml.ASTRootNode@5b6ec132, 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/temp2331522136747598646.xml

  /tmp/out/BIOMD0000000912_sim.sedml

  false

  cbit.vcell.solver.ode.CVodeSolverStandalone@718607eb

  Finished: SOLVER_FINISHED:completed

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

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

  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 (12.2 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://biosimulators.org/conventions/status

Log:

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

  Sep 20, 2021 4:12:54 PM java.util.prefs.FileSystemPreferences$1 run

  INFO: Created user preferences directory.

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

  TempPath Created: /tmp/vcell_temp_add4c6d8-6c2a-43b6-b775-d62430a4d38d7262186325284257352

  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@51fadaff, name=time, getId()=data_gen_time]

  DataGenerator [math=org.jmathml.ASTRootNode@401f7633, name=T, getId()=data_gen_T]

  DataGenerator [math=org.jmathml.ASTRootNode@31ff43be, name=E, getId()=data_gen_E]

  DataGenerator [math=org.jmathml.ASTRootNode@5b6ec132, 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/temp2544981541342653354.xml

  /tmp/out/BIOMD0000000912_sim.sedml

  false

  cbit.vcell.solver.ode.CVodeSolverStandalone@718607eb

  Finished: SOLVER_FINISHED:completed

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

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

  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 (12.2 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://biosimulators.org/conventions/status

Log:

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

  Sep 20, 2021 4:13:07 PM java.util.prefs.FileSystemPreferences$1 run

  INFO: Created user preferences directory.

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

  TempPath Created: /tmp/vcell_temp_e81497d4-306d-4518-a85c-2d6264823e187436129855378684255

  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@51fadaff, name=time, getId()=data_gen_time]

  DataGenerator [math=org.jmathml.ASTRootNode@401f7633, name=T, getId()=data_gen_T]

  DataGenerator [math=org.jmathml.ASTRootNode@31ff43be, name=E, getId()=data_gen_E]

  DataGenerator [math=org.jmathml.ASTRootNode@5b6ec132, 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/temp8342435051738639439.xml

  /tmp/out/BIOMD0000000912_sim.sedml

  false

  cbit.vcell.solver.ode.CVodeSolverStandalone@718607eb

  Finished: SOLVER_FINISHED:completed

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

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

  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 (12.2 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://biosimulators.org/conventions/status

Log:

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

  Sep 20, 2021 4:13:19 PM java.util.prefs.FileSystemPreferences$1 run

  INFO: Created user preferences directory.

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

  TempPath Created: /tmp/vcell_temp_375fd60f-4725-4ad3-af1d-e6c1f739f86b1884206239226050025

  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@51fadaff, name=time, getId()=data_gen_time]

  DataGenerator [math=org.jmathml.ASTRootNode@401f7633, name=T, getId()=data_gen_T]

  DataGenerator [math=org.jmathml.ASTRootNode@31ff43be, name=E, getId()=data_gen_E]

  DataGenerator [math=org.jmathml.ASTRootNode@5b6ec132, 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/temp7746440286395952052.xml

  /tmp/out/BIOMD0000000912_sim.sedml

  false

  cbit.vcell.solver.ode.CVodeSolverStandalone@718607eb

  Finished: SOLVER_FINISHED:completed

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

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

  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 
- 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/1254243083). 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/1254243083).
jonrkarr commented 3 years ago

@moraru @danv61 the 3 failed test cases appear to be due to the same issue, that the data for SED-ML plots is not being exported as expected. Sample results for the Caravagna OMEX file are here. I copied this to virtualcell/vcell#81 as well.

moraru commented 3 years ago

@jonrkarr this appears to be a side effect of fixing warnings generated by the validator about "unexpected reports"

when plot outputs are present reports were being generated with ids corresponding to the plots and dataset ids corresponding to all curve elements, and packaged into the reports zip file; the interpretation of the warning was that they should not be present and were therefore discarded

moraru commented 3 years ago

The message body above was not correctly formatted. url must be a property of image. @moraru this likely needs to be corrected in your submission action.

indeed, cut and paste error missing two spaces for proper indent

moraru commented 3 years ago

@jonrkarr this appears to be a side effect of fixing warnings generated by the validator about "unexpected reports"

when plot outputs are present reports were being generated with ids corresponding to the plots and dataset ids corresponding to all curve elements, and packaged into the reports zip file; the interpretation of the warning was that they should not be present and were therefore discarded

should be fixed in 7.4.0.22