Submit Neuron 8.0.0

id: neuron
version: 8.0.0
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_pyNeuroML/f5ea344d28c171a1a00918cac841a995e3fc5f68/biosimulators-neuron.json
specificationsPatch:
version: 8.0.0
image:
url: ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0
validateImage: true
commitSimulator: true

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

The specifications of your simulator is valid!

Summary of tests

Executed 72 test cases

Passed 30 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
docker_image.SingularityImageExecutesSimulationsSuccessfully
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
sedml.SimulatorSupportsDataSetsWithDifferentShapes
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 0 test cases

Skipped 42 test cases:

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
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/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
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
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
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:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsComputeModelChanges
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

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (4.2 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'
  - 'BUNDLE_OUTPUTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.DeclaresSupportedEnvironmentVariables (1.9 s)
Test if a Docker image declares the environment variables that is supports
Warnings:
Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'
  - 'BUNDLE_OUTPUTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.HasBioContainersLabels (0.6 s)
Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
The Docker image should have the following BioContainers labels:
  extra.identifiers.biotools

Log:

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (13.8 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Warnings:
Unexpected reports were produced:
  simulation.sedml/plot

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

    Plots (1):

      plot: 4 curves

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Tasks (1):

    Succeeded: 1

    Skipped: 0

    Failed: 0

  Outputs (2):

    Succeeded: 2

    Skipped: 0

    Failed: 0

Skips
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3972
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/Elowitz-Nature-2000-Repressilator (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: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:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 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/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000086

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000086

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

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/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

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 (0.0 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

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027, KISAO_0000030

Log:

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

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

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000030

Log:

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

Format: format_2585
Algorithm: KISAO_0000027

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000027

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:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
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:

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log:

sedml.SimulatorProducesLinear3DPlots (0.8 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 (1.0 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 (0.8 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements.
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log:

sedml.SimulatorSupportsAlgorithmParameters (0.8 s)
Test that a simulator supports setting the values of parameters of algorithms
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

sedml.SimulatorSupportsComputeModelChanges (0.9 s)
Test that a simulator supports compute model changes
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log:

sedml.SimulatorSupportsModelAttributeChanges (0.8 s)
Test that a simulator supports changes to the attributes of model elements
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log:

sedml.SimulatorSupportsRepeatedTasksWithChanges (1.0 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log:

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.7 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
'cython_function_or_method' object has no attribute 'rpartition'

Log:

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (9.7 s)
Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

  - The SED-ML file at location `simulation.sedml` may be invalid.

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `pyNeuroML` was not able to execute `/tmp/tmpgp5j57qq.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5743M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmphoy9u_gc.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmphoy9u_gc.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmprc_epljx, /tmp, /tmp, /tmp/tmprc_epljx]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:42  (INFO) Loading LEMS file from: /tmp/tmphoy9u_gc.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:42  (INFO) Reading from: /tmp/tmphoy9u_gc.xml

      pyNeuroML >>>  jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (10.1 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

  - The SED-ML file at location `simulation.sedml` may be invalid.

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `pyNeuroML` was not able to execute `/tmp/tmpjacilata.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5742M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmplsc1xxfu.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmplsc1xxfu.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpx2ota6yf, /tmp, /tmp, /tmp/tmpx2ota6yf]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:43  (INFO) Loading LEMS file from: /tmp/tmplsc1xxfu.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:43  (INFO) Reading from: /tmp/tmplsc1xxfu.xml

      pyNeuroML >>>  jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (10.1 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

  - The SED-ML file at location `simulation.sedml` may be invalid.

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `pyNeuroML` was not able to execute `/tmp/tmpi2ka882d.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5744M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmphsfflqk8.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmphsfflqk8.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmph3trb_u8, /tmp, /tmp, /tmp/tmph3trb_u8]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:43  (INFO) Loading LEMS file from: /tmp/tmphsfflqk8.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:43  (INFO) Reading from: /tmp/tmphsfflqk8.xml

      pyNeuroML >>>  jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (10.2 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

  - The SED-ML file at location `simulation.sedml` may be invalid.

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `pyNeuroML` was not able to execute `/tmp/tmpvexp5idb.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5742M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp335afa23.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp335afa23.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpiczjpgko, /tmp, /tmp, /tmp/tmpiczjpgko]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:43  (INFO) Loading LEMS file from: /tmp/tmp335afa23.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:43  (INFO) Reading from: /tmp/tmp335afa23.xml

      pyNeuroML >>>  jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (9.8 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

  - The SED-ML file at location `simulation.sedml` may be invalid.

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `pyNeuroML` was not able to execute `/tmp/tmpcs0b9798.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5740M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpa5yt57fb.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpa5yt57fb.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmp4dd4mvy8, /tmp, /tmp, /tmp/tmp4dd4mvy8]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:43  (INFO) Loading LEMS file from: /tmp/tmpa5yt57fb.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:43  (INFO) Reading from: /tmp/tmpa5yt57fb.xml

      pyNeuroML >>>  jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (10.6 s)
Test that a simulator supports nested repeated tasks
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

  - The SED-ML file at location `simulation.sedml` may be invalid.

