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.

action_error = 'Action error'[source]
approved = 'Approved'[source]
invalid = 'Invalid'[source]
validated = 'Validated'[source]
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

id[source]

id of simulator (e.g., tellurium or vcell)

Type

str

version[source]

version of simulator (e.g., 2.1.6)

Type

str

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

validate_image[source]

if True, validate Docker image

Type

bool

commit_simulator[source]

if True, commit simulator to database

Type

bool

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

to_tuple()[source]

Tuple representation of a person

Returns

tuple representation of a person

Return type

tuple of str

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.query.get_simulator_version_specs(id)[source]

Get the specifications of the versions of a simulator in the BioSimulators registry

Parameters

id (str) – simulator id

Returns

specifications of the registered versions of the simulator

Return type

list of dict

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) – simulator

  • gh_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