Submit Vcell <IP_ADDRESS>

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

Thank you @bilalshaikh42 for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job will be available here. The results of the validation of your tool will also be saved as a JSON file.A link to this file will be available from the "Artifacts" section at the bottom of this page.

The specifications of your simulator is valid!

Summary of tests

Executed 67 test cases

Passed 27 test cases:

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

Failed 1 test cases:

docker_image.SingularityImageExecutesSimulationsSuccessfully

Skipped 39 test cases:

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

Failures
docker_image.SingularityImageExecutesSimulationsSuccessfully (12.8 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:

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (1.2 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

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

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

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

Log:

docker_image.HasBioContainersLabels (3.3 s)
Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
The Docker image should have the following BioContainers labels:
  extra.identifiers.biotools

Log:

docker_image.HasOciLabels (15.0 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 (10.8 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 25, 2021 10:51:58 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_287c1329-a9a8-48ab-a70d-4ea3a06b95062329525684898417349

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp5772049153365007004.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

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

Finished: SOLVER_FINISHED:completed

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

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

Ignoring unsupported output `Figure_1` while CSV generation.

Generating report `report`.

Python 3.8.5

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (21.0 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 25, 2021 10:52:09 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_bd72f7d4-377d-4bcd-aa05-1aee23befa673902161018358172831

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Successful translation: SED-ML file simulation_1.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Succesful model import: SBML file /tmp/temp2377614361024808671.xml

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

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

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

Ignoring unsupported output `Figure_3a` while CSV generation.

Ignoring unsupported output `Figure_3b` while CSV generation.

Ignoring unsupported output `Figure_3c` while CSV generation.

Ignoring unsupported output `Figure_3d` while CSV generation.

Generating report `report`.

Python 3.8.5

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (20.0 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 25, 2021 10:52:30 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_e22995ac-70db-483e-93d4-5c94832ec7194249505711039461071

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Successful translation: SED-ML file simulation_1.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Succesful model import: SBML file /tmp/temp7818861936382815675.xml

/tmp/out/simulation_1.sedml

false

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

Finished: SOLVER_FINISHED:completed

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

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

Ignoring unsupported output `Figure_3a` while CSV generation.

Ignoring unsupported output `Figure_3b` while CSV generation.

Ignoring unsupported output `Figure_3c` while CSV generation.

Ignoring unsupported output `Figure_3d` while CSV generation.

Generating report `report`.

Python 3.8.5

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (48.2 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 25, 2021 10:53:43 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_5a1c06f4-159a-47fe-a96a-fcbe30f6cc7c4466014668881382492

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Successful translation: SED-ML file simulation.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Succesful model import: SBML file /tmp/temp3794986932334762061.xml

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

Succesful model import: SBML file /tmp/temp4196208162233755703.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/temp1499201947654976370.xml

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

Succesful model import: SBML file /tmp/temp798905520849109548.xml

/tmp/out/simulation.sedml

false

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

Finished: SOLVER_FINISHED:completed

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

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

Solver status: 3

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

values are:

A = NaN

C = Infinity

PrmA = Infinity

PrmA_bound = -Infinity

PrmR = Infinity

PrmR_bound = -Infinity

R = -Infinity

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

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

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

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

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

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@fd413fb

Finished: SOLVER_FINISHED:completed

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

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

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

Finished: SOLVER_FINISHED:completed

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

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

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

Finished: SOLVER_FINISHED:completed

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

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

Ignoring unsupported output `plot2d_Fig_1a` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation.

Ignoring unsupported output `plot2d_Euler_default` while CSV generation.

Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation.

Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation.

Generating report `report_Fig_1a`.

Generating report `report_low_delta_R_det`.

Generating report `report_Euler_default`.

Generating report `report_Euler_small_step_size`.

Generating report `report_Fig_1_c`.

Generating report `report_low_delta_R_stoch`.

