biosimulators_utils package¶
Subpackages¶
- biosimulators_utils.archive package
- biosimulators_utils.biosimulations package
- biosimulators_utils.combine package
- biosimulators_utils.gh_action package
- biosimulators_utils.kisao package
- biosimulators_utils.licensing package
- biosimulators_utils.log package
- biosimulators_utils.model_lang package
- Subpackages
- biosimulators_utils.model_lang.bngl package
- biosimulators_utils.model_lang.cellml package
- biosimulators_utils.model_lang.lems package
- biosimulators_utils.model_lang.neuroml package
- biosimulators_utils.model_lang.rba package
- biosimulators_utils.model_lang.sbml package
- biosimulators_utils.model_lang.smoldyn package
- biosimulators_utils.model_lang.xpp package
- Subpackages
- biosimulators_utils.omex_meta package
- biosimulators_utils.ref package
- biosimulators_utils.report package
- biosimulators_utils.sedml package
- Submodules
- biosimulators_utils.sedml.data_model module
- biosimulators_utils.sedml.exceptions module
- biosimulators_utils.sedml.exec module
- biosimulators_utils.sedml.io module
- biosimulators_utils.sedml.math module
- biosimulators_utils.sedml.model_utils module
- biosimulators_utils.sedml.utils module
- biosimulators_utils.sedml.validation module
- biosimulators_utils.sedml.warnings module
- biosimulators_utils.simulator package
- Submodules
- biosimulators_utils.simulator.cli module
- biosimulators_utils.simulator.data_model module
- biosimulators_utils.simulator.environ module
- biosimulators_utils.simulator.exceptions module
- biosimulators_utils.simulator.exec module
- biosimulators_utils.simulator.io module
- biosimulators_utils.simulator.specs module
- biosimulators_utils.simulator.utils module
- biosimulators_utils.simulator_registry package
- biosimulators_utils.utils package
- biosimulators_utils.viz package
- biosimulators_utils.xml package
Submodules¶
biosimulators_utils.config module¶
Common configuration for simulation tools
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2020-12-29
- Copyright
2020, Center for Reproducible Biomedical Modeling
- License
MIT
- class biosimulators_utils.config.Config(OMEX_METADATA_INPUT_FORMAT=OmexMetadataInputFormat.rdfxml, OMEX_METADATA_OUTPUT_FORMAT=OmexMetadataOutputFormat.rdfxml_abbrev, OMEX_METADATA_SCHEMA=OmexMetadataSchema.biosimulations, VALIDATE_OMEX_MANIFESTS=True, VALIDATE_SEDML=True, VALIDATE_SEDML_MODELS=True, VALIDATE_IMPORTED_MODEL_FILES=True, VALIDATE_OMEX_METADATA=True, VALIDATE_IMAGES=True, VALIDATE_RESULTS=True, ALGORITHM_SUBSTITUTION_POLICY=AlgorithmSubstitutionPolicy.SIMILAR_VARIABLES, COLLECT_COMBINE_ARCHIVE_RESULTS=False, COLLECT_SED_DOCUMENT_RESULTS=False, SAVE_PLOT_DATA=True, REPORT_FORMATS=[<ReportFormat.h5: 'h5'>], VIZ_FORMATS=[<VizFormat.pdf: 'pdf'>], H5_REPORTS_PATH='reports.h5', REPORTS_PATH='reports.zip', PLOTS_PATH='plots.zip', BUNDLE_OUTPUTS=True, KEEP_INDIVIDUAL_OUTPUTS=True, LOG=True, LOG_PATH='log.yml', BIOSIMULATORS_API_ENDPOINT='https://api.biosimulators.org/', BIOSIMULATIONS_API_ENDPOINT='https://api.biosimulations.org/', BIOSIMULATIONS_API_AUTH_ENDPOINT='https://auth.biosimulations.org/oauth/token', BIOSIMULATIONS_API_AUDIENCE='api.biosimulations.org', VERBOSE=False, DEBUG=False)[source]¶
Bases:
object
Configuration
- OMEX_METADATA_INPUT_FORMAT[source]¶
format to validate OMEX Metadata files against
- Type
OmexMetadataInputFormat
- OMEX_METADATA_OUTPUT_FORMAT[source]¶
format to export OMEX Metadata files
- Type
OmexMetadataOutputFormat
- OMEX_METADATA_SCHEMA[source]¶
schema to validate OMEX Metadata files against
- Type
OmexMetadataSchema
- VALIDATE_OMEX_MANIFESTS[source]¶
whether to validate OMEX manifests during the validation of COMBINE/OMEX archives
- Type
bool
- VALIDATE_SEDML[source]¶
whether to validate SED-ML files during the validation of COMBINE/OMEX archives
- Type
bool
- VALIDATE_SEDML_MODELS[source]¶
whether to validate models referenced by SED-ML files during the validation of COMBINE/OMEX archives
