Submit VCell <IP_ADDRESS>

id: vcell
version: <IP_ADDRESS>
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_VCell/14226e2f85acdb7f3e9abd39017faa0121200689/biosimulators.json
specificationsPatch:
version: <IP_ADDRESS>
image:
url: ghcr.io/biosimulators/biosimulators_vcell/vcell:<IP_ADDRESS>
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 here. The results of the validation of your tool will also be saved as a JSON file.A link to this file will be available from the "Artifacts" section at the bottom of this page.

The specifications of your simulator is valid!

Summary of tests

Executed 67 test cases

Passed 26 test cases:

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

Failed 2 test cases:

docker_image.SingularityImageExecutesSimulationsSuccessfully
results_report.SimulatorGeneratesReportsOfSimulationResults

Skipped 39 test cases:

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

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (1.4 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

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

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

Log:

cli.CliDisplaysHelpInline (2.2 s)
Test that a command-line interface provides inline help.
Warnings:
Command-line interface should support the `-h` option for displaying help inline.

The command-line interface displayed the following when executed with `-h`:

  Invalid arguments: [-h, , , , , ]

Command-line interface should support the `--help` option for displaying help inline.

The command-line interface displayed the following when executed with `--help`:

  Invalid arguments: [--help, , , , , ]

Log:

cli.CliDisplaysVersionInformationInline (1.8 s)
Test that a command-line interface provides version information inline.
Warnings:
Command-line interface should support the `-v` option for displaying version information inline.

The command-line interface displayed the following when executed with `-v`:

  Invalid arguments: [-v, , , , , ]

Command-line interface should support the `--version` option for displaying version information inline.

The command-line interface displayed the following when executed with `--version`:

  Invalid arguments: [--version, , , , , ]

Log:

docker_image.HasBioContainersLabels (0.4 s)
Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
The Docker image should have the following BioContainers labels:
  extra.identifiers.biotools

Log:

docker_image.HasOciLabels (0.5 s)
Test that a Docker image has Open Container Initiative (OCI) labels with metadata about the image
Warnings:
The Docker image should have the following Open Container Initiative (OCI) labels:
  org.opencontainers.image.created
  org.opencontainers.image.revision

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (14.6 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

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

Plots were not produced:
  BIOMD0000000912_sim.sedml/plot_1

Extra plots were produced:
  BIOMD0000000912_sim.sedml/Figure_1

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

Jun 24, 2021 4:55:20 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_ff16ada0-a9b3-4220-9904-6c24a5431d7e7178151003226030692

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  1 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp4521958127400789429.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@1b70203f

Finished: SOLVER_FINISHED:completed

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

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

Ignoring unsupported output `Figure_1` while CSV generation.

Generating report `report`.

Python 3.6.9

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (25.3 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000086

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

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

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

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

Jun 24, 2021 4:55:35 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_6e180ffb-57b1-45cf-a776-d1d0647ff7826995376429100899108

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  4 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file simulation_1.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Succesful model import: SBML file /tmp/temp1326540115010029863.xml

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

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

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

Ignoring unsupported output `Figure_3a` while CSV generation.

Ignoring unsupported output `Figure_3b` while CSV generation.

Ignoring unsupported output `Figure_3c` while CSV generation.

Ignoring unsupported output `Figure_3d` while CSV generation.

Generating report `report`.

Python 3.6.9

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (25.1 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

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

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

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

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

Jun 24, 2021 4:56:00 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_774cfa44-c5c1-4107-9427-af132f48cea17063641112854097942

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  4 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file simulation_1.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Succesful model import: SBML file /tmp/temp8836057759911866578.xml

/tmp/out/simulation_1.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@3b4825f0

Finished: SOLVER_FINISHED:completed

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

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

Ignoring unsupported output `Figure_3a` while CSV generation.

Ignoring unsupported output `Figure_3b` while CSV generation.

Ignoring unsupported output `Figure_3c` while CSV generation.

Ignoring unsupported output `Figure_3d` while CSV generation.

Generating report `report`.

