biosimulators_utils.simulator_registry package¶
Submodules¶
biosimulators_utils.simulator_registry.data_model module¶
Data model for submitting simulators to the BioSimulators registry
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2020-12-06
- Copyright
2020, Center for Reproducible Biomedical Modeling
- License
MIT
- class biosimulators_utils.simulator_registry.data_model.IssueLabel(value)[source]¶
Bases:
str
,enum.Enum
An enumeration.
- class biosimulators_utils.simulator_registry.data_model.SimulatorSubmission(id=None, version=None, specifications_url=None, specifications_patch=None, validate_image=False, commit_simulator=False, validated=False, approved=False, committed=False)[source]¶
Bases:
object
Submission of a simulator to the BioSimulators registry
- specifications_url[source]¶
URL for the specifications of the version of the simulator (e.g., https://raw.githubusercontent.com/biosimulators/Biosimulators_tellurium/2.1.6/biosimulators.json)
- Type
str
- specifications_patch[source]¶
superseding specifications to those at
specifications_url
- Type
dict
- is_equal(other)[source]¶
Determine if two submissions are equal
- Parameters
other (
SimulatorSubmission
) – another submission- Returns
True
, if two submissions are equal- Return type
bool
biosimulators_utils.simulator_registry.process_submission module¶
Methods for processing submissions to the BioSimulators registry
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2020-12-06
- Copyright
2020, Center for Reproducible Biomedical Modeling
- License
MIT
- biosimulators_utils.simulator_registry.process_submission.get_simulator_submission_from_gh_issue_body(body)[source]¶
Get a simulator submission from the YAML-structured data in an issue
- Parameters
body (
str
) – body of a GitHub issue for the submission of a simulator- Returns
simulator submission
- Return type
SimulatorSubmission
biosimulators_utils.simulator_registry.query module¶
Methods for querying the BioSimulators registry
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2020-12-06
- Copyright
2020, Center for Reproducible Biomedical Modeling
- License
MIT
biosimulators_utils.simulator_registry.submit module¶
Methods for submitting simulators to the BioSimulators registry
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2020-12-06
- Copyright
2020, Center for Reproducible Biomedical Modeling
- License
MIT
- biosimulators_utils.simulator_registry.submit.build_gh_issue_body(submission)[source]¶
Build the body of a GitHub issue for the submission of a simulator
- Parameters
submission (
SimulatorSubmission
) – simulator- Returns
body for a GitHub issue for the submission of a simulator
- Return type
str
- biosimulators_utils.simulator_registry.submit.submit_simulator_to_biosimulators_registry(simulator, gh_username, gh_access_token)[source]¶
Submit a version of a simulation tool for review for inclusion in the BioSimulators registry. This will create a GitHub issue which the BioSimulators Team will use to review your submission.
This method requires a GitHub access and personal access token. This access token must have the public_repo scope. Instructions for creating an access token are available in the GitHub documentation <https://docs.github.com/en/free-pro-team@latest/github/authenticating-to-github/creating-a-personal-access-token>_.
- Parameters
simulator (
SimulatorSubmission
) – simulatorgh_username (
str
) – GitHub username (e.g., jonrkarr)gh_access_token (
str
) – GitHub personal access token.
- Raises
requests.exceptions.HTTPError – if the simulator is not successfully submitted for review