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (3):

      __repeated_task_0

      __repeated_task_1

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (3):

    Succeeded: 1

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `pyNeuroML` was not able to execute `/tmp/tmp8zzehbcu.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5739M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp_qyjq1gz.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp_qyjq1gz.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmp661nyqq5, /tmp, /tmp, /tmp/tmp661nyqq5]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:43  (INFO) Loading LEMS file from: /tmp/tmp_qyjq1gz.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:43  (INFO) Reading from: /tmp/tmp_qyjq1gz.xml

      pyNeuroML >>>  jNeuroML >>

    `pyNeuroML` was not able to execute `/tmp/tmp23n9sz2t.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5740M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpimjaz9ef.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpimjaz9ef.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmp5itly_2l, /tmp, /tmp, /tmp/tmp5itly_2l]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:43  (INFO) Loading LEMS file from: /tmp/tmpimjaz9ef.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:43  (INFO) Reading from: /tmp/tmpimjaz9ef.xml

      pyNeuroML >>>  jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (10.8 s)
Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their order attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes.
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Task `__repeated_task_1` may be invalid.

    - The outputs of the sub-tasks have different shapes.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

  - The SED-ML file at location `simulation.sedml` may be invalid.

    - Task `__repeated_task_1` may be invalid.

      - The outputs of the sub-tasks have different shapes.

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (3):

      __repeated_task_0

      __repeated_task_1

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (3):

    Succeeded: 1

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `pyNeuroML` was not able to execute `/tmp/tmp_9cflv9w.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5736M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpynytkip0.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpynytkip0.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmptuf4m8k0, /tmp, /tmp, /tmp/tmptuf4m8k0]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:43  (INFO) Loading LEMS file from: /tmp/tmpynytkip0.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:43  (INFO) Reading from: /tmp/tmpynytkip0.xml

      pyNeuroML >>>  jNeuroML >>

    `pyNeuroML` was not able to execute `/tmp/tmpk4h6hsse.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5736M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpz31860_m.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpz31860_m.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpx43jsmti, /tmp, /tmp, /tmp/tmpx43jsmti]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:43  (INFO) Loading LEMS file from: /tmp/tmpz31860_m.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:43  (INFO) Reading from: /tmp/tmpz31860_m.xml

      pyNeuroML >>>  jNeuroML >>

sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (9.9 s)
Test that a simulator supports repeated tasks over vector ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The SED document is potentially incorrect.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: The COMBINE/OMEX archive may be invalid.

  - The SED-ML file at location `simulation.sedml` may be invalid.

    - Output `__repeated_task_report` may be invalid.

      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.

  warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 1

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    `pyNeuroML` was not able to execute `/tmp/tmp9l688rhq.xml`:

      pyNeuroML >>> *** Problem running command:

      pyNeuroML >>>        Command 'java -Xmx5737M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpfdnljg8a.xml"  -nogui -I ''' returned non-zero exit status 1.

      pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

      pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpfdnljg8a.xml with jLEMS, NO GUI mode...

      pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

      pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmp0row1f62, /tmp, /tmp, /tmp/tmp0row1f62]

      pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

      pyNeuroML >>>  jNeuroML >>

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

      pyNeuroML >>>  jNeuroML >>  	at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

      pyNeuroML >>>  jNeuroML >>  	at org.neuroml.JNeuroML.main(JNeuroML.java:595)

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:44  (INFO) Loading LEMS file from: /tmp/tmpfdnljg8a.xml

      pyNeuroML >>>  jNeuroML >>  INFO Aug 21,2021 19:44  (INFO) Reading from: /tmp/tmpfdnljg8a.xml

      pyNeuroML >>>  jNeuroML >>

sedml.SimulatorSupportsSubstitutingAlgorithms (30.5 s)
Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:AlgorithmSubstitutionPolicy.SAME_METHOD. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:AlgorithmSubstitutionPolicy.NONE.
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

  Unknown error

Log:
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    No algorithm can be substituted for 'LSODA' (KISAO_0000088) at substitution policy 'NONE'. Algorithms can only be substituted for the following algorithms:

      KISAO_0000019: CV ...

The image for your simulator is valid!

Your submission was committed to the BioSimulators registry. Thank you!
Future submissions of subsequent versions of neuron to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.


Fixes documentation message for EnforcedShorthandSyntax: consistent

EnforcedShorthandSyntax: consistent behave more like either than always
Why is it not like always:

consistent allows regular and shorthand hash syntax, but not mixed
always     allows only the shorthand syntax

=> consistent does not behave like `always
Why is like either:

consistent allows regular and shorthand hash syntax, but not mixed
either     allows regular and shorthand hash syntax.

=> consistent is similar to either but does not allow mixing syntax.
Replace this text with a summary of the changes in your PR.
The more detailed you are, the better.

Before submitting the PR make sure the following are checked:

[x] The PR relates to only one subject with a clear title and description in grammatically correct, complete sentences.
[x] Wrote good commit messages.
[x] Commit message starts with [Fix #issue-number] (if the related issue exists).
[x] Feature branch is up-to-date with master (if not - rebase it).
[x] Squashed related commits together.
[ ] Added tests.
[ ] Ran bundle exec rake default. It executes all tests and runs RuboCop on its own code.
[ ] Added an entry (file) to the changelog folder named {change_type}_{change_description}.md if the new code introduces user-observable changes. See changelog entry format for details.

This update looks good. Can you update the config/default.yml as well?
https://github.com/rubocop/rubocop/blob/aa65208d54944334f18f8e7c955c276ebe634dd9/config/default.yml#L3860

@lucianghinda I triggered the re-run to the failing test because it's a flaky test. This should solve it. Thank you!


Update nimcuda.nimble

I am working on removing old deprecated stuff from Nim, like pre- 1.0 or so,
your package is on important packages list and still uses Deprecated ospaths.
:)

Thank you


Change event prop callbacks

https://github.com/pinterest/gestalt/issues/354

Deploy preview for gestalt ready!
Built with commit f2830157a78ddf2063d29506cb164735fa8f4eae
https://deploy-preview-359--gestalt.netlify.com


Gradients with Token-Referenced Variables Do Not Update Correctly When Applying Theme with “Resolved Values

Describe the bug
When using variables connected to tokens inside gradients, they do not update correctly when applying a theme from the plugin using “Resolved values.” Regular color fills work fine, but gradients fail to update as expected.
To Reproduce

Create a gradient token with referring base color tokens
now create styles and variables with the Create styles with variable references option.
now apply the gradient token on any frame
change the applied current tokens as to resolved values, no variables or styles in the plugin and click on the apply to selection button.
Now click on the fill-in Figma and see the error

Expected behavior
selecting the resolved values, no variables or styles, shouldn't apply any variables or styles to the elements.
Screenshots or Screencasts
https://github.com/user-attachments/assets/87dd1000-dab6-4b48-9696-92f456f9074d

This is causing problems when swapping themes for big selections as we need to go individually and fix the issue for every element using a gradient.

Still reproducible in V 2.2.2


[Feature Request]: Improve Package.html

Is there an existing issue for this?

[X] I have searched the existing issues

Feature Description
Improve the card designs, make sections separate, fix navbar
Use Case
For choosing packages on the page, this will improve the experience
Benefits
No response
Add ScreenShots
No response
Priority
High
Record

[X] I have read the Contributing Guidelines
[X] I'm a GSSOC'24 contributor
[ ] I'm a VSOC'24 contributor
[X] I have starred the repository

@apu52
hey, I'd like to contribute in this issue.
I have read the Contributing Guidelines.
I'm a GSSOC'24 contributor.
I have starred the repository.


Update svg background

Set the svg background to white so it can be showing clearly
in dark mode.
Signed-off-by: Lan Luo<EMAIL_ADDRESS>

Codecov Report

Merging #3756 (dfb976a) into main (627239c) will decrease coverage by 21.03%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##             main    #3756       +/-   ##
===========================================
- Coverage   64.69%   43.65%   -21.04%
===========================================
  Files         279      210       -69
  Lines       39784    36043     -3741
===========================================
- Hits        25738    15736    -10002
- Misses      12051    19161     +7110
+ Partials     1995     1146      -849

Flag
Coverage Δ

kind-e2e-tests
?

unit-tests
43.65% <ø> (-0.06%)
:arrow_down:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files
Coverage Δ

pkg/ovs/openflow/default.go
0.00% <0.00%> (-100.00%)
:arrow_down:

pkg/util/runtime/runtime.go
0.00% <0.00%> (-100.00%)
:arrow_down:

pkg/agent/openflow/groups.go
0.00% <0.00%> (-100.00%)
:arrow_down:

pkg/ovs/openflow/ofctrl_pipeline.go
0.00% <0.00%> (-95.84%)
:arrow_down:

pkg/ovs/openflow/logs.go
10.34% <0.00%> (-89.66%)
:arrow_down:

pkg/agent/controller/networkpolicy/reject.go
0.00% <0.00%> (-85.89%)
:arrow_down:

pkg/agent/nodeportlocal/k8s/annotations.go
0.00% <0.00%> (-84.45%)
:arrow_down:

pkg/apis/controlplane/register.go
0.00% <0.00%> (-83.34%)
:arrow_down:

pkg/agent/client.go
0.00% <0.00%> (-76.75%)
:arrow_down:

pkg/flowaggregator/certificate.go
0.00% <0.00%> (-75.53%)
:arrow_down:

... and 198 more

@antoninbas  looks like this fix only help on local VS code, it doesn't work on browser, should we  also add *.svg.png file with white background for those images?

@antoninbas I refined the fix and change the background in the svg directly, this works for browser, could you please review? thanks.

/skip-all


Functorizing Zinc

Problem
currently we cant change AST repr of contract/hash/key/address depending on the user input and we need a way to provide functionality to work with those values to interpreter module
Solution
Functorize Zinc_types and Zinc_interpreter by  executor module (dummy name for now).As of right now  with this pr we represent everything as strings during compilation and testing, but for example when we will be using it in Deku we would be able to use our internal representations of hash/contract/address/key and related functionality from Deku.
Related

#300

Hm, that should've been a PR :sweat_smile: my bad.


Compression via ffmpeg only on demand

Describe the feature
Description
The README has instructions on how to do a compressed stream via runOnReady. I assume this means ffmpeg will unconditionally run whether there are consumers for the compressed stream or not. This starts to slowdown my Pi 4 with just two stream (I have a bunch of other stuff running, of course).
My question/request is: can I start and kill the compressed stream based on whether it's being used or not?

Look at runOnDemand. It's explained in the config file

Run on demand does not work with startOnReady

Even if it did, the compressed stream would be started when the raw stream
is accessed. This is not efficient. I want the compressed stream to only
start when it's actually requested and shut down when it's not used.
On Wed, Mar 15, 2023, 12:35 AM raypanggh @.***> wrote:

Look at runOnDemand. It's explained in the config file
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Ffmpeg will start compressing the stream when the raw stream is
requested. I don't want to compress the stream if the compressed version is
not being used.
On Wed, Mar 15, 2023, 2:58 PM raypanggh @.***> wrote:

Not following the requirement.
I don't see any reference to startOnReady, only runOnReady.
Why not use runOnDemand? Ffmpeg will only start when the stream is
requested. And it will be shut down when there are no consumers.
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Can you share your config so I can understand the use case?

This is an example of one stream that I need a compressed version of. As you can see, runOnReady is started when the uncompressed stream is ready. If I combine sourceOnDemand with runOnReady, the compressed stream won't start unless the raw stream is requested. That does not make sense. Also, we cannot control ffmpeg to only compress on demand because it's started from the raw stream, not from the compressed path.
paths:
 all:
   publishUser: <redacted>
   publishPass: <redacted>
 1/unicast/compressed:
  readUser: <redacted>
  readPass: <redacted>
 1/unicast:
   readUser: root
   readPass: <redacted>
   source: rtsp://root:<redacted>@<ip>:8554/unicast
   sourceOnDemand: no
   sourceProtocol: udp
   runOnReady: ffmpeg -i rtsp://<redacted>:<redacted>@localhost:$RTSP_PORT/$RTSP_PATH -c:v h264_v4l2m2m -b:v 600k -max_muxing_queue_size 1024 -f rtsp rtsp://localhost:$RTSP_PORT/$RTSP_P>
   runOnReadyRestart: yes

Could you not make 1/unicast simply an RTSP proxy for rtsp://root:@:8554/unicast, and then have 1/unicast/compressed call ffmpeg via runOnDemand?
I'm imagining this:
1/unicast/compressed:
  runOnDemand: ffmpeg -i rtsp://<redacted>:<redacted>@localhost:$RTSP_PORT/1/unicast -c:v h264_v4l2m2m -b:v 600k -max_muxing_queue_size 1024 -f rtsp rtsp://localhost:$RTSP_PORT/$RTSP_PATH
  runOnDemandRestart: yes
1/unicast:
   source: rtsp://root:<redacted>@<ip>:8554/unicast
   sourceOnDemand: no # or yes if you don't want the bandwidth consumption if nobody is using the uncompressed source
   sourceProtocol: udp

This way the 1/unicast (the uncompressed stream) is always available, and only if 1/unicast/compressed is requested does ffmpeg kick in.

Tried it, but it didn't work:
Mar 15 16:57:50 raspberrypi rtsp-simple-server[5540]: 2023/03/15 16:57:50 INF [RTSP] [conn <IP_ADDRESS>:56752] closed (no one is publishing to path '3/unicast/compressed')

 3/unicast/compressed:
  readUser: <redacted>
  readPass: <redacted>
  runOnReady: ffmpeg -i rtsp://<redacted>:<redacted>@localhost:$RTSP_PORT/3/unicast -c:v h264_v4l2m2m -b:v 600k -max_muxing_queue_size 1024 -f rtsp rtsp://localhost:$RTSP_PORT/$RTSP_PATH
  runOnReadyRestart: yes
 3/unicast:
   readUser: <redacted>
   readPass: <redacted>
   source: rtsp://<redacted>:<redacted>@<ip>:8554/unicast
   sourceOnDemand: yes
   sourceProtocol: udp

Am I doing something wrong?

Hmm, it looks alright.
Try sourceOnDemand: no.
I suspect that 3/unicast isn't working because nothing is requesting it. As a result, 3/unicast/compressed won't work, as that relies on 3/unicast to be running.
Also you want runOnDemand, not runOnReady. runOnReady will leave you with the compressed stream running all the time.
If this doesn't work, I'll have a play with such a setup on my side and see if I can get it working.

Oh also you'll probably need to specify the credentials for publishing to 3/unicast/compressed, if you've got publishUser/publishPass configured.
-f rtsp rtsp://:@localhost:$RTSP_PORT/$RTSP_PATH
Try turning off all your authentication temporarily to eliminate that from the problem.

It works with your suggestions (but I also had to change ffmpeg params to the same ones in the README as mine were causing an empty stream)


next(CDXFetcherIter) hangs when cc request returns 400/404

OS: Windows 10
Python 3.8.5
cdx_toolkit 0.9.29
requests 2.24.0
So recently iterations on CDXFetcherIter hang on some urls, below is an example:
url = 'http://www.illinoishomepage.net/news/local-news/man-who-fell-through-ice-dies'
cdx = cdx_toolkit.CDXFetcher(source='cc')
next(cdx.iter(url, from_ts='201301',to='201709'))

And it turns out that on my machine, this request always returns 404:
cc_url = 'https://index.commoncrawl.org/CC-MAIN-2017-34-index'
params = {'to': '20170930235959', 'url': 'http://www.illinoishomepage.net/news/local-news/man-who-fell-through-ice-dies', 'output': 'json', 'page': 0, 'from': '20130101000000'}
headers = {'User-Agent': 'pypi_cdx_toolkit/installed-from-git'}
resp = requests.get(cc_url, params=params, headers=headers,
                                timeout=(30., 30.), allow_redirects=False)

And because of the way 404 is handled, CDXFetcherIter.get_more() will run this request over and over again with increasing page but self.captures remains [], causing the loop to hang.
I don't know if it's a temporary common crawl server error or it's related to my local connection. but same error last for 3 days now. So I think adding an option to limit number of pages or number of retries of get_more() would be nice. Thank you!

I did not use cdx server api before so I don't know its behavior before but it seems that with a large page number, the request would eventually return 400, for example with page=0
https://index.commoncrawl.org/CC-MAIN-2020-50-index?url=http%3A%2F%2Fwww.illinoishomepage.net%2Fnews%2Flocal-news%2Fman-who-fell-through-ice-dies&output=json&page=0
return 404, text is "error no capture".
But with page=1,
https://index.commoncrawl.org/CC-MAIN-2020-50-index?url=http%3A%2F%2Fwww.illinoishomepage.net%2Fnews%2Flocal-news%2Fman-who-fell-through-ice-dies&output=json&page=1
returns 400 and get_more() will move to next endpoint.
But for my example above, for CC-MAIN-2017-34-index, no matter what the page number is, for example, page=1000000, https://index.commoncrawl.org/CC-MAIN-2017-34-index?url=http%3A%2F%2Fwww.illinoishomepage.net%2Fnews%2Flocal-news%2Fman-who-fell-through-ice-dies&output=json&page=1000000
still returns 404 with text "error no capture". And get_more() will keep increasing the page number and retry.

I did not use cdx server api before so I don't know its behavior before but it seems that with a large page number, the request would eventually return 400, for example with page=0
https://index.commoncrawl.org/CC-MAIN-2020-50-index?url=http%3A%2F%2Fwww.illinoishomepage.net%2Fnews%2Flocal-news%2Fman-who-fell-through-ice-dies&output=json&page=0
return 404, text is "error no capture".
But with page=1,
https://index.commoncrawl.org/CC-MAIN-2020-50-index?url=http%3A%2F%2Fwww.illinoishomepage.net%2Fnews%2Flocal-news%2Fman-who-fell-through-ice-dies&output=json&page=1
returns 400 and get_more() will move to next endpoint.
But for my example above, for CC-MAIN-2017-34-index, no matter what the page number is, for example, page=1000000, https://index.commoncrawl.org/CC-MAIN-2017-34-index?url=http%3A%2F%2Fwww.illinoishomepage.net%2Fnews%2Flocal-news%2Fman-who-fell-through-ice-dies&output=json&page=1000000
still returns 404 with text "error no capture". And get_more() will keep increasing the page number and retry.

Sebastian fixed this bug on the Common Crawl side, it was a missing index file for just that one index. It happened because the index moved to a new server recently. Thanks for finding it!
I will add some kind of guard to the code, so this infinite loop is at least a visible infinite loop.

Sebastian fixed this bug on the Common Crawl side, it was a missing index file for just that one index. It happened because the index moved to a new server recently. Thanks for finding it!
I will add some kind of guard to the code, so this infinite loop is at least a visible infinite loop.


Failed to install in ubuntu 18

Already installed python 3 and set allies for python. But while trying to configure with ./configure && make it is producing following error.
rm -f LINUX_5.4.0-1009-aws_DBG/st.h
cp public.h LINUX_5.4.0-1009-aws_DBG/st.h
sed "s/<EMAIL_ADDRESS>< st.pc.in > st.pc
make[1]: Leaving directory '/home/ubuntu/srs/trunk/objs/Platform-Linux-5.4.0-SRS3/st-srs'
Installing CherryPy-3.2.4
auto/depends.sh: line 410: python: command not found
build CherryPy-3.2.4 failed, ret=127

I agree with that...   same problem.
and also this pb:
./objs/srs -c conf/srs.conf
-bash: ./objs/srs: No such file or directory


Support for time data type questions in SDC

Is your feature request related to a problem? Please describe.
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
Describe the solution you'd like
A clear and concise description of what you want to happen.
Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.
Additional context
Add any other context or screenshots about the feature request here.
Would you like to work on the issue?
Please state if this issue should be assigned to you or who you think could help to solve this issue.

Hi @LZRS and @pld ,
I’m interested in working on this issue. Could you please let me know if it's still available and if there are any specific guidelines or pointers to keep in mind? Thank you!

Hi @VishalGawade1,
Sorry for responding to this a bit late. The ticket has been assigned to you, and start working on it.
You'll be adding support for type time for Questionnaire.item.type. Currently supported item types are described here

@aditya-07 has some bandwidth and can do this


Error when processing any line where the value has a comma

Parser Version: 1.3.0
Java version: 8
In the example below, PARAMX will be break the parser.
...
ADD MONAME: PARAM1=VALUE1, PARAM2="VALUE3", PARAMX="Some string with, comas"
...

Fixed by PR #3


OpenGL/GLFW error building GLMakie

Hello, I wanted to give a try to Makie but I got the following error while trying to install it:
(@v1.5) pkg> build GLMakie
   Building ModernGL → `~/.julia/packages/ModernGL/rVuW2/deps/build.log`
   Building FFTW ────→ `~/.julia/packages/FFTW/DMUbN/deps/build.log`
   Building GLMakie ─→ `~/.julia/packages/GLMakie/4EXKe/deps/build.log`
┌ Error: Error building `GLMakie`:
│ libGL error: MESA-LOADER: failed to open iris (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri)
│ libGL error: failed to load driver: iris
│ libGL error: MESA-LOADER: failed to open iris (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri)
│ libGL error: failed to load driver: iris
│ libGL error: MESA-LOADER: failed to open swrast (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri)
│ libGL error: failed to load driver: swrast
│ init error of GLFW
│ ERROR: LoadError: OpenGL/GLFW wasn't installed correctly. This likely means,
│ you don't have an OpenGL capable Graphic Card,
│ you don't have the newest video driver installed,
│ or the GLFW build failed. If you're on linux and `]build` GLFW failed,
│ try manually adding `sudo apt-get install libglfw3` and then `]build GLMakie`.
│ If you're on a headless server, you still need to install x-server and
│ proper GPU drivers. You can take inspiration from this article
│ on how to get Makie running on a headless system:
│ https://nextjournal.com/sdanisch/makie-1.0
│ If you don't have a GPU, there is also a Cairo software backend
│ for Makie which you can use:
│ https://github.com/JuliaPlots/CairoMakie.jl.
│ Please check the below error and open an issue at:
│ https://github.com/JuliaPlots/GLMakie.jl.
│ After you fixed your OpenGL install, please run `]build GLMakie` again!
│ GLMakie will still load, but will be disabled as a default backend for Makie
│
│ Stacktrace:
│  [1] error(::String) at ./error.jl:33
│  [2] top-level scope at /home/lobianco/.julia/packages/GLMakie/4EXKe/deps/build.jl:63
│  [3] include(::String) at ./client.jl:457
│  [4] top-level scope at none:5
│ in expression starting at /home/lobianco/.julia/packages/GLMakie/4EXKe/deps/build.jl:31
│ caused by [exception 1]
│ GLFWError (VERSION_UNAVAILABLE): GLX: Failed to create context: GLXBadFBConfig
│ Stacktrace:
│  [1] _ErrorCallbackWrapper(::Int32, ::Cstring) at /home/lobianco/.julia/packages/GLFW/CBo9c/src/callback.jl:43
│  [2] CreateWindow(::Int64, ::Int64, ::String, ::GLFW.Monitor, ::GLFW.Window) at /home/lobianco/.julia/packages/GLFW/CBo9c/src/glfw3.jl:499
│  [3] GLFW.Window(; name::String, resolution::Tuple{Int64,Int64}, debugging::Bool, major::Int64, minor::Int64, windowhints::Array{Tuple{UInt32,Int64},1}, contexthints::Array{Tuple{UInt32,Integer},1}, visible::Bool, focus::Bool, fullscreen::Bool, monitor::Nothing, share::GLFW.Window) at /home/lobianco/.julia/packages/GLFW/CBo9c/src/glfw3.jl:344
│  [4] top-level scope at /home/lobianco/.julia/packages/GLMakie/4EXKe/deps/build.jl:34
│  [5] include(::String) at ./client.jl:457
│  [6] top-level scope at none:5
└ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:942

I am on a recent Dell Ubuntu 20.04 Laptop with Intel graphical card and I do already have libglfw3 to the newest version (3.3.2-1). I did also installed everything in the list on  https://nextjournal.com/sdanisch/makie-1.0 (and I don't know nothing of graphical terms.. OpenGL, GLX, GLFW, Cairo.....).

This seems to be this issue: https://github.com/JuliaGL/GLFW.jl/issues/198


DSEGOG-261 Use ObjectIds in ExperimentModel

This PR changes the _id in the ExperimentModel to use ObjectIds. Previously, this field was filled with a concatenation of the experiment ID and the part number. However, in the simulated EPAC data, experiment IDs for maintenance periods are stored as maintenance. In the case of the generated data, they were all experiments with a part number of 1.
Given current discussions regarding parts, it's unclear if this'll be the case in production so I've decided to move to using ObjectIds. We use these in the user session functionality so wasn't too bad to make this change (I was a bit scared of them before). Even the tests didn't require too much work!

I've made the suggested changes and the CI has passed. I've marked this PR for re-review


Add toy data

By adding toy data as functions, e.g. ms.load_oresund_comparer() or ms.load_dataset("oresund"), we could make it easier to get started with modelskill and easier to write documentation. Similar to https://scikit-learn.org/stable/datasets/toy_dataset.html or https://docs.xarray.dev/en/stable/generated/xarray.tutorial.load_dataset.html#xarray.tutorial.load_dataset or https://seaborn.pydata.org/generated/seaborn.load_dataset.html

Another elegant way to store datasets is in a data module like plotly: https://plotly.com/python-api-reference/generated/plotly.data.html in our case it could be:
cc = ms.data.oresund()
cc = ms.data.vistula()


UI: fix spacing on password reset form

:heart: Thank you for your contribution!
Description

Please describe briefly your pull request.

Before and after

Before and after

Once this is merged I'll remove the reset-password rule as it will no longer be used
Checklist
Ticks in all boxes and 🟢 on all GitHub actions status checks are required to merge:

[ ] I'm aware of the code of conduct.
[ ] I've created logical separate commits and followed the commit message format.
[ ] I've added relevant test cases.
[ ] I've added relevant documentation.
[ ] I've marked translation strings.
[ ] I've identified the copyright holder(s) and updated copyright headers for touched files (>15 lines contributions).
[ ] I've NOT included third-party code (copy/pasted source code or new dependencies).

If you have added third-party code (copy/pasted or new dependencies), please reach out to an architect.

Frontend

[ ] I've followed the CSS/JS and React guidelines.
[ ] I've followed the web accessibility guidelines.
[ ] I've followed the user interface guidelines.

Reminder
By using GitHub, you have already agreed to the GitHub’s Terms of Service including that:

You license your contribution under the same terms as the current repository’s license.
You agree that you have the right to license your contribution under the current repository’s license.

CI seems broken 🥶  can you have a look?

This should be merged after https://github.com/inveniosoftware/invenio-theme/pull/401


QC for variants is falsely finding errors

For instance,
  patient #320
    variants
     warnings:
     ·Expected a VCF record, a VRS CNV, or an expression with `hgvs.c`
but had an error retrieving any from patient
KBG39[PMID_36446582_KBG39].
Remove variant from testing
     ·Patient PMID_36446582_KBG39 has no variants to work with

but this phenopacket has
  "expressions": [
                  {
                    "syntax": "hgvs.c",
                    "value": "NM_013275.6:c.1893dup"
                  },
                  {
                    "syntax": "hgvs.g",
                    "value": "NC_000016.10:g.89284654dup"
                  }
                ],
                "vcfRecord": {
                  "genomeAssembly": "hg38",
                  "chrom": "chr16",
                  "pos": "89284648",
                  "ref": "G",
                  "alt": "GT"
                },

Is it the phenopacket in question located here?
https://github.com/monarch-initiative/genophenocorr/blob/KBG/notebooks/ANKRD11/phenopackets/PMID_36446582_KBG39.json
If so, then the warning is a true positive - there is indeed no variant to work with there.


builder: use structured logging for maven output

http://development.wombatsecurity.com/development/2018/04/06/logging-maven-to-json/

//cc @astefanutti

It complements #580 for integration logging.

I am looking at this.

So, I got that working. The original link does not work, but the page is archived on wayback machine.

There are a few caveats, though:

We lose the old non-parseable Maven output, since we have to remove the maven slf4j adapter
The container is slightly bigger
The build process is slightly longer and more prune to fail due to downloading extra dependencies for maven itself
Although it outputs in json format, it's not the same json format as the one in the operator logs. We may need to tune it - or allow the user to tune it - so it can be parseable.

Great! I think these are acceptable, compared to having the operator log fully JSONified.
Just to be sure, what do you mean exactly by 4?
The first value is to have full JSON for the operator log. Then, the second requirement would be to enable correlation for the Build logs, that are interleaved into the operator reconcile loop. To meed that requirement, it'd be useful to add a build correlation key. Or to find another mechanism, so that SOPs or users can quickly pick into the build and reconciliation for a particular resource.

Thanks!

Great! I think these are acceptable, compared to having the operator log fully JSONified.
Just to be sure, what do you mean exactly by 4?

Basically, what I meant is that the JSON for the build log and the JSON for the operator logs are different.
{"level":"info","ts":1620106986.5145833,"logger":"camel-k.controller.kamelet","msg":"Invoking action monitor","request-namespace":"camel-colorization","request-name":"cassandra-sink","api-version":"camel.apache.
org/v1alpha1","kind":"Kamelet","ns":"camel-colorization","name":"cassandra-sink"}

The maven logs are slightly different and we'll have to adjust that to make them look the same (either by modifying the logback configuration or consuming them).

The first value is to have full JSON for the operator log. Then, the second requirement would be to enable correlation for the Build logs, that are interleaved into the operator reconcile loop. To meed that requirement, it'd be useful to add a build correlation key. Or to find another mechanism, so that SOPs or users can quickly pick into the build and reconciliation for a particular resource.

I see. It makes sense. If I understand it correctly, this is just the first part: just printing the maven logs in JSON format.
To make it truly useful, we'll have to consume and process that maven JSON format so we can normalize it and correlate it. So, IMHO, the next step would be to work on that.
Do you think it makes sense to split that into 2 tasks (and, consequently, in 2 contributions)?

2. The container is slightly bigger

3. The build process is slightly longer and more prune to fail due to downloading extra dependencies for maven itself

Cane we eventually make a pre-build container image with all the required bits already there ?

@orpiske

Do you think it makes sense to split that into 2 tasks (and, consequently, in 2 contributions)?

Whatever works best for you. Having the Maven logs JSONified is already an improvement, so it can be merged and have it followed by other contributions.

@lburgazzoli

Can we eventually make a pre-build container image with all the required bits already there?

My understanding is that the image here is the operator one. So it'll be updated to have all the bits.

Whatever works best for you. Having the Maven logs JSONified is already an improvement, so it can be merged and have it followed by other contributions.

Deal, thanks. I'll clean it up and send the current implement today for review.

@lburgazzoli

Can we eventually make a pre-build container image with all the required bits already there?

My understanding is that the image here is the operator one. So it'll be updated to have all the bits.

That's correct.


Define security for a report or a folder

It should be possible to define the roles' membership at the level of an item (folder, report, ...)

Currently we support setting security by inheritance (membership is added to existing security of the parent)

https://ci.appveyor.com/project/CdricLCharlier/ssrsdeploy/build/0.8.0-unstable.14.build.75


fixed the replication of navbar buttons

Fixed the navbar replication of buttons, and also added mobile responsiveness for the same.

pls add the hacktober accepted tag , nice working with you @codingkatty


minecraft-server imageTag rpi3 ran into issues with rcon-cli

helm install stable/minecraft --version 1.1.6 --set=imageTag=rpi3 --set minecraftServer.eula=true --generate-name

I saw the following problem in the logs.
Running as uid=1000 gid=1000 with /data as 'drwxrwxrwx    6 0        0             4096 Feb  2 17:41 /data'
Checking version information.
Checking type information.
server.properties already created, skipping
Checking for JSON files.
Copying any mods over...
Setting initial memory to 512M and max to 512M
Starting the Minecraft server...
2020/02/02 17:42:55 Stopping with rcon-cli
2020/02/02 17:42:55 ERROR Failed to stop using rcon-cli exit status 1
2020/02/02 17:42:55 Sending 'stop' to Minecraft server...
2020/02/02 17:42:55 Waiting for completion...

I tried 1.15.2 yesterday on my RaspberryPi 3 and it failed miserably. I had to power-cycle the entire RaspberryPi to even ssh back to it. The logs you reported don't indicate an rcon-cli problem; instead the problem is that the minecraft server itself is not ready or responsive enough to even respond to rcon connections/operations.
I thought I would try an older version, 1.12.2, and even that maxes out one of the cores without making any visible progress:

Finally, I tried 1.7.10 and it starts up slowly but is actually making progress through the "Preparing spawn area" steps.


Open new Tab

Hi,
Can I open a new tab instead of opening a new window?
Best.

Not with how this module works. You would need OS and browser specific scripting, for example, using AppleScript to open a new tab in Chrome.


add all-settled in promise

Fixes #31083
It's toooooooooo hard to write ten overload

seems ci is broken

Fixed merge conflicts, let's see how CI goes

♥ line ending problems

Anything else needs me to update?🤔

🙋🏻♂


Some user experience

Firstly, I am not an English-speaking user, and my window ratio is relatively unusual (3456x1200), so my issue may not be common for everyone.
When I am using it, only equipped items can be recognized, which is very strange. I don't know where the problem is coming from.
Regarding the recognition of affixes and dot-affixes_X, I have tried cropping the image myself to achieve better recognition results. For users who cannot use the presets, it is not a good experience to replace them one by one. Perhaps you could add a tab in the DEBUG interface for re-capturing existing affixes? For example: 1. Select the affix. 2. Click the replace button, and the program starts monitoring clipboard events. 3. The user manually takes a screenshot. 4. The program pops up a preview and a prompt asking whether to replace it.
These are my user experiences, and I hope they are useful to you. Thank you for sharing your ideas.

Thanks for your feedback. The next update will make it easier to get it working for different resolutions. That will most likely fix your issue with equipped items as well.
But I have to solve some crashes first before I can release it.

Perhaps you could add a tab in the DEBUG interface for re-capturing existing affixes?

Windows has a build in feature that works easy enough I think.
If you press Shift + Windows + S the snipping tool will open which allows you to draw a rectangle around the affix and save it.
I have also plans to add a download manage in the app to directly download system presets for each resolution created by the community.

Glad to receive your reply.
I know that Windows has a built-in screenshot function, and in fact, that's what I use to take screenshots. I'm also happy to see that you support users replacing local files to make them more localized and customizable. However, as you know, there are dozens to hundreds of different affixes in D4, and replacing them one by one with screenshots is not a very enjoyable preparation work. Additionally, I'm not sure if different file formats, such as PNG and JPEG, would affect recognition efficiency.

However, as you know, there are dozens to hundreds of different affixes in D4, and replacing them one by one with screenshots is not a very enjoyable preparation work.

Indeed, combining the different item types and affixes you would need hundreds of images. Luckily this is only the first version of the app. It now uses images so everyone can expand it themselves with the affixes they like. Also it supports all languages without any effort.
When this version is stable enough with some basic features I'll start working on a version 2 which uses OCR.
Then you'll only need a few images to detect the tooltip and the remaining part will be converted from image to text.

I'm glad there will be future versions. I'm a bit eager for them. Thank you for your hard work. I don't have any more questions. Have a great day!


Fixing akktors bug

Pull Request Test Coverage Report for Build 330

0 of 4 (0.0%)  changed or added relevant lines in 2 files are covered.
2 unchanged lines in 1 file lost coverage.
Overall coverage increased (+0.4%) to 35.513%

Changes Missing Coverage
Covered Lines
Changed/Added Lines
%

master/src/main/scala/com/github/jaitl/crawler/master/config/TorRequestController.scala
0
1
0.0%

master/src/main/scala/com/github/jaitl/crawler/master/config/ResourceBalancer.scala
0
3
0.0%

Files with Coverage Reduction
New Missed Lines
%

master/src/main/scala/com/github/jaitl/crawler/master/queue/QueueTaskBalancer.scala
2
66.67%

Totals

Change from base Build 328:
0.4%

Covered Lines:
277

Relevant Lines:
780

💛  - Coveralls