Python 3.6.9

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (57.9 s)
Required model formats and simulation algorithms for SED tasks:

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

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

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

Jun 24, 2021 4:57:31 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_df3f38dd-759e-4d46-afee-bad1b44489297923865186429866142

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 4 model(s), 6 simulation(s), 6 task(s), 6  report(s),  6 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file simulation.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Succesful model import: SBML file /tmp/temp5476421137362832260.xml

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

Succesful model import: SBML file /tmp/temp786238515853865870.xml

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

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

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

Succesful model import: SBML file /tmp/temp4873027184798180571.xml

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

Succesful model import: SBML file /tmp/temp3692137389867704793.xml

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@62b09715

Finished: SOLVER_FINISHED:completed

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

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

Solver status: 3

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

values are:

A = NaN

C = Infinity

PrmA = Infinity

PrmA_bound = -Infinity

PrmR = Infinity

PrmR_bound = -Infinity

R = -Infinity

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

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

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

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

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

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@4391a2d8

Finished: SOLVER_FINISHED:completed

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

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

cbit.vcell.solver.stoch.GibsonSolver@384fda47

Finished: SOLVER_FINISHED:completed

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

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

cbit.vcell.solver.stoch.GibsonSolver@433d9680

Finished: SOLVER_FINISHED:completed

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

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

Ignoring unsupported output `plot2d_Fig_1a` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation.

Ignoring unsupported output `plot2d_Euler_default` while CSV generation.

Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation.

Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation.

Generating report `report_Fig_1a`.

Generating report `report_low_delta_R_det`.

Generating report `report_Euler_default`.

Generating report `report_Euler_small_step_size`.

Generating report `report_Fig_1_c`.

Generating report `report_low_delta_R_stoch`.

Python 3.6.9

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (40.8 s)
Required model formats and simulation algorithms for SED tasks:

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

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

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

Jun 24, 2021 4:56:25 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_05878f76-dce7-4fa5-b357-14b57cd30b606503428040877953236

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 2 model(s), 4 simulation(s), 4 task(s), 4  report(s),  5 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file simulation.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Succesful model import: SBML file /tmp/temp2047352836815813872.xml

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

Succesful model import: SBML file /tmp/temp6993040086241039118.xml

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

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

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@5b47731f

Finished: SOLVER_FINISHED:completed

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

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

Solver status: 3

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

values are:

A = NaN

C = Infinity

PrmA = Infinity

PrmA_bound = -Infinity

PrmR = Infinity

PrmR_bound = -Infinity

R = -Infinity

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

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

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

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

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

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@76f881d9

Finished: SOLVER_FINISHED:completed

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

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

Ignoring unsupported output `Figure_2ab` while CSV generation.

Ignoring unsupported output `plot2d_Fig_1a` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation.

Ignoring unsupported output `plot2d_Euler_default` while CSV generation.

Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation.

Generating report `report_Fig_1a`.

Generating report `report_low_delta_R_det`.

Generating report `report_Euler_default`.

Generating report `report_Euler_small_step_size`.

Python 3.6.9

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (24.4 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000027

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

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

Jun 24, 2021 4:57:06 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_6692b9e9-3ae6-4f84-852b-6d8dbe375a116921724297640105160

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 2 model(s), 2 simulation(s), 2 task(s), 2  report(s),  2 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file simulation.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Succesful model import: SBML file /tmp/temp1123725324387605984.xml

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

Succesful model import: SBML file /tmp/temp3493085633756150377.xml

cbit.vcell.solver.stoch.GibsonSolver@3f92c349

Finished: SOLVER_FINISHED:completed

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

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

cbit.vcell.solver.stoch.GibsonSolver@9d200de

Finished: SOLVER_FINISHED:completed

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

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

Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation.

Generating report `report_Fig_1_c`.

Generating report `report_low_delta_R_stoch`.

Python 3.6.9

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

Failures
docker_image.SingularityImageExecutesSimulationsSuccessfully (13.9 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives
Exception:
Simulator did not produce the following reports:
  - `BIOMD0000000912_sim.sedml/report`

Log:

results_report.SimulatorGeneratesReportsOfSimulationResults (10.1 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.
Exception:
`uri` of HDF5 data set `BIOMD0000000912_sim.sedml/report` must be `BIOMD0000000912_sim.sedml/report`, not `./BIOMD0000000912_sim.sedml/report`.

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

Jun 24, 2021 4:54:28 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_002ba53c-b6b9-4117-8ea4-5920c9d7c00a2959002003866540318

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp4326384223160847279.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@6650813a

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.6.9

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

Skips
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (10.4 s)
Test that simulator logs the execution of COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.

More information: https://biosimulators.org/conventions/status

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

Jun 24, 2021 4:54:38 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_465e7dcb-b059-434b-91dc-47f66bb54cdd5417586627715939221

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp108809343679564191.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@6650813a

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.6.9

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (10.1 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.