Python 3.8.5

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (33.2 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 25, 2021 10:52:50 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_e87d7aad-3932-49a3-b8ca-b66c0906313c6493525222056716405

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Successful translation: SED-ML file simulation.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Succesful model import: SBML file /tmp/temp4606602387840354572.xml

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

Succesful model import: SBML file /tmp/temp1435477795180921283.xml

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

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

/tmp/out/simulation.sedml

false

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

Finished: SOLVER_FINISHED:completed

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

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

Solver status: 3

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

values are:

A = NaN

C = Infinity

PrmA = Infinity

PrmA_bound = -Infinity

PrmR = Infinity

PrmR_bound = -Infinity

R = -Infinity

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

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

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

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

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

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@7ae0cc89

Finished: SOLVER_FINISHED:completed

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

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

Ignoring unsupported output `Figure_2ab` while CSV generation.

Ignoring unsupported output `plot2d_Fig_1a` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation.

Ignoring unsupported output `plot2d_Euler_default` while CSV generation.

Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation.

Generating report `report_Fig_1a`.

Generating report `report_low_delta_R_det`.

Generating report `report_Euler_default`.

Generating report `report_Euler_small_step_size`.

Python 3.8.5

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (19.6 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 25, 2021 10:53:23 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_0093b0ee-9ceb-4e8b-b462-cdca24ae60f01953241588455720225

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Successful translation: SED-ML file simulation.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Succesful model import: SBML file /tmp/temp6198600441799979807.xml

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

Succesful model import: SBML file /tmp/temp6686389509231961889.xml

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

Finished: SOLVER_FINISHED:completed

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

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

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

Finished: SOLVER_FINISHED:completed

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

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

Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation.

Generating report `report_Fig_1_c`.

Generating report `report_low_delta_R_stoch`.

Python 3.8.5

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

Skips
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (8.6 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 25, 2021 10:51:23 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_30fac526-81d1-4eb4-a0af-2f96e5ecc23b6226698110342178886

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp3472731790402295432.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

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

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.8.5

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (8.7 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 25, 2021 10:51:32 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_c50fe89e-5975-498c-a5d7-a05bef312d64814773793438356456

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp5783735917743831139.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

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

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.8.5

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (8.6 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 25, 2021 10:51:40 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_962bb3fe-c5f1-492e-88cf-3858e2dba8dd3886178281442318904

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp922694011302039398.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

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

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.8.5

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (8.6 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 25, 2021 10:51:49 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_0da976e8-e47e-4624-94f9-376cfb95f91556372872265051394

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp7440137445536200016.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

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

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.8.5

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

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

Format: format_3972
Algorithm: KISAO_0000263

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

Log:

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

Format: format_3972
Algorithm: KISAO_0000019

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

Log:

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

Format: format_3240
Algorithm: KISAO_0000019

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

Log:

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

Format: format_9004
Algorithm: KISAO_0000019

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

Log:

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

Format: format_9004
Algorithm: KISAO_0000030

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

Log:

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

Format: format_2585
Algorithm: KISAO_0000088

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

Log:

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

Format: format_2585
Algorithm: KISAO_000019

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

Log:

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

Format: format_2585
Algorithm: KISAO_0000496

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

Log:

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

Format: format_2585
Algorithm: KISAO_0000560

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

Log:

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

Format: format_2585
Algorithm: KISAO_0000560

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

Log:

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

Format: format_2585
Algorithm: KISAO_0000029

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

Log:

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

Format: format_2585
Algorithm: KISAO_0000437

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

Log:

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

Format: format_2585
Algorithm: KISAO_0000449

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

Log:

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

Format: format_9001
Algorithm: KISAO_0000057

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

Log:

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

  Unknown error

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

Jun 25, 2021 10:47:12 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_996fd9dc-075d-4860-a421-40633d88568b2880116998349573383

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

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

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

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

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

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

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

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

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

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

Error importing from SBML : no SBML source.

Unable to initialize bioModel for the given selection

Error importing from SBML : no SBML source.

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

  Unknown error

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

Jun 25, 2021 10:47:14 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_3a17cc6a-55cc-406e-928b-a0169404b1c65008499514590976654

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

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

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

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

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

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

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

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

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

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

Error importing from SBML : no SBML source.

Unable to initialize bioModel for the given selection

Error importing from SBML : no SBML source.

