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

Bases: 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

get_uri()[source]#

Get a standard URI for the citation (e.g. http://identifiers.org/doi/10.1007/BF00713556).

Returns:: formatted URI
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: str | None = None, label: str | None = None, caption: str | None = None, filename: str | None = 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

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
License:: MIT

biosimulators_utils.ref.utils.get_pubmed_central_open_access_graphics(id, dirname, session=<module 'requests' from '/home/runner/work/Biosimulators_utils/Biosimulators_utils/.venv/lib/python3.10/site-packages/requests/__init__.py'>)[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 '/home/runner/work/Biosimulators_utils/Biosimulators_utils/.venv/lib/python3.10/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