More information: https://biosimulators.org/conventions/status

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

Jun 24, 2021 4:54:49 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_834dc3fd-a04b-4c6d-9972-c912438b584b3814014605404177110

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp7074806795958090734.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@6650813a

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.6.9

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (10.3 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.

More information: https://biosimulators.org/conventions/status

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

Jun 24, 2021 4:54:59 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_cb68e6b5-3ef4-4924-99ac-d5ea89fad2391745154620245252172

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp1735475273517230635.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@6650813a

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.6.9

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (10.9 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.

More information: https://biosimulators.org/conventions/status

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

Jun 24, 2021 4:55:09 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_ba2f8421-7bae-4e7e-b2ac-68c115a9b3223679344026643117305

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp6868827189902742939.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@6650813a

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.6.9

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

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

Format: format_3972
Algorithm: KISAO_0000263

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

Log:

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

Format: format_3972
Algorithm: KISAO_0000019

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

Log:

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

Format: format_3240
Algorithm: KISAO_0000019

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

Log:

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

Format: format_9004
Algorithm: KISAO_0000019

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

Log:

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

Format: format_9004
Algorithm: KISAO_0000030

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

Log:

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

Format: format_2585
Algorithm: KISAO_0000088

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

Log:

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

Format: format_2585
Algorithm: KISAO_000019

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

Log:

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

Format: format_2585
Algorithm: KISAO_0000496

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

Log:

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

Format: format_2585
Algorithm: KISAO_0000560

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

Log:

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

Format: format_2585
Algorithm: KISAO_0000560

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

Log:

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

Format: format_2585
Algorithm: KISAO_0000029

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

Log:

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

Format: format_2585
Algorithm: KISAO_0000437

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

Log:

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

Format: format_2585
Algorithm: KISAO_0000449

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

Log:

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

Format: format_9001
Algorithm: KISAO_0000057

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

Log:

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (2.6 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1).
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_vcell/vcell:<IP_ADDRESS>' could not execute the archive:

  Unknown error

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

Jun 24, 2021 4:50:49 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_b1d7548f-c03b-4703-a889-dd1b9c2c7b591126762642505276877

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

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

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

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

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

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

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

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

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

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

Error importing from SBML : no SBML source.

Unable to initialize bioModel for the given selection

Error importing from SBML : no SBML source.

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (2.6 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1) and inherit the changes of the model.
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_vcell/vcell:<IP_ADDRESS>' could not execute the archive:

  Unknown error

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

Jun 24, 2021 4:50:51 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_5f9facb4-ad9c-49be-b558-f8fe0a4944528472726419065970867

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

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

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

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

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

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

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

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

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

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

Error importing from SBML : no SBML source.

Unable to initialize bioModel for the given selection

Error importing from SBML : no SBML source.

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

Log:

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

Log:

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (10.3 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements.
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

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

Jun 24, 2021 4:51:42 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_fb26aba8-6a0a-4ed4-841f-03f8dc3c9ffc8996983979367654951

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp2469040150277333659.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@1b70203f

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.6.9

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsComputeModelChanges (11.2 s)
Test that a simulator supports compute model changes
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

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

Jun 24, 2021 4:52:03 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_9cf71f4c-8ff5-4e09-bd50-162865f64f355171783964828107138

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp5636380941198463649.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@736ac09a

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.6.9

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (13.3 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp0hp0_k84/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

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

Jun 24, 2021 4:52:14 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_b1f93dc5-6949-4881-bc51-531b7b29992d1674221892825002938

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp5055978146094522955.xml

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

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@17f460bb

Finished: SOLVER_FINISHED:completed

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

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

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@5fa05212

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report__copy_2`.