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

Log:

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

Log:

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (8.6 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 25, 2021 10:47:57 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_fc78cfe7-0b3e-447e-87d6-bb795b2f37d18728712919595644482

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp3480702731302124281.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

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

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.8.5

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsComputeModelChanges (9.4 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 25, 2021 10:48:14 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_41a26a2a-1735-4681-9a03-eb0f80451a423561331481464207266

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp4206614518829452491.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

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

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.8.5

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (11.0 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/tmp4nzmyaq8/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 25, 2021 10:48:24 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_9702d876-605a-482b-9ff8-2a2a7725efdd7863579562671077127

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp6013116500156504883.xml

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

/tmp/out/BIOMD0000000912_sim.sedml

false

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

Finished: SOLVER_FINISHED:completed

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

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

/tmp/out/BIOMD0000000912_sim.sedml

false

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

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report__copy_2`.

Python 3.8.5

Traceback (most recent call last):

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

    fire.Fire({

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

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

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

    component, remaining_args = _CallAndUpdateTrace(

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

    component = fn(*varargs, **kwargs)

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

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

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

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

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

HDF conversion failed

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsDataSetsWithDifferentShapes (11.1 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/tmpm5rby0n6/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 25, 2021 10:48:35 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_66bccf06-a128-47da-b414-3c8817747caf6022397743353109324

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp857512743111335306.xml

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

/tmp/out/BIOMD0000000912_sim.sedml

false

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

Finished: SOLVER_FINISHED:completed

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

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

/tmp/out/BIOMD0000000912_sim.sedml

false

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

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Traceback (most recent call last):

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

    fire.Fire({

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

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

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

    component, remaining_args = _CallAndUpdateTrace(

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

    component = fn(*varargs, **kwargs)

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

    report_frames = get_report_dataframes(all_report_dataref, result_out_dir)

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

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

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

    return _read(filepath_or_buffer, kwds)

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

    return parser.read(nrows)

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

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

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

    data = self._reader.read(nrows)

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

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

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

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

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

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

Python 3.8.5

Traceback (most recent call last):

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

    fire.Fire({

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

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

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

    component, remaining_args = _CallAndUpdateTrace(

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

    component = fn(*varargs, **kwargs)

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

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

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

    return _read(filepath_or_buffer, kwds)

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

    return parser.read(nrows)

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

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

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

    data = self._reader.read(nrows)

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

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

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

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

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

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

HDF conversion failed

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsModelAttributeChanges (16.7 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 25, 2021 10:48:53 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_cd99afba-ddea-468f-bec8-0a21b9374a533870576228348859084

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

Successful translation: SED-ML file BIOMD0000000912_sim.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

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

SBML Import: no assignment rules.

SBML Import: no assignment rules.

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

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

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

Succesful model import: SBML file /tmp/temp7694451166807267953.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@f9b5552

Finished: SOLVER_FINISHED:completed

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

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

Generating report `report`.

Python 3.8.5

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsRepeatedTasksWithChanges (11.4 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/tmp7d2asegn/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 25, 2021 10:50:24 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_a5536707-a872-4875-a1fd-10c7b1b859a75380924307225957161

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

java.lang.NullPointerException

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

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

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

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

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

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

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

SED-ML processing for /tmp/vcell_temp_a5536707-a872-4875-a1fd-10c7b1b859a75380924307225957161/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 25, 2021 10:50:26 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_b5849309-a709-4378-b0c8-8870f08454165244170885252777103

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

java.lang.NullPointerException

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

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

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

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

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

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

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

SED-ML processing for /tmp/vcell_temp_b5849309-a709-4378-b0c8-8870f08454165244170885252777103/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

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

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

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

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

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

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

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

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (4.2 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp2j6m9u5d/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 25, 2021 10:50:28 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_657de256-313d-4d69-a5d6-0f52b9f1ca345117705603678303445

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

java.lang.NullPointerException

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

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

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

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

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

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

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

SED-ML processing for /tmp/vcell_temp_657de256-313d-4d69-a5d6-0f52b9f1ca345117705603678303445/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 25, 2021 10:50:30 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_5e7bb006-50a7-455c-b637-333745f0404f9087301452090720590

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

java.lang.NullPointerException

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

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

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

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

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

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

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

SED-ML processing for /tmp/vcell_temp_5e7bb006-50a7-455c-b637-333745f0404f9087301452090720590/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

