Closed jonrkarr closed 3 years ago
Thank you @jonrkarr 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 is available here.
The specifications of your simulator is valid!
Executed 35 test cases
Passed 10 test cases:
cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
Failed 16 test cases:
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
exec_status_report.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint
results_report.SimulatorGeneratesReportsOfSimultionResults
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Skipped 9 test cases:
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
(2.9 s)Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.
Exception:
The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.4' could not execute the archive:
Unknown error
Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
simulation_1.sedml:
Tasks (1):
simulation_1
Reports (1):
simulation_1: 20 data sets
Executing SED-ML file 0: simulation_1.sedml
Found 1 tasks
simulation_1
Executing task 1: simulation_1
argument 'solver=<class 'gillespy2.solvers.numpy.ssa_solver.NumPySSASolver'>' to run() failed. Reason Given: name 'Clog' is not defined
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
(3.1 s)Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files.
Exception:
The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.4' could not execute the archive:
Unknown error
Log:
Found 2 SED-ML documents with 2 models, 2 simulations, 2 tasks, 2 reports, and 0 plots:
__copy__simulation_1.sedml:
Tasks (1):
simulation_1
Reports (1):
simulation_1: 20 data sets
simulation_1.sedml:
Tasks (1):
simulation_1
Reports (1):
simulation_1: 20 data sets
Executing SED-ML file 0: __copy__simulation_1.sedml
Found 1 tasks
simulation_1
Executing task 1: simulation_1
argument 'solver=<class 'gillespy2.solvers.numpy.ssa_solver.NumPySSASolver'>' to run() failed. Reason Given: name 'Clog' is not defined
exec_status_report.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
(2.8 s)Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.
Exception:
The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.4' could not execute the archive:
Unknown error
Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
simulation_1.sedml:
Tasks (1):
simulation_1
Reports (1):
simulation_1: 20 data sets
Executing SED-ML file 0: simulation_1.sedml
Found 1 tasks
simulation_1
Executing task 1: simulation_1
argument 'solver=<class 'gillespy2.solvers.numpy.ssa_solver.NumPySSASolver'>' to run() failed. Reason Given: name 'Clog' is not defined
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint
(2.8 s)Required model formats and simulation algorithms for SED tasks:
Format: format_2585
Algorithm: KISAO_0000029
Exception:
The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.4' could not execute the archive:
Unknown error
Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
simulation_1.sedml:
Tasks (1):
simulation_1
Reports (1):
simulation_1: 20 data sets
Executing SED-ML file 0: simulation_1.sedml
Found 1 tasks
simulation_1
Executing task 1: simulation_1
argument 'solver=<class 'gillespy2.solvers.numpy.ssa_solver.NumPySSASolver'>' to run() failed. Reason Given: name 'Clog' is not defined
results_report.SimulatorGeneratesReportsOfSimultionResults
(2.8 s)Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.
Exception:
The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.4' could not execute the archive:
Unknown error
Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
simulation_1.sedml:
Tasks (1):
simulation_1
Reports (1):
simulation_1: 20 data sets
Executing SED-ML file 0: simulation_1.sedml
Found 1 tasks
simulation_1
Executing task 1: simulation_1
argument 'solver=<class 'gillespy2.solvers.numpy.ssa_solver.NumPySSASolver'>' to run() failed. Reason Given: name 'Clog' is not defined
sedml.SimulatorProducesLinear2DPlots
(2.8 s)Test that a simulator produces linear 2D plots
Exception:
The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.4' could not execute the archive:
Unknown error
Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
simulation_1.sedml:
Tasks (1):
simulation_1
Plots (1):
plot_0: 20 curves
Executing SED-ML file 0: simulation_1.sedml
Found 1 tasks
simulation_1
Executing task 1: simulation_1
argument 'solver=<class 'gillespy2.solvers.numpy.ssa_solver.NumPySSASolver'>' to run() failed. Reason Given: name 'Clog' is not defined
sedml.SimulatorProducesLinear3DPlots
(2.8 s)Test that a simulator produces linear 3D plots
Exception:
The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.4' could not execute the archive:
Unknown error
Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
simulation_1.sedml:
Tasks (1):
simulation_1
Plots (1):
plot_0: 20 surfaces
Executing SED-ML file 0: simulation_1.sedml
Found 1 tasks
simulation_1
Executing task 1: simulation_1
argument 'solver=<class 'gillespy2.solvers.numpy.ssa_solver.NumPySSASolver'>' to run() failed. Reason Given: name 'Clog' is not defined
sedml.SimulatorProducesLogarithmic2DPlots
(2.8 s)Test that a simulator produces logarithmic 2D plots
Exception:
The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.4' could not execute the archive:
Unknown error
Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
simulation_1.sedml:
Tasks (1):
simulation_1
Plots (1):
plot_0: 20 curves
Executing SED-ML file 0: simulation_1.sedml
Found 1 tasks
simulation_1
Executing task 1: simulation_1
argument 'solver=<class 'gillespy2.solvers.numpy.ssa_solver.NumPySSASolver'>' to run() failed. Reason Given: name 'Clog' is not defined
sedml.SimulatorProducesLogarithmic3DPlots
(2.9 s)Test that a simulator produces logarithmic 3D plots
Exception:
The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.4' could not execute the archive:
Unknown error
Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
simulation_1.sedml:
Tasks (1):
simulation_1
Plots (1):
plot_0: 20 surfaces
Executing SED-ML file 0: simulation_1.sedml
Found 1 tasks
simulation_1
Executing task 1: simulation_1
argument 'solver=<class 'gillespy2.solvers.numpy.ssa_solver.NumPySSASolver'>' to run() failed. Reason Given: name 'Clog' is not defined
sedml.SimulatorProducesMultiplePlots
(2.8 s)Test that a simulator produces multiple plots
Exception:
The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.4' could not execute the archive:
Unknown error
Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 2 plots:
simulation_1.sedml:
Tasks (1):
simulation_1
Plots (2):
plot_0: 10 curves
plot_1: 10 curves
Executing SED-ML file 0: simulation_1.sedml
Found 1 tasks
simulation_1
Executing task 1: simulation_1
argument 'solver=<class 'gillespy2.solvers.numpy.ssa_solver.NumPySSASolver'>' to run() failed. Reason Given: name 'Clog' is not defined
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
(2.8 s)Test that that the curated number of output dimensions matches the actual number of output dimensions
Exception:
The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.4' could not execute the archive:
Unknown error
Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
simulation_1.sedml:
Tasks (1):
simulation_1
Reports (1):
simulation_1: 20 data sets
Executing SED-ML file 0: simulation_1.sedml
Found 1 tasks
simulation_1
Executing task 1: simulation_1
argument 'solver=<class 'gillespy2.solvers.numpy.ssa_solver.NumPySSASolver'>' to run() failed. Reason Given: name 'Clog' is not defined
sedml.SimulatorSupportsModelAttributeChanges
(2.8 s)Test that a simulator supports changes to the attributes of model elements
Exception:
The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.4' could not execute the archive:
Unknown error
Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
simulation_1.sedml:
Tasks (1):
simulation_1
Reports (1):
simulation_1: 20 data sets
Executing SED-ML file 0: simulation_1.sedml
Found 1 tasks
simulation_1
Executing task 1: simulation_1
argument 'solver=<class 'gillespy2.solvers.numpy.ssa_solver.NumPySSASolver'>' to run() failed. Reason Given: name 'Clog' is not defined
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
(2.9 s)Test that a simulator supports the core elements of SED: models, simulations, tasks, data generators for individual variables, and reports
Exception:
The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.4' could not execute the archive:
Unknown error
Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
simulation_1.sedml:
Tasks (1):
simulation_1
Reports (1):
simulation_1: 20 data sets
Executing SED-ML file 0: simulation_1.sedml
Found 1 tasks
simulation_1
Executing task 1: simulation_1
argument 'solver=<class 'gillespy2.solvers.numpy.ssa_solver.NumPySSASolver'>' to run() failed. Reason Given: name 'Clog' is not defined
sedml.SimulatorSupportsMultipleReportsPerSedDocument
(2.8 s)Test that a simulator supports multiple reports per SED document
Exception:
The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.4' could not execute the archive:
Unknown error
Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 2 reports, and 0 plots:
simulation_1.sedml:
Tasks (1):
simulation_1
Reports (2):
report_1: 10 data sets
report_2: 11 data sets
Executing SED-ML file 0: simulation_1.sedml
Found 1 tasks
simulation_1
Executing task 1: simulation_1
argument 'solver=<class 'gillespy2.solvers.numpy.ssa_solver.NumPySSASolver'>' to run() failed. Reason Given: name 'Clog' is not defined
sedml.SimulatorSupportsMultipleTasksPerSedDocument
(3.1 s)Test that a simulator supports multiple tasks per SED document
Exception:
The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.4' could not execute the archive:
Unknown error
Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:
simulation_1.sedml:
Tasks (2):
simulation_1
simulation_1__test_suite_copy
Reports (2):
simulation_1: 20 data sets
simulation_1__test_suite_copy: 20 data sets
Executing SED-ML file 0: simulation_1.sedml
Found 2 tasks
simulation_1
simulation_1__test_suite_copy
Executing task 1: simulation_1
argument 'solver=<class 'gillespy2.solvers.numpy.ssa_solver.NumPySSASolver'>' to run() failed. Reason Given: name 'Clog' is not defined
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
(2.8 s)Test that a simulator supports time courses with non-zero output start times
Exception:
The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.4' could not execute the archive:
Unknown error
Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
simulation_1.sedml:
Tasks (1):
simulation_1
Reports (1):
simulation_1: 20 data sets
Executing SED-ML file 0: simulation_1.sedml
Found 1 tasks
simulation_1
Executing task 1: simulation_1
argument 'solver=<class 'gillespy2.solvers.numpy.ssa_solver.NumPySSASolver'>' to run() failed. Reason Given: name 'Clog' is not defined
cli.CliDescribesSupportedEnvironmentVariablesInline
(11.2 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:
cli.CliDisplaysVersionInformationInline
(3.9 s)Test that a command-line interface provides version information inline.
Warnings:
Command-line interface should support the `-v` option for displaying version information inline.
The command-line interface displayed the following when executed with `-v`:
GillesPy2: 1.5.4, CLI: 0.1.16, Python: 3.7.9, OS: Linux debian 10.7 5.4.0-1032-azure, Machine: x86_64
Command-line interface should support the `--version` option for displaying version information inline.
The command-line interface displayed the following when executed with `--version`:
GillesPy2: 1.5.4, CLI: 0.1.16, Python: 3.7.9, OS: Linux debian 10.7 5.4.0-1032-azure, Machine: x86_64
Log:
docker_image.DeclaresSupportedEnvironmentVariables
(2.0 s)Test if a Docker image declares the environment variables that is supports
Warnings:
Docker images for simulation tools should declare the environment variables that they support.
The Docker image does not declare the following standard environment variables recognized by BioSimulators:
- 'ALGORITHM_SUBSTITUTION_POLICY'
If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.
Note, support for these environment variables is optional. Simulation tools are not required to support these variables.
Log:
docker_image.HasBioContainersLabels
(1.1 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:
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
(2.9 s)Test that a simulator supports multiple time courses with non-zero initial times
Warnings:
The image 'ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.4' could not execute the archive:
Unknown error
Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
simulation_1.sedml:
Tasks (1):
simulation_1
Reports (1):
simulation_1: 20 data sets
Executing SED-ML file 0: simulation_1.sedml
Found 1 tasks
simulation_1
Executing task 1: simulation_1
Initial simulation time 50.0 is not supported. Initial time must be 0.
- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
Rejecting GillesPy2 1.5.4 because it doesn't correctly handle species with ids that include "ln". This is fixed in GillesPy2 1.5.7.
id: gillespy2 version: 1.5.4 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_GillesPy2/e5db0434dc18125b8147f1335cb3c85a5e16e45b/biosimulators.json specificationsPatch: version: 1.5.4 image: url: ghcr.io/biosimulators/biosimulators_gillespy2/gillespy2:1.5.4 validateImage: true commitSimulator: true