Python 3.6.9

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 355, in <module>

    'genPlotPdfs': gen_plot_pdfs,

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire

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

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire

    target=component.__name__)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 165, in exec_sed_doc

    data_set_results[data_set.id] = data_set_df.loc[data_set.label, :].to_numpy(dtype ='float64')

  File "/usr/local/lib/python3.6/dist-packages/pandas/core/base.py", line 846, in to_numpy

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

  File "/usr/local/lib/python3.6/dist-packages/numpy/core/_asarray.py", line 83, in asarray

    return array(a, dtype, copy=False, order=order)

ValueError: could not convert string to float: 'NaN.9'

HDF conversion failed

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsDataSetsWithDifferentShapes (13.3 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpqzzaq68w/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

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

Jun 24, 2021 4:52:27 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_d7e9cdeb-25ff-4ac8-af5d-5e26011621dc1326176760371134372

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp4636465672216878199.xml

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

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@51671b08

Finished: SOLVER_FINISHED:completed

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

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

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@3f3ddbd9

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 355, in <module>

    'genPlotPdfs': gen_plot_pdfs,

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire

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

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire

    target=component.__name__)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 305, in gen_plot_pdfs

    report_frames = get_report_dataframes(all_report_dataref, result_out_dir)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 281, in get_report_dataframes

    report_frames[report] = pd.read_csv(os.path.join(result_out_dir, report + ".csv")).T.reset_index()

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 688, in read_csv

    return _read(filepath_or_buffer, kwds)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 460, in _read

    data = parser.read(nrows)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 1198, in read

    ret = self._engine.read(nrows)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 2157, in read

    data = self._reader.read(nrows)

  File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader.read

  File "pandas/_libs/parsers.pyx", line 862, in pandas._libs.parsers.TextReader._read_low_memory

  File "pandas/_libs/parsers.pyx", line 918, in pandas._libs.parsers.TextReader._read_rows

  File "pandas/_libs/parsers.pyx", line 905, in pandas._libs.parsers.TextReader._tokenize_rows

  File "pandas/_libs/parsers.pyx", line 2042, in pandas._libs.parsers.raise_parser_error

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

Python 3.6.9

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 355, in <module>

    'genPlotPdfs': gen_plot_pdfs,

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire

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

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire

    target=component.__name__)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 145, in exec_sed_doc

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

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 688, in read_csv

    return _read(filepath_or_buffer, kwds)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 460, in _read

    data = parser.read(nrows)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 1198, in read

    ret = self._engine.read(nrows)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 2157, in read

    data = self._reader.read(nrows)

  File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader.read

  File "pandas/_libs/parsers.pyx", line 862, in pandas._libs.parsers.TextReader._read_low_memory

  File "pandas/_libs/parsers.pyx", line 918, in pandas._libs.parsers.TextReader._read_rows

  File "pandas/_libs/parsers.pyx", line 905, in pandas._libs.parsers.TextReader._tokenize_rows

  File "pandas/_libs/parsers.pyx", line 2042, in pandas._libs.parsers.raise_parser_error

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

HDF conversion failed

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsModelAttributeChanges (11.6 s)
Test that a simulator supports changes to the attributes of model elements
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

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

Jun 24, 2021 4:52:40 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_abe48ea5-4235-4ea8-9934-a4a7fec1b9f48057603363592372729

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp112255578102530229.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@59712875

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.6.9

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsRepeatedTasksWithChanges (5.2 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpgpzbxczz/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

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

Jun 24, 2021 4:53:27 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_40e20a29-3a95-4fa5-bb7a-3a402ca0b2a38951353855151365674

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

java.lang.NullPointerException

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

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

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

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

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

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

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

SED-ML processing for /tmp/vcell_temp_40e20a29-3a95-4fa5-bb7a-3a402ca0b2a38951353855151365674/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

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

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

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

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

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

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

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

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

Jun 24, 2021 4:53:29 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_ba55b075-dca9-4ebe-bfbc-5d694630186c431380527027675451

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

java.lang.NullPointerException

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

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

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

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

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

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

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

SED-ML processing for /tmp/vcell_temp_ba55b075-dca9-4ebe-bfbc-5d694630186c431380527027675451/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

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

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

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

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

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

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

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

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (5.1 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpelhb0wrh/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

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

Jun 24, 2021 4:53:32 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_9f71d71d-50fd-4b58-8f02-48936536f7946049062724026759022

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

java.lang.NullPointerException

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

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

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

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

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

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

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

SED-ML processing for /tmp/vcell_temp_9f71d71d-50fd-4b58-8f02-48936536f7946049062724026759022/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

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

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

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

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

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

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

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

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

Jun 24, 2021 4:53:35 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_8356a37d-a1f3-4a1d-8bd0-f9763200003a7342235570207708579

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

java.lang.NullPointerException

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

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

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

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

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

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

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

SED-ML processing for /tmp/vcell_temp_8356a37d-a1f3-4a1d-8bd0-f9763200003a7342235570207708579/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

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

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

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

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

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

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

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

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (2.5 s)
Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpiiyv3jg_/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

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

Jun 24, 2021 4:53:37 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_ecf4f43e-b1c4-4661-8539-3bd973163c5f4228332730251493866

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

java.lang.NullPointerException

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

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

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

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

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

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

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

SED-ML processing for /tmp/vcell_temp_ecf4f43e-b1c4-4661-8539-3bd973163c5f4228332730251493866/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

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

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

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

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

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

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

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

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (2.5 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpht2fcz6n/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

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

Jun 24, 2021 4:53:40 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_735bdb7e-ebab-4a89-a447-8965550dc87c4730293696720212926

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

java.lang.NullPointerException

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

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

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

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

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

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

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

SED-ML processing for /tmp/vcell_temp_735bdb7e-ebab-4a89-a447-8965550dc87c4730293696720212926/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

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

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

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

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

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

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

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

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (2.4 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpooasxc6r/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

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

Jun 24, 2021 4:53:42 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_34ce1323-a995-4a44-883f-5a9b38693fd14611959773889465034

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

java.lang.NullPointerException

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

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

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

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

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

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

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

SED-ML processing for /tmp/vcell_temp_34ce1323-a995-4a44-883f-5a9b38693fd14611959773889465034/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

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

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

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

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

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

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

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

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (2.5 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpqcj_qqp6/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

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

Jun 24, 2021 4:53:45 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_c7a563c5-508b-4a98-987a-b9588c5302d9302672191160155883

Python 3.6.9

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

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

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

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

SED-ML version level not supported, import may fail

java.lang.NullPointerException

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

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

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

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

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

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

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

SED-ML processing for /tmp/vcell_temp_c7a563c5-508b-4a98-987a-b9588c5302d9302672191160155883/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

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

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

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

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

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

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

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

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (2.5 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpwnricps2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

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

Jun 24, 2021 4:53:47 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_125f04c2-2f4f-4565-a1b1-940c446c32575161592068049912966

Python 3.6.9

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

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

cl ...

- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
-
- The complete log of your validation/submission job, including further information about the failure, is available [here](https://github.com/biosimulators/Biosimulators/actions/runs/968698325). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/968698325).


Closes issue 30

Hi @elray1,
I checked the code with matts files. The error that matt initially got:
state.as_of_truth.date is undefined
An error occurred while rendering the page. Check developer tools console for details.

no longer shows up. The graphs disappear when the dates end (the arrays become empty) and the site no longer crashes.


Slider not acting responsive

We have on one page 2 jcarousels. This is working fine. One is working as an vertical slider and one as an horizontal (only visible on mobile < 768px). But the one for mobile is not acting responsive.
For both carousels we have different stylings defined.When we put the "vertical" class on the mobile, the image is acting responsive....
We narrowed it down to the width option of the ul-element:
.mcarousel ul { width: 20000em; }
When we change that in "height", the image is acting responsive (but of course all images are stacked under eachother....
You kan see at http://jsfiddle.net/andrenl/8anskuo6/1/

Looks like .jcarousel li also need a max-width: 100%.

Hi Jan,
max-width on the li-element does not have any effect... I'm puzzled. Below the CSS styling on the elements... (they call mcarousel). Any other suggestions?
.mcarousel {
position: relative;
overflow: hidden;
}
.mcarousel ul {
width: 20000em;
position: relative;
list-style: none;
margin: 0;
padding: 0;
}
.mcarousel li {
float: left;
}
.mcarousel li img{
display: block;
height: auto !important;
-webkit-border-top-right-radius: 26px;
border-top-right-radius: 26px;
}

Hi
I created an jsfiddle:
http://jsfiddle.net/andrenl/8anskuo6/1/
The silder is working, but not resizing...(responsive)

Hi,
I've added an function to solve the issue; it works in our specific case; in other cases it would need a minor changes (like the width/height ratio and the id of the carousel).
function resizeMobileImg() {
var width = jQuery('#mobilecarousel').width();
var height = Math.floor(width * 0.6656051);
$('#mobilecarousel ul li img').height(height).width(width);
}
example:
http://jsfiddle.net/andrenl/8anskuo6/5/

This is much like the repsonsive carousel example: http://sorgalla.com/jcarousel/examples/responsive/


VPN Gateway packet capture documentation should have more information about SAS URL

Current documentation is really vague about SAS URL and the linked Powershell documentation does not really help. The following information should be mentioned on this page:

SAS URL must include container name. Otherwise packet capture will use the current year as the name of the container
Named container must exist on the target storage account. Otherwise, dump will fail with Error: An internal error occured. The response did not contain any data. Please check storage for the capture.

the linked page: https://docs.microsoft.com/en-us/powershell/module/az.network/stop-azvirtualnetworkgatewaypacketcapture?view=azps-7.1.0

Document Details
⚠ Do not edit this section. It is required for docs.microsoft.com ➟ GitHub issue linking.

ID: 85090bbe-facd-f493-9817-b639df44f345
Version Independent ID: 29832cb6-6676-147d-5d5f-fccbd55b2fba
Content: Configure packet capture for VPN Gateway - Azure VPN Gateway
Content Source: articles/vpn-gateway/packet-capture.md
Service: vpn-gateway
GitHub Login: @anzaman
Microsoft Alias: alzam

Thanks for the feedback! I have assigned the issue to the content author to investigate further and update the document as appropriate.

The examples on the linked page do show how to set the $sasurl variable and include the container name.

Does this mean that no documentation clarifications will be done?
How can I connect the product team for

adding similar information on the portal
enhance the error message?

we will add portal instructions for stopping packet capture and can specify that SAS URL must be include container name.

Cool.
I had to check logs of the target storage account to understand why stopping packet capture failed.
Afterward, I read the Powershell section of the documentation and found the linked page.

#please-close

The portal instructions are still missing. I wasted 2 hours trying to get a packet trace to save to a URL and eventually gave up and had to resort to blind guesswork to solve my network issue. It should not be this hard to save a packet trace somewhere - usually when we're doing packet traces its because we are under pressure to solve a problem.   Such a garbage feature of VNG

I am currently having this issue as well. My experience with Azure in the last three 3months that I started using is that many basic things that should ordinarily be a walk in the pack are surprisingly difficult to troubleshoot. After years of work on GCP and AWS. I didn't find things too hard to solve like Azure. There are many good things about Azure though.


Strong name everything.

https://github.com/aspnet/dnx/issues/2615
cc @davidfowl @pranavkm @Eilon @muratg @moozzyk

Hi @cesarbs, I'm your friendly neighborhood .NET Foundation Pull Request Bot (You can call me DNFBOT). Thanks for your contribution!
You've already signed the contribution license agreement. Thanks!
The agreement was validated by .NET Foundation and real humans are currently evaluating your PR.
TTYL, DNFBOT;


[Review only] MLHR 1957 hbase input

@sandeepdeshmukh
Can you please review?

Incorporated review comments.
@PramodSSImmaneni @sandeepdeshmukh
Please review.

@gauravgopi123 / @PramodSSImmaneni  Could you please review?

@PramodSSImmaneni
Can you please review? Once you approve, I can squash the commits.


API should not return an error status when a protocol is cancelled

overview
Currently, when a protocol is cancelled, the API correctly reports a "cancelled" status, and then emits an error. It should continue to report the "cancelled" status, but not emit an error.

This was resolved in PAPIv1 by #3721. If this is still a problem in PAPIv2 we should open a new ticket


[BUG] [WCAG] requests/new - Validation error contrast ratio is too low.

Describe the bug
The validation error text's colour does not contrast the background enough to meet WCAG compliance. The current contrast is 3.27:1. This is only an acceptable contrast ratio for fonts over 18px.
Found on https://reach4help-staging-web-client.firebaseapp.com/requests/new
Possibly an issue on all pages in which validation errors appear.
To Reproduce
Steps to reproduce the behavior:

Navigate to the requests/new page.
Trigger a validation error.
Open console (F12) and turn on the inspector.
4a (with Axe add-on). Hover over the validation error. Notice that the hover-inspector fails the contrast compliance test.
4b (without Axe). Click on the validation error. Copy and paste the colour hex codes of the text and the background into a contrast checker (link provided below) [text: FF4D4F, background: ffffff ]
5b. Notice that the contrast ratio fails the contrast compliance test.

Expected behavior
Contrast ratio meets WCAG requirements (4.5:1) of text under 18px on all text.
Screenshots

Desktop (please complete the following information):

Windows 10 - Chrome

Additional context
To check contrast: https://contrastchecker.com/
WCAG quick reference on contrast: https://www.w3.org/WAI/WCAG21/quickref/#contrast-minimum

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