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

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

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

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

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

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

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

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (2.0 s)
Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpc7s5ro9s/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 25, 2021 10:50:33 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_1f76fbe0-51f0-43bc-bb91-495fcc3c74812129826662868091691

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

java.lang.NullPointerException

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

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

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

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

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

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

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

SED-ML processing for /tmp/vcell_temp_1f76fbe0-51f0-43bc-bb91-495fcc3c74812129826662868091691/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

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

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

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

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

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

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

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

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (2.0 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp9jlnaudi/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 25, 2021 10:50:35 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_a6f9ad72-a702-4ef2-af1b-3c60eedf38866906193849321974843

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

java.lang.NullPointerException

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

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

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

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

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

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

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

SED-ML processing for /tmp/vcell_temp_a6f9ad72-a702-4ef2-af1b-3c60eedf38866906193849321974843/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 (2.0 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmphpd14efx/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 25, 2021 10:50:37 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_512f3445-b902-4323-bc3c-0e96b0d3e9e47006213424590643054

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

java.lang.NullPointerException

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

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

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

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

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

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

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

SED-ML processing for /tmp/vcell_temp_512f3445-b902-4323-bc3c-0e96b0d3e9e47006213424590643054/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 (2.1 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/tmpvdz199o_/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 25, 2021 10:50:39 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_1efcfa21-0584-40f7-a654-aa733c02ae116033680376585343093

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

java.lang.NullPointerException

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

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

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

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

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

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

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

SED-ML processing for /tmp/vcell_temp_1efcfa21-0584-40f7-a654-aa733c02ae116033680376585343093/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

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

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

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

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

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

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

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

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (2.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp075oklkz/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 25, 2021 10:50:41 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_2e0618ce-6fd9-488d-ae7d-75abf20fac8a6398749831104357480

Python 3.8.5

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

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

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

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

SED-ML version level not supported, import may fail

java.lang.NullPointerException

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

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

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

	at org.jli ...

- 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/972900792). 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/972900792).

@jonrkarr All the tests have passed except for the singularity conversion. But I think that error is due to an error in the action caused by the xvfb script. Could you confirm? VCell is ready to push to biosimulators/vcell if so.


design idea

Instead of providing trySetLen and some procs that produce exceptions and some that don't, consider this design instead: Data that does not fit the string is cut off and the string is made to end in \0xff or similar so that it's easy enough to see that a cut had been made. This is almost what Turbo Pascal did except that it added no visible marker.

There's a proc called addTruncate which does almost what you're saying, minus the terminator. That does remind me though, Beef was suggesting to me that I make strings null-terminated under the hood for ease of use with C. I'm not sure if that's something I want to do uniformly, but I was considering having a conditional compilation flag for null terminated strings. What do you think?

It's a bad idea, avoid. Clients of your libraries must then agree on the state of compilation flag.

Using a compilation flag is a horrible idea indeed, I more meant doing it globally or encoding it into a type.
type
  StackStringImpl[Size: static int, isTerminated: static bool] = object
    ...
  StackString[Size: static int] = StackStringImpl[Size, false]
  NulledStackString[Size: static int] = StackStringImpl[Size, True]

Sounds like overkill to me. Just make it zero terminated and then it can be passed to C strings.

Yeah, I'm thinking null-terminated is the best ultimately, since I expect a lib like this would end up being used in environments where you're passing strings to and from C. Are normal Nim strings null-terminated? @Araq

Yes normal Nim strings are null terminated, almost every sane string does.

@beef331 Seems like a legacy thing that stuck and became necessary

Correct but there are more important fights to win. ;-)

@Araq @beef331 Done


Rpa

Support NoBubble for vertex4
Add electron-phonon coupling vertex4
Clean-up
Fix Hubbard-atom test

Codecov Report

Merging #120 (12331a3) into master (6254e8e) will decrease coverage by 10.41%.
The diff coverage is 41.79%.

:exclamation: Current head 12331a3 differs from pull request most recent head 42bf0be. Consider uploading reports for the commit 42bf0be to get more accurate results

:exclamation: Your organization is not using the GitHub App Integration. As a result you may experience degraded service beginning May 15th. Please install the Github App Integration for your organization. Read more.
@@             Coverage Diff             @@
##           master     #120       +/-   ##
===========================================
- Coverage   66.42%   56.01%   -10.41%
===========================================
  Files          32       55       +23
  Lines        1930     3233     +1303
===========================================
+ Hits         1282     1811      +529
- Misses        648     1422      +774

Impacted Files
Coverage Δ

src/FeynmanDiagram.jl
75.00% <ø> (ø)

src/common_new.jl
0.00% <0.00%> (ø)

src/computational_graph/eval.jl
0.00% <0.00%> (ø)

src/computational_graph/operation.jl
0.00% <0.00%> (ø)

src/computational_graph/optimize.jl
0.00% <0.00%> (ø)

src/diagram_tree/DiagTree.jl
14.28% <ø> (ø)

src/diagram_tree/io.jl
66.66% <0.00%> (ø)

src/diagram_tree/operation.jl
76.56% <0.00%> (ø)

src/expression_tree/ExpressionTree.jl
100.00% <ø> (ø)

src/frontend/GV_diagrams/readfile.jl
0.00% <ø> (ø)

... and 31 more


Ability to configure prepend text - like time stamp

Wondering if there's any settings.  Would like the ability to prepend a time stamp to the entry entered.
i.e. result:
[08:32] This is a test entry

This is now in the settings.


Set up /register route with hashed password

Implement the /register route in the backend API using Express. Ensure passwords are hashed using bcrypt or a similar library before saving them in the database.
Reference:

JWT Authentication in Express
Mongoose with Express

I would like to work on this !

Fixed in #23


[CHORE] normalize the cosine bf

Description of changes
Summarize the changes made by this PR.

Improvements & Bug fixes

...

New functionality

...

Test plan
How are these changes tested?

[ ] Tests pass locally with pytest for python, yarn test for js, cargo test for rust

Documentation Changes
Are all docstrings for user-facing APIs updated if required? Do we need to make documentation changes in the docs repository?

[!WARNING]
This pull request is not mergeable via GitHub because a downstack PR is open. Once all requirements are satisfied, merge this PR as a stack on Graphite.
Learn more

#2206  👈
#2205
#2204
main

This stack of pull requests is managed by Graphite. Learn more about stacking.

Join @HammadB and the rest of your teammates on  Graphite


pdf export / print

Bug Report
When I try to print a webpage using firefox or chrome, only the first page is printed. Maybe this is a gitbooks issue, so it would be handy to have pdfs of each article which one could download.
Description
Steps to Reproduce
Steps to reproduce the behavior:

Go to 'https://www.algorithm-archive.org/contents/gaussian_elimination/gaussian_elimination.html'
Show print preview of firefox/chrome

Expected behavior
the full webpage should be shown or there should be a pdf available to download.

For Algorithm Archive Developers

[x] The bug can be reproduced
[x] The bug can be fixed (if not, please explain why not in a comment below)
[x] There is a timeline to fix the bug
[x] The bug has been fixed (Please link the PR)

This has been fixed in #777 (I just forgot to close the issue). Thanks for bringing it up!


www/caddy: Remove port from subdomain since it is unsupported.

Fixes: https://github.com/opnsense/plugins/issues/4024

The subdomain port field has been removed, since it is unsupported. Subdomains track their ports from their parent wildcard domain.
Filling this field out currently will result in site block that does not work properly, since it will not route requests to the upstream.

Merged, thanks!

Only one way to find out:
# opnsense-patch -c plugins c1d162d5681

If it doesn't apply then nothing bad happens.
Cheers,
Franco

@no-usernames-left there is too much going on at the moment to deliver a clean backport. caddy software was updated to 2.8.4 for the upcoming 24.1.9 and there's some overlap in functionality that I don't want to break on a Friday

@fichtner There is nothing in here that needs to be hotfixed right now. Just leaving the port empty in the subdomain is enough. There are a lot of people who use it like that.
Still surprised it took half a year to notice this. XD


Allow using existing key file on login

If the given key on login in empty, keep the existing key file rather
than overwriting it with an empty file. This is useful if you log out
and want to log in again and still use the same key, or if you have
copied over the key file rather than providing it as input.
Before the first commit, an empty key file would be created if key
wasn't specified, and after that commit, the key file would not be
created if the key wasn't specified and stay empty if it was empty.
With the second commit the log command checks the key file if a key is
not specified and exits with an error message if either the key file
couldn't be opened or is empty. If a key is specified, the key file is
just created with it as before.
(Btw, great talk at fosdem!)

