Package of tools for formatting publication data and accessing data from PubMed's Entrez tool
- entrez - streamlines BioPython
- citations - creates citations for 6 different types using IMS standards
- date - formats dates into our desired format
- sanitizer - mostly useful for forcing unicode compliance in python2
Citations are based on a standard defined by PubMed https://www.ncbi.nlm.nih.gov/books/NBK7256/. For some publication types, passing the italicize parameter with a True value will return HTML with italic tagged journals or conference names.
The journals module uses the PMC source file https://www.ncbi.nlm.nih.gov/pmc/journals/?format=csv to construct a library of journals keyed by abbreviation or full title.
[3.0.1] - 22 Aug 2019
- journals module reconfigured to not write to disk on startup
[3.0] - 12 Aug 2019
- Exlusively supports python 3
[2.1] - unreleased
- Redesign of citation with abstract behavior.
- "italicize" option has been replaced with an "html" option and does not do any safe escape
- add docstrings to citation functions
[2.0.2] - 25 Jan 2019
- Revert safe_unicode use but have it be only applicable for python 2. Not an issue in python 3
- Unescape all fields except title and abstract if using the "escape" parameter. Those two fields are treated as HTML if escape is false all other fields are plain text
[2.0] - 17 October 2018
- Six implementation with support for python 2 and 3 [hoskins]
[1.7] - 10 May 2018
- Refactor some entrez functions to make it more obvious what the API endpoints are
- Convert docstring of all intended end point functions to reST
- Add ability to find publication by PMC ID. This is done by querying the PMC database
- Refactor generate_search_query slightly
[1.6] - 1 March 2018
- Fixed the book REST API calls to allow for failure
- book REST API calls now use requests module
- the isbndb.com database is now a paