Submit Vcell <IP_ADDRESS>

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

Thank you @bilalshaikh42 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 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 from the "Artifacts" section at the bottom of this page.

The specifications of your simulator is valid!

Failures
docker_image.SingularityImageExecutesSimulationsSuccessfully (15.4 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives
Exception:
Simulator did not produce the following reports:
  - `BIOMD0000000912_sim.sedml/report`

Log:

Summary of tests

Executed 67 test cases

Passed 27 test cases:

cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 1 test cases:

docker_image.SingularityImageExecutesSimulationsSuccessfully

Skipped 39 test cases:

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsComputeModelChanges
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
sedml.SimulatorSupportsDataSetsWithDifferentShapes
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsRepeatedTasksWithChanges
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
sedml.SimulatorSupportsSubstitutingAlgorithms
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

Skips
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (8.9 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

Jun 26, 2021 4:50:53 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_3c56f187-c549-4542-bca5-49172f5ff5853829361190366474369

Python 3.8.5

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

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

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/temp7607655551491558351.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@3b582111

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.8.5

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (9.0 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

Jun 26, 2021 4:51:02 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_4fcc8b36-2730-42ea-86b3-0359809a41b25617481574274673357

Python 3.8.5

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

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

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/temp1941780878381236173.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@3b582111

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.8.5

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (9.0 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

Jun 26, 2021 4:51:11 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_c2557f05-7cde-4b5d-b080-73b0713b5c931818583408644878325

Python 3.8.5

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

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

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/temp1943830452396644509.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@3b582111

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.8.5

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (9.0 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

Jun 26, 2021 4:51:20 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_ec42b21d-bbbb-4dac-a3c3-efb42ba33f253145677122002995130

Python 3.8.5

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

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

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/temp2271638921274137794.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@3b582111

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.8.5

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:

Format: format_3972
Algorithm: KISAO_0000263

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000263

Log:

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000088

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_000019

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000496

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000496

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000029

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000029

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000437

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000437

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log:

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9001
Algorithm: KISAO_0000057

Reason for skip:
Case requires model formats format_9001 and simulation algorithms KISAO_0000057

Log:

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (2.2 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1).
Reason for skip:
The image 'ghcr.io/virtualcell/biosimulators_vcell:<IP_ADDRESS>' could not execute the archive:

  Unknown error

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

Jun 26, 2021 4:47:35 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_3e49b387-1f04-4f36-a444-a4b71301947f730087370459338787

Python 3.8.5

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 2 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

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

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

[Fatal Error] :1:1: Content is not allowed in prolog.

[Fatal Error] :1:1: Content is not allowed in prolog.

java.lang.RuntimeException: Error importing from SBML : no SBML source.

	at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:448)

	at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:685)

	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:66)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:188)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Error importing from SBML : no SBML source.

Unable to initialize bioModel for the given selection

Error importing from SBML : no SBML source.

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (2.3 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1) and inherit the changes of the model.
Reason for skip:
The image 'ghcr.io/virtualcell/biosimulators_vcell:<IP_ADDRESS>' could not execute the archive:

  Unknown error

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

Jun 26, 2021 4:47:37 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_162aaf8f-96f7-44ea-b9be-fa84c2014ce22676641685625808531

Python 3.8.5

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 2 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

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

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

[Fatal Error] :1:1: Content is not allowed in prolog.

[Fatal Error] :1:1: Content is not allowed in prolog.

java.lang.RuntimeException: Error importing from SBML : no SBML source.

	at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:448)

	at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:685)

	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:66)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:188)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Error importing from SBML : no SBML source.

Unable to initialize bioModel for the given selection

Error importing from SBML : no SBML source.

sedml.SimulatorProducesLinear3DPlots (0.3 s)
Test that a simulator produces linear 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

sedml.SimulatorProducesLogarithmic3DPlots (0.3 s)
Test that a simulator produces logarithmic 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (9.0 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements.
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

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

Jun 26, 2021 4:48:22 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_45540835-66e2-473a-8c3c-ddf04290bd107068241410577596594

Python 3.8.5

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

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

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/temp5687899185194980055.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@3c49fab6

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.8.5

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsComputeModelChanges (9.7 s)
Test that a simulator supports compute model changes
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

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

Jun 26, 2021 4:48:40 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_c678b180-ecb5-44c7-b9e6-2bafd69002fc7900294732734508723

Python 3.8.5

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

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

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/temp5717491415868941784.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@69eb86b4

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.8.5

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (11.4 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpp0tlrwgk/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

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

Jun 26, 2021 4:48:49 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_289524b8-8be1-46c5-b711-bd17fe009ec96630851897069070608

Python 3.8.5

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), 2 simulation(s), 2 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

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/temp6377262230628971370.xml

Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@88a8218

Finished: SOLVER_FINISHED:completed

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

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

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@7e053511

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.

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

Generating report `report__copy_2`.

Python 3.8.5

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 372, in <module>

    fire.Fire({

  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire

    component, remaining_args = _CallAndUpdateTrace(

  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 176, in exec_sed_doc

    data_set_results[data_set.id] = data_set_df.loc[data_set.label, :].to_numpy(

  File "/usr/local/lib/python3.8/dist-packages/pandas/core/base.py", line 610, in to_numpy

    result = np.asarray(self._values, dtype=dtype)

ValueError: could not convert string to float: 'NaN.1'

HDF conversion failed

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsDataSetsWithDifferentShapes (11.4 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpedzm8l78/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

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

Jun 26, 2021 4:49:01 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_51c9b073-3481-4598-a220-a58beb83915b3627906822137638430

Python 3.8.5

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), 2 simulation(s), 2 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

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/temp513793542558270097.xml

Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@515f4131

Finished: SOLVER_FINISHED:completed

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

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

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@2472c7d8

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.

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

Generating report `report`.

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 372, in <module>

    fire.Fire({

  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire

    component, remaining_args = _CallAndUpdateTrace(

  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 329, in gen_plot_pdfs

    report_frames = get_report_dataframes(all_report_dataref, result_out_dir)

  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 298, in get_report_dataframes

    report_frames[report] = pd.read_csv(os.path.join(

  File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 610, in read_csv

    return _read(filepath_or_buffer, kwds)

  File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 468, in _read

    return parser.read(nrows)

  File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 1057, in read

    index, columns, col_dict = self._engine.read(nrows)

  File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 2036, in read

    data = self._reader.read(nrows)

  File "pandas/_libs/parsers.pyx", line 756, in pandas._libs.parsers.TextReader.read

  File "pandas/_libs/parsers.pyx", line 771, in pandas._libs.parsers.TextReader._read_low_memory

  File "pandas/_libs/parsers.pyx", line 827, in pandas._libs.parsers.TextReader._read_rows

  File "pandas/_libs/parsers.pyx", line 814, in pandas._libs.parsers.TextReader._tokenize_rows

  File "pandas/_libs/parsers.pyx", line 1951, in pandas._libs.parsers.raise_parser_error

pandas.errors.ParserError: Error tokenizing data. C error: Expected 12 fields in line 5, saw 22

Python 3.8.5

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 372, in <module>

    fire.Fire({

  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire

    component, remaining_args = _CallAndUpdateTrace(

  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 156, in exec_sed_doc

    data_set_df = pd.read_csv(report_filename).transpose()

  File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 610, in read_csv

    return _read(filepath_or_buffer, kwds)

  File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 468, in _read

    return parser.read(nrows)

  File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 1057, in read

    index, columns, col_dict = self._engine.read(nrows)

  File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers.py", line 2036, in read

    data = self._reader.read(nrows)

  File "pandas/_libs/parsers.pyx", line 756, in pandas._libs.parsers.TextReader.read

  File "pandas/_libs/parsers.pyx", line 771, in pandas._libs.parsers.TextReader._read_low_memory

  File "pandas/_libs/parsers.pyx", line 827, in pandas._libs.parsers.TextReader._read_rows

  File "pandas/_libs/parsers.pyx", line 814, in pandas._libs.parsers.TextReader._tokenize_rows

  File "pandas/_libs/parsers.pyx", line 1951, in pandas._libs.parsers.raise_parser_error

pandas.errors.ParserError: Error tokenizing data. C error: Expected 12 fields in line 5, saw 22

HDF conversion failed

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsModelAttributeChanges (10.0 s)
Test that a simulator supports changes to the attributes of model elements
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

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

Jun 26, 2021 4:49:12 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_b7b6c4ae-9b83-4171-983f-a73f74ec89d14323637279034387868

Python 3.8.5

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

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

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/temp1318398154505745115.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@f9b5552

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.8.5

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsRepeatedTasksWithChanges (4.2 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp3c52v61r/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

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

Jun 26, 2021 4:49:52 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_adb42c4b-ac6f-4ba2-bc6f-b00ee0c8829a4820965407873390501

Python 3.8.5

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

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_adb42c4b-ac6f-4ba2-bc6f-b00ee0c8829a4820965407873390501/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

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

Jun 26, 2021 4:49:54 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_17199969-8386-4c00-8f6c-2d7f5ef626406297133664266569057

Python 3.8.5

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

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_17199969-8386-4c00-8f6c-2d7f5ef626406297133664266569057/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (4.2 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpkfdlbaad/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

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

Jun 26, 2021 4:49:56 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_084b4054-10fa-4d8a-b648-6d14f480c6056063360917302670601

Python 3.8.5

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

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_084b4054-10fa-4d8a-b648-6d14f480c6056063360917302670601/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

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

Jun 26, 2021 4:49:58 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_e1f90cdb-1f11-45cb-9edc-d98f204c37727123263085572247947

Python 3.8.5

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

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_e1f90cdb-1f11-45cb-9edc-d98f204c37727123263085572247947/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (2.0 s)
Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp2_499gbs/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

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

Jun 26, 2021 4:50:00 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_6562cb02-6efe-4339-9de1-6cc530b4a7462309194450202056623

Python 3.8.5

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

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_6562cb02-6efe-4339-9de1-6cc530b4a7462309194450202056623/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (2.0 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpqit5yr_z/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

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

Jun 26, 2021 4:50:02 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_02f60652-a5a4-4621-8a62-6d98bb3be6d82162640908496496450

Python 3.8.5

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

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_02f60652-a5a4-4621-8a62-6d98bb3be6d82162640908496496450/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (2.1 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpdbee3mlo/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

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

Jun 26, 2021 4:50:04 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_846d15b5-c87c-4c3e-87a2-0e4aca333c711637777780172213934

Python 3.8.5

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

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_846d15b5-c87c-4c3e-87a2-0e4aca333c711637777780172213934/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (2.0 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpa6hgxtr_/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

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

Jun 26, 2021 4:50:07 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_7a2f92fc-616c-4bc3-9016-c8359d3872ef513277914077260442

Python 3.8.5

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

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_7a2f92fc-616c-4bc3-9016-c8359d3872ef513277914077260442/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (2.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp28upjqqa/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

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

Jun 26, 2021 4:50:09 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_edf967da-6abb-41dc-af70-b3febcb975a83506480011498383763

Python 3.8.5

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

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.read ...

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (1.2 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'

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.HasBioContainersLabels (0.2 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 (11.1 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Warnings:
Unexpected reports were produced:
  BIOMD0000000912_sim.sedml/Figure_1

Plots were not produced:
  BIOMD0000000912_sim.sedml/plot_1

Extra plots were produced:
  BIOMD0000000912_sim.sedml/Figure_1

Log:
VCell CLI input archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex

Jun 26, 2021 4:51:29 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_aca1853e-ade3-430b-bbe9-29ed1cc1275a1506688950526671559

Python 3.8.5

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),  1 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

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/temp1272236983774958035.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@3c49fab6

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations__BIOMD0000000912' Task 'Caravagna2010'.

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

Ignoring unsupported output `Figure_1` while CSV generation.

Generating report `report`.

Python 3.8.5

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (21.6 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000086

Warnings:
Unexpected reports were produced:
  simulation_1.sedml/Figure_3a
  simulation_1.sedml/Figure_3b
  simulation_1.sedml/Figure_3c
  simulation_1.sedml/Figure_3d

Plots were not produced:
  simulation.sedml/Figure_3a
  simulation.sedml/Figure_3b
  simulation.sedml/Figure_3c
  simulation.sedml/Figure_3d

Extra plots were produced:
  simulation_1.sedml/Figure_3a
  simulation_1.sedml/Figure_3b
  simulation_1.sedml/Figure_3c
  simulation_1.sedml/Figure_3d

Log:
VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex

Jun 26, 2021 4:51:40 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_5f1978f1-3dfc-418c-af4a-207799f261493609633731246530108

Python 3.8.5

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),  4 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file simulation_1.sedml

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

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='task_1') is compatible, solver match found in ontology: 'KISAO:0000086' matched to RungeKuttaFehlberg

Succesful model import: SBML file /tmp/temp4696677445158657060.xml

final tolerance=0.1 final threshold=0.060000000000000005, 552 remaining (keepAtMost=1000)

Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg__Ciliberto2003_Morphogenesis' Task 'simulation 1'.

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

Ignoring unsupported output `Figure_3a` while CSV generation.

Ignoring unsupported output `Figure_3b` while CSV generation.

Ignoring unsupported output `Figure_3c` while CSV generation.

Ignoring unsupported output `Figure_3d` while CSV generation.

Generating report `report`.

Python 3.8.5

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (20.7 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Warnings:
Unexpected reports were produced:
  simulation_1.sedml/Figure_3a
  simulation_1.sedml/Figure_3b
  simulation_1.sedml/Figure_3c
  simulation_1.sedml/Figure_3d

Plots were not produced:
  simulation.sedml/Figure_3a
  simulation.sedml/Figure_3b
  simulation.sedml/Figure_3c
  simulation.sedml/Figure_3d

Extra plots were produced:
  simulation_1.sedml/Figure_3a
  simulation_1.sedml/Figure_3b
  simulation_1.sedml/Figure_3c
  simulation_1.sedml/Figure_3d

Log:
VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex

Jun 26, 2021 4:52:02 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_712491e0-9998-4e87-ba84-1f3f17ac445f907986252888324718

Python 3.8.5

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),  4 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file simulation_1.sedml

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

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='task_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp8374274963090180960.xml

/tmp/out/simulation_1.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@2582b0ef

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous__Ciliberto2003_Morphogenesis' Task 'simulation 1'.

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

Ignoring unsupported output `Figure_3a` while CSV generation.

Ignoring unsupported output `Figure_3b` while CSV generation.

Ignoring unsupported output `Figure_3c` while CSV generation.

Ignoring unsupported output `Figure_3d` while CSV generation.

Generating report `report`.

Python 3.8.5

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (49.3 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000027
Format: format_2585
Algorithm: KISAO_0000030

Warnings:
Unexpected reports were produced:
  simulation.sedml/plot2d_Euler_default
  simulation.sedml/plot2d_Euler_small_step_size
  simulation.sedml/plot2d_Fig_1_c
  simulation.sedml/plot2d_Fig_1a
  simulation.sedml/plot2d_low_delta_R_det
  simulation.sedml/plot2d_low_delta_R_stoch

Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex

Jun 26, 2021 4:53:17 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_24976273-9e32-46ee-9a1f-8012154fabe62053051095462905595

Python 3.8.5

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 4 model(s), 6 simulation(s), 6 task(s), 6  report(s),  6 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file simulation.sedml

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

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='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp2748512280880942615.xml

Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp3714335919994003331.xml

Task (id='tsk_0_2') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler

Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler

Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson

Succesful model import: SBML file /tmp/temp7120643092569007271.xml

Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson

Succesful model import: SBML file /tmp/temp738592591054751742.xml

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@67332b1e

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_0'.

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

Solver status: 3

Solver message: simulation failed at time=1.3: consider using smaller default or max time step.

values are:

A = NaN

C = Infinity

PrmA = Infinity

PrmA_bound = -Infinity

PrmR = Infinity

PrmR_bound = -Infinity

R = -Infinity

Failed execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_2'.

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

final tolerance=0.1 final threshold=0.09, 885 remaining (keepAtMost=1000)

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_3'.

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

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@fd413fb

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic_0' Task 'tsk_0_1'.

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

cbit.vcell.solver.stoch.GibsonSolver@30bf26df

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_stochastic' Task 'tsk_1_0'.

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

cbit.vcell.solver.stoch.GibsonSolver@7f4596d0

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_stochastic_0' Task 'tsk_1_1'.

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

Ignoring unsupported output `plot2d_Fig_1a` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation.

Ignoring unsupported output `plot2d_Euler_default` while CSV generation.

Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation.

Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation.

Generating report `report_Fig_1a`.

Generating report `report_low_delta_R_det`.

Generating report `report_Euler_default`.

Generating report `report_Euler_small_step_size`.

Generating report `report_Fig_1_c`.

Generating report `report_low_delta_R_stoch`.

Python 3.8.5

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (34.3 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000030

Warnings:
Unexpected reports were produced:
  simulation.sedml/Figure_2ab
  simulation.sedml/plot2d_Euler_default
  simulation.sedml/plot2d_Euler_small_step_size
  simulation.sedml/plot2d_Fig_1a
  simulation.sedml/plot2d_low_delta_R_det

Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex

Jun 26, 2021 4:52:23 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_3a34d340-f9d0-4ca3-87fc-82e1035715477810163258391702759

Python 3.8.5

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 2 model(s), 4 simulation(s), 4 task(s), 4  report(s),  5 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file simulation.sedml

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

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='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp3002592570872166023.xml

Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp6705495048546217714.xml

Task (id='tsk_0_2') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler

Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@53ce2392

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic' Task 'tsk_0_0'.

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

Solver status: 3

Solver message: simulation failed at time=1.3: consider using smaller default or max time step.

values are:

A = NaN

C = Infinity

PrmA = Infinity

PrmA_bound = -Infinity

PrmR = Infinity

PrmR_bound = -Infinity

R = -Infinity

Failed execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic' Task 'tsk_0_2'.

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

final tolerance=0.1 final threshold=0.09, 885 remaining (keepAtMost=1000)

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic' Task 'tsk_0_3'.

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

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@d4df0e

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic_0' Task 'tsk_0_1'.

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

Ignoring unsupported output `Figure_2ab` while CSV generation.

Ignoring unsupported output `plot2d_Fig_1a` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation.

Ignoring unsupported output `plot2d_Euler_default` while CSV generation.

Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation.

Generating report `report_Fig_1a`.

Generating report `report_low_delta_R_det`.

Generating report `report_Euler_default`.

Generating report `report_Euler_small_step_size`.

Python 3.8.5

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (20.2 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000027

Warnings:
Unexpected reports were produced:
  simulation.sedml/plot2d_Fig_1_c
  simulation.sedml/plot2d_low_delta_R_stoch

Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex

Jun 26, 2021 4:52:57 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_453605da-9a9f-43f1-abea-7608b566358b2433895261978193595

Python 3.8.5

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 2 model(s), 2 simulation(s), 2 task(s), 2  report(s),  2 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file simulation.sedml

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

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='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson

Succesful model import: SBML file /tmp/temp4120759162150131376.xml

Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson

Succesful model import: SBML file /tmp/temp6490845679918022361.xml

cbit.vcell.solver.stoch.GibsonSolver@646811d6

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM__ODE_stochastic' Task 'tsk_1_0'.

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

cbit.vcell.solver.stoch.GibsonSolver@4ba89729

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM__ODE_stochastic_0' Task 'tsk_1_1'.

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

Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation.

Generating report `report_Fig_1_c`.

Generating report `report_low_delta_R_stoch`.

Python 3.8.5

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

- 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 [here](https://github.com/biosimulators/Biosimulators/actions/runs/974521714). 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/974521714).


Metadata parsing support for pip components.

Codecov Report
Attention: 81 lines in your changes are missing coverage. Please review.

Comparison is base (848944d) 59.81% compared to head (f7e0ae1) 59.67%.

Files
Patch %
Lines

.../PackageDetails/ComponentDetailsUtils/PypiUtils.cs
59.11%
54 Missing and 11 partials :warning:

...t.Sbom.Api/PackageDetails/PackageDetailsFactory.cs
0.00%
16 Missing :warning:

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #461      +/-   ##
==========================================
- Coverage   59.81%   59.67%   -0.14%
==========================================
  Files         248      249       +1
  Lines        7560     7733     +173
  Branches      901      931      +30
==========================================
+ Hits         4522     4615      +93
- Misses       2626     2695      +69
- Partials      412      423      +11

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.


Tabular: Added unit tests for models

Issue #, if available:
Description of changes:

Added unit tests for models
FastAI NN unit tests are disabled at present since required dependencies are not installed during test runs on CI.

By submitting this pull request, I confirm that you can use, modify, copy, and redistribute this contribution, under the terms of your choice.

Job PR-764-1 is done.
Docs are uploaded to http://autogluon-staging.s3-website-us-west-2.amazonaws.com/PR-764/1/index.html

Not sure if it's worthwhile, but we could also test individual models' HPO & bagging capabilities.

Job PR-764-3 is done.
Docs are uploaded to http://autogluon-staging.s3-website-us-west-2.amazonaws.com/PR-764/3/index.html

Not sure if it's worthwhile, but we could also test individual models' HPO & bagging capabilities.

I think this is reasonable, but we need to be careful about the time testing all of these things requires.


[Tooltip] Fix broken arrow position in rtl

Fixes https://github.com/mui-org/material-ui/issues/27858 The fix was to prevent some styles from flipping in rtl. As /* @noflip */ is working only with string templates, I've added the isRtl prop and added the appropriate styles based on it.
Isolated codesandbox examples
Codesandbox in RTL on master:
https://codesandbox.io/s/material-demo-forked-qh2ds?file=/demo.js

Codesandbox in RTL on next:
https://codesandbox.io/s/basictooltip-material-demo-forked-5gc67?file=/demo.js

Codesandbox using the packages in the PR:
https://codesandbox.io/s/basictooltip-material-demo-forked-44bhg?file=/demo.js

-----
Docs demos:
Next docs 😢 :

Current PR docs:

Looks great. I guess the change of behavior between v4 and v5 is linked to the flip option that we do no longer have available

ah I didn’t noticed it, but yes, looks like it comes from it. We missed to catch it during the migration.

I guess we need to go through every component that had this or rather check every usage of flip: false from master against the behavior of next.

Yes will do this today


remove hidden posts from /posts

Fix for #2623

Another tip: If you include Fix #2623 in your PR description, you can "link" this PR to that issue, and when it's merged, the linked issue can be closed automatically by GitHub.
See GitHub documentation on linked PRs.


Many of you are asking about the following:

Images/Attributed Strings in Tables
Swift 4.0 Support
more...

I am working a lot on the upcoming release of 1.0.0 where all these questions are answered.
Please stay with me, but keep it in mind!
I will put this in this issue so I can reference to it.

@techprimate-phil any approx ETA?

@marbetschar Preparing it right now, going to release now, as all elements are now working properly. More test cases and pixel testing will be necessary afterwards

Just released version 1.0.0


fix gcp with perfix

Problem description:
Yor already handles fixing of certain label values based on the GCP constraints. Like '/' gets converted to '__' for git_file label value. But if yor argument tag-prefix is specified, this handling does not work.
Solution description:
Checking whether there is a prefix in the tags and appropriate treatment
fixes:https://github.com/bridgecrewio/yor/issues/444

Looks good!
Please look at the lint issues to see if they relate to you.


Autocomplete in a modal

Hello everyone,
I'm posting because i notice something when you want to create an autocompletion for an input text in a modal.
The autocompletion window which shows us the suggestions is display behind the input.
The way i use to get around this is to change the .autocomplete-content property margin-top : -15px to 0.
Thanks !

Can you provide a way to reproduce it?
Thanks
Closed due inactivity, feel free to reopen it if it is still necessary.


New release

Hey @mcg1969
I have deployed internally and use successfully #172 for 10 days. So I was wondering if you could do a release including it?

Note: regarding your previous attempt to switch to noarch and #177, a solution to set the default kernelspec manager maybe Automatic installation
I did not try it for other option than the activation of a server extension - so I am not sure it will be usable here.

Agreed, will get this done

Thanks @mcg1969

2.3.0 is tagged


Feature/wpds 978 add avatar component

What I did

Avatar will be added in the feature/WPDS-978-create-avatar-component branch


Plumb contexts into health checks

Related to #4110

See individual commit messages for details.

This needs a rebase @corhere


Add basic Travis integration

Travis CI proudly uses Slackin at https://chat.travis-ci.com/ , fwiw :smiley_cat:
For full effect, this will also require the equivalent of:
gem install travis
travis enable -r rauchg/slackin

@meatballhat “Not a permitted channel.”
Probably because channel-specific sign-ups have a maximum of five users. :)

:+1:


mqsicreatebar not found

I sourced mqsiprofile.
For packaging BARs there's only mqsipackagebar, the mqsicreatebar is not found.
I'm new to IIB and this image, am I missing something?
I tried both base and mq-client images.
The command I used to start container:
docker run --rm -it -e IIB_LICENSE=accept --entrypoint bash dennisseidel/iib-bestpractice-runtimes:<IP_ADDRESS>-mqclient

@tsutsarin-fuib Hi image does currently not support the mounting of code and the create of the bar file inside the container.
What you can do is the following steps:

Build the bar file external
Create a dockerfile that inherits from dennisseidel/iib-bestpractice-runtimes:<IP_ADDRESS>-mqclient and that copies your barflies into the image COPY workspace/BARfiles/app.bar /iibProjects/ in the how to section described

Thanks!
What if I make PR that includes Dockerfile with IBM Integration Toolkit for building bars inside the container?

@tsutsarin-fuib Then we can merge it into the repo, and I think I / many people would be very thankful :-)
I planned on have such an image anyway not for running in in production, but for the build step in the DevOps Pipeline. So that would be great.

Can be reopend if problem is still relevant.


PMD-IDEA v1.9.0 is not compatible with IntelliJ IDEA 2022.3

Tested on Windows with Build #IU-223.7571.182, built on November 29, 2022
IntelliJ IDEA refuses to load the plugin:

Plugin 'PMD-IDEA' (version '1.9.0') is not compatible with the current version of the IDE, because it requires build 222.* or older but the current build is IU-223.7571.182

Same for IntelliJ 2023.1. Is this a simple version bump in the manifest (but #31 has gotten test failures when it attempted that), or is more work required? Do you still plan to support this useful plugin, or is it effectively dead?


Make "Definition" field non mandatory for NHS Business Definitions, Supporting Information and XML Schema Constraints Pages

Currently when a NHS Business Definition, Supporting Information or XML Schema Constraints Page is created we have to add Code (the name of the NHS Business Definition) and Definition (the same as the name).
Can "Definition" be set as non mandatory?

@pjmonks - this still isn't working. It is still wanting a definition. See #472 and #473


Pig Latin transform

This transformation translates the original text into pig latin. Resulting sentences retain the same meaning as the original sentences, and are modified only on the word level. While the resulting sentences can still be interpreted by an English-speaking human annotator with some effort, the transformation yields sentences which are completely different on the word level from the original sentence.
@vinayprabhu @rteehas @jjangsangy

Thank you for the comments! I've fetched the current upstream commits and included your suggestion for using a translation probability. Accordingly, the transformation now meaningfully uses max_outputs.

Thanks for the additions, looks good to me!

Thanks @csinva! I've also added evaluation results to the readme. Using the same evaluation procedure as shown in the leaderboard, text classification models are substantially less robust to the PigLatin transform than all of the leading transformations for evaluating robustness.

Transformation
roberta-base-SST-2
bert-base-uncased-QQP
roberta-large-mnli
roberta-base-imdb

PigLatin
94.0->60.0 (-34.0)
92.0->68.0 (-24.0)
91.0->50.0 (-41.0)
95.0->32.0 (-63.0)

BackTranslation
94.0->91.0 (-3.0)
92.0->90.0 (-2.0)
91.0->87.0 (-4.0)
95.0->92.0 (-3.0)

ButterFingersPerturbation
94.0->89.0 (-5.0)
92.0->89.0 (-3.0)
91.0->88.0 (-3.0)
95.0->93.0 (-2.0)

ChangePersonNamedEntities
94.0->94.0 (0.0)
92.0->92.0 (0.0)
91.0->89.0 (-2.0)
95.0->95.0 (0.0)

CloseHomophonesSwap
94.0->91.0 (-3.0)
92.0->88.0 (-4.0)
91.0->89.0 (-2.0)
95.0->96.0 (1.0)

DiscourseMarkerSubstitution
94.0->94.0 (0.0)
92.0->92.0 (0.0)
91.0->91.0 (0.0)
95.0->95.0 (0.0)

MixedLanguagePerturbation
94.0->90.0 (-4.0)
92.0->86.0 (-6.0)
91.0->86.0 (-5.0)
95.0->91.0 (-4.0)

PunctuationWithRules
94.0->94.0 (0.0)
92.0->92.0 (0.0)
91.0->91.0 (0.0)
95.0->90.0 (-5.0)

ReplaceNumericalValues
94.0->94.0 (0.0)
92.0->92.0 (0.0)
91.0->90.0 (-1.0)
95.0->95.0 (0.0)

SentenceReordering
94.0->95.0 (1.0)
92.0->93.0 (1.0)
nan
95.0->94.0 (-1.0)

Thank you very much for the changes! This PR looks great and is a very important addition to NL-Augmenter. Also thanks to @csinva and @afnanmmir for the reviews! I am merging this now. @nick11roberts, please create a separate PR to add the keywords for your PR - I will merge it directly!

Thank you very much for the changes! This PR looks great and is a very important addition to NL-Augmenter. Also thanks to @csinva and @afnanmmir for the reviews! I am merging this now. @nick11roberts, please create a separate PR to add the keywords for your PR - I will merge it directly!

Thank you @kaustubhdhole, and my apologies for the delay on the keywords! Please see https://github.com/GEM-benchmark/NL-Augmenter/pull/299 for the newly added keywords.


Feat/app navigation

This pull request closes #56
Video Demo of Navigating:
https://github.com/Jrod7938/TxTchangeApp/assets/46418742/3279af14-9b8f-40f0-97d5-dfe933846a41

This is good. I just think it's missing some top and bottom padding. Is there a way to do this?

Okay one more thing, can you move the logo and the text further to the left to match the other side?

padding values and app bar prevent alignment to the left