Seems ok, I'm a little skeptical on it's value, but I'm overall not against this

(you can ignore the clippy failure, being fixed in #686)

Seems ok, I'm a little skeptical on it's value, but I'm overall not against this

I'd argue that the first commit is useful at least. After registering, I logged out and in again because I like to confirm that the login works and got the credentials I expect. On the key prompt, I assumed it would just use the existing key if I didn't specify anything, so I ended up with an empty key file.
The second commit could be better. I think it makes sense to verify that the key is valid on login, but it would be better to actually verify that it's a valid key. Just checking that it's not empty isn't that useful, especially since you shouldn't end up with an empty key after the first commit. (And I see now that the sync panics if the key isn't valid, so there shouldn't be any security concern with an empty/weak key here).
If we were to add a check that the key is valid, I think it would make sense to also do that check for key values specified at the prompt.


unused_ddic: TABL used in EXPORT

It does not recognize usage in EXPORT ... TO DATABASE table (same for IMPORT/DELETE, I think).

@mbtools try again 2.77.3 published

Works 👍


maven: update gpg key

Signed-off-by: slievrly<EMAIL_ADDRESS>
Ⅰ. Describe what this PR did
gpg key  out of date,  re-generate

Ⅱ. Does this pull request fix one issue?

Ⅲ. Why don't you add test cases (unit test/integration test)?
Ⅳ. Describe how to verify it
Ⅴ. Special notes for reviews

Codecov Report

Merging #3662 (0193cd2) into develop (1c0fccd) will decrease coverage by 0.18%.
The diff coverage is n/a.

:exclamation: Current head 0193cd2 differs from pull request most recent head c08fe7c. Consider uploading reports for the commit c08fe7c to get more accurate results

@@              Coverage Diff              @@
##             develop    #3662      +/-   ##
=============================================
- Coverage      51.99%   51.81%   -0.19%
+ Complexity      3511     3501      -10
=============================================
  Files            639      639
  Lines          21181    21156      -25
  Branches        2630     2588      -42
=============================================
- Hits           11014    10962      -52
  Misses          9080     9080
- Partials        1087     1114      +27

Impacted Files
Coverage Δ
Complexity Δ

...ource/sql/struct/cache/AbstractTableMetaCache.java
72.41% <0.00%> (-17.25%)
8.00% <0.00%> (-1.00%)

...obuf/convertor/BranchRegisterRequestConvertor.java
90.47% <0.00%> (-9.53%)
3.00% <0.00%> (ø%)

...otobuf/convertor/BranchReportRequestConvertor.java
90.90% <0.00%> (-9.10%)
3.00% <0.00%> (ø%)

...obuf/convertor/BranchRollbackRequestConvertor.java
92.00% <0.00%> (-8.00%)
3.00% <0.00%> (ø%)

...otobuf/convertor/GlobalBeginResponseConvertor.java
92.59% <0.00%> (-7.41%)
3.00% <0.00%> (ø%)

...ava/io/seata/server/metrics/MetricsSubscriber.java
72.58% <0.00%> (-6.46%)
6.00% <0.00%> (-1.00%)

...otobuf/convertor/GlobalCommitRequestConvertor.java
93.75% <0.00%> (-6.25%)
3.00% <0.00%> (ø%)

...otobuf/convertor/GlobalStatusRequestConvertor.java
93.75% <0.00%> (-6.25%)
3.00% <0.00%> (ø%)

...obuf/convertor/GlobalRollbackRequestConvertor.java
93.75% <0.00%> (-6.25%)
3.00% <0.00%> (ø%)

...protobuf/convertor/RegisterTMRequestConvertor.java
94.73% <0.00%> (-5.27%)
3.00% <0.00%> (ø%)

... and 29 more