biosimulators_utils.ref package¶
Submodules¶
biosimulators_utils.ref.data_model module¶
Data model for references (e.g., journal articles, books)
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2021-09-05
- Copyright
2021, Center for Reproducible Biomedical Modeling
- License
MIT
- class biosimulators_utils.ref.data_model.JournalArticle(pubmed_id: Optional[str] = None, pubmed_central_id: Optional[str] = None, doi: Optional[str] = None, authors: List[str] = <factory>, title: Optional[str] = None, journal: Optional[str] = None, volume: Optional[str] = None, issue: Optional[str] = None, pages: Optional[str] = None, year: Optional[int] = None, date: Optional[str] = None)[source]¶
Bases:
biosimulators_utils.ref.data_model.Reference
Journal article
biosimulators_utils.ref.utils module¶
Methods for working with references (e.g., journal articles, books)
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2021-09-05
- Copyright
2021, Center for Reproducible Biomedical Modeling
- License
MIT
- biosimulators_utils.ref.utils.get_pubmed_central_open_access_graphics(id, dirname, session=<module 'requests' from '/opt/hostedtoolcache/Python/3.9.9/x64/lib/python3.9/site-packages/requests/__init__.py'>, max_num_ftp_tries=3)[source]¶
Get the open access graphics for a publication in PubMed Central
- Parameters
id (
str
) – PubMed Central iddirname (
str
) – path to save imagessession (
requests.session.Session
) – requests session
- Returns
list of graphics
- Return type
list
ofPubMedCentralOpenAccesGraphic
- biosimulators_utils.ref.utils.get_reference(pubmed_id=None, doi=None, cross_ref_session=<module 'requests' from '/opt/hostedtoolcache/Python/3.9.9/x64/lib/python3.9/site-packages/requests/__init__.py'>)[source]¶
Get data about a reference by its PubMed id and/or DOI
- Parameters
pubmed_id (
str
, optional) – PubMed iddoi (
str
, optional) – DOIsession (
requests.sessions.Session
, optional) – requests session
- Returns
data about a reference
- Return type
JournalArticle