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

pubmed_id[source]

PubMed id

Type

str

pubmed_central_id[source]

PubMed Central id

Type

str

doi[source]

DOI

Type

str

authors[source]

authors

Type

list of str

title[source]

title

Type

str

journal[source]

journal

Type

str

volume[source]

volume

Type

str

issue[source]

issue

Type

str

pages[source]

pages

Type

str

year[source]

year

Type

str

date[source]

publication date

Type

str

authors: List[str][source]
date: str = None[source]
doi: str = None[source]
get_citation()[source]

Format a citation for a reference (e.g., “Authors. Title. Journal volume, issue: pages (year)”.).

Returns

formatted citation for a reference

Return type

str

issue: str = None[source]
journal: str = None[source]
pages: str = None[source]
pubmed_central_id: str = None[source]
pubmed_id: str = None[source]
title: str = None[source]
volume: str = None[source]
year: int = None[source]
class biosimulators_utils.ref.data_model.PubMedCentralOpenAccesGraphic(id: Optional[str] = None, label: Optional[str] = None, caption: Optional[str] = None, filename: Optional[str] = None)[source]

Bases: object

A PubMed Central open access graphic

id[source]

PubMed Central id

Type

str

label[source]

label (e.g., Figure 1)

Type

str

caption[source]

caption

Type

str

filename[source]

local path to JPEG file for graphic

Type

str

caption: str = None[source]
filename: str = None[source]
id: str = None[source]
label: str = None[source]
class biosimulators_utils.ref.data_model.Reference[source]

Bases: abc.ABC

abstract get_citation()[source]

Get a human-readable citation for a reference

Returns

human-readable citation

Return type

str

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 id

  • dirname (str) – path to save images

  • session (requests.session.Session) – requests session

Returns

list of graphics

Return type

list of PubMedCentralOpenAccesGraphic

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 id

  • doi (str, optional) – DOI

  • session (requests.sessions.Session, optional) – requests session

Returns

data about a reference

Return type

JournalArticle