biosimulations_bigg package

Submodules

biosimulations_bigg.config module

biosimulations_bigg.config.get_config(source_api_endpoint='http://bigg.ucsd.edu/api/v2', source_model_file_endpoint='http://bigg.ucsd.edu/static', source_map_file_endpoint='http://bigg.ucsd.edu/escher_map_json', source_dirname=None, source_license_filename=None, sessions_dirname=None, final_dirname=None, curators_filename=None, issues_filename=None, status_filename=None, thumbnails_filename=None, extra_visualizations_filename=None, project_ids=None, first_project=0, max_projects=None, max_num_reactions=None, max_thumbnails=None, update_project_sources=False, update_combine_archives=False, update_simulations=False, update_simulation_runs=False, simulate_projects=True, publish_projects=True, entrez_delay=5.0, bucket_endpoint=None, bucket_name=None, bucket_access_key_id=None, bucket_secret_access_key=None, biosimulations_api_client_id=None, biosimulations_api_client_secret=None, dry_run=False)[source]

Get a configuration

Parameters

  • (obj (extra_visualizations_filename) – str, optional): endpoint for retrieving metadata about BiGG models

  • (obj – str, optional): endpoint for retrieving files for BiGG models

  • (obj – str, optional): endpoint for retrieving files for Escher visualizations

  • (obj – str, optional): directory where source models, metabolic flux maps, and thumbnails should be stored

  • (obj – str, optional): path to BiGG license to copy into COMBINE/OMEX archives

  • (obj – str, optional): directory where cached HTTP sessions should be stored

  • (obj – str, optional): directory where created SED-ML, metadata, and COMBINE/OMEX archives should be stored

  • (obj – str, optional): path which describes the people who helped curator the repository

  • (obj – str, optional): path to issues which prevent some models from being imported

  • (obj – str, optional): path to save the import status of each project

  • (obj – str, optional): path to curated list of good thumbnails

  • (obj – str, optional): path to curated list of additional Escher diagrams to use with projects

  • project_ids (list of str, optional) – ids of projects to import

  • first_project (int, optional) – iteration through projects at which to begin importing

  • max_projects (int, optional) – maximum number of projects to download, convert, execute, and submit; used for testing

  • max_num_reactions (int, optional) – maximum size model to import; used for testing

  • max_thumbnails (int, optional) – maximum number of thumbnails to use; used for testing

  • update_project_sources (bool, optional) – whether to update the source files for the projects; used for testing

  • update_combine_archives (bool, optional) – whether to update COMBINE archives even if they already exist; used for testing

  • update_simulations (bool, optional) – whether to re-run COMBINE archives even if they have already been run; used for testing

  • update_simulation_runs (bool, optional) – whether to update projects even if they have already been imported; used for testing

  • simulate_projects (bool, optional) – whether to simulate projects; used for testing

  • publish_projects (bool, optional) – whether to pushlish projects; used for testing

  • entrez_delay (float, optional) – delay in between Entrez queries

  • bucket_endpoint (str, optional) – endpoint for storage bucket

  • bucket_name (str, optional) – name of storage bucket

  • bucket_access_key_id (str, optional) – key id for storage bucket

  • bucket_secret_access_key (str, optional) – access key for storage bucket

  • biosimulations_api_client_id (str, optional) – id for client to the BioSimulations API

  • biosimulations_api_client_secret (str, optional) – secret for client to the BioSimulations API

  • dry_run (bool, optional) – whether to submit projects to BioSimulations or not; used for testing

Returns

dict: configuration

Return type

obj

biosimulations_bigg.core module

biosimulations_bigg.core.import_projects(config)[source]

Download the source database, convert into COMBINE/OMEX archives, simulate the archives, and submit them to BioSimulations

Parameters

config (dict) – configuration