- Type
bool
- VALIDATE_OMEX_METADATA[source]¶
whether to validate OMEX metadata (RDF files) during the validation of COMBINE/OMEX archives
- Type
bool
- VALIDATE_IMAGES[source]¶
whether to validate the images in COMBINE/OMEX archives during their validation
- Type
bool
- VALIDATE_RESULTS[source]¶
whether to validate the results of simulations following their execution
- Type
bool
- COLLECT_COMBINE_ARCHIVE_RESULTS[source]¶
whether to assemble an in memory data structure with all of the simulation results of COMBINE/OMEX archives
- Type
bool
- COLLECT_SED_DOCUMENT_RESULTS[source]¶
whether to assemble an in memory data structure with all of the simulation results of SED documents
- Type
bool
- SAVE_PLOT_DATA[source]¶
whether to save data for plots alongside data for reports in CSV/HDF5 files
- Type
bool
- H5_REPORTS_PATH[source]¶
path to save reports in HDF5 format relative to base output directory
- Type
str
- REPORTS_PATH[source]¶
path to save zip archive of reports relative to base output directory
- Type
str
- BUNDLE_OUTPUTS[source]¶
indicates whether bundles of report and plot outputs should be produced
- Type
bool
- KEEP_INDIVIDUAL_OUTPUTS[source]¶
indicates whether the individual output files should be kept
- Type
bool
biosimulators_utils.data_model module¶
Core data model
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2020-12-06
- Copyright
2020, Center for Reproducible Biomedical Modeling
- License
MIT
- class biosimulators_utils.data_model.Identifier(namespace=None, id=None, url=None)[source]¶
Bases:
object
An identifier
- is_equal(other)[source]¶
Determine if identifiers are equal
- Parameters
other (
Identifier
) – another identifier- Returns
True
, if two identifiers are equal- Return type
bool
- class biosimulators_utils.data_model.OntologyTerm(namespace=None, id=None, url=None)[source]¶
Bases:
biosimulators_utils.data_model.Identifier
Term in an ontology
- class biosimulators_utils.data_model.Person(given_name=None, other_name=None, family_name=None)[source]¶
Bases:
object
A person
biosimulators_utils.exceptions module¶
Standard exceptions issued by biosimulation tools
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2020-12-29
- Copyright
2020, Center for Reproducible Biomedical Modeling
- License
MIT
biosimulators_utils.image module¶
Utilities for working with Docker images
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2020-12-06
- Copyright
2020, Center for Reproducible Biomedical Modeling
- License
MIT
- biosimulators_utils.image.convert_docker_image_to_singularity(docker_image, singularity_filename=None)[source]¶
Convert a locally cached Docker image to a Singularity image.
Remotely published Docker images (e.g., images published to Docker Hub, GitHub Container Registry, etc.) should first be pulled (e.g., using
pull_docker_image
ordocker pull {image}
).- Parameters
docker_image (
str
) –singularity_filename (
str
, optional) – file name for saving Singularity image
- Returns
path where Singularity image was saved
- Return type
str
- biosimulators_utils.image.get_docker_image(docker_client, tag, pull=True)[source]¶
Get a Docker image for a simulator
- Parameters
docker_client (
docker.client.DockerClient
) – Docker clienttag (
str
) – tag (e.g.,biosimulators/tellurium
) or URL (ghcr.io/biosimulators/tellurium
) for a Docker image of a simulator
- Returns
Docker image
- Return type
docker.models.images.Image
- biosimulators_utils.image.login_to_docker_registry(registry, username, password)[source]¶
Login to a Docker registry
- Parameters
registry (
str
) – registry (e.g., ghcr.io)username (
str
) – user namepassword (
str
) – password
- Returns
Docker client
- Return type
docker.client.DockerClient
biosimulators_utils.warnings module¶
Standard warnings issued by biosimulation tools
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2020-12-29
- Copyright
2020, Center for Reproducible Biomedical Modeling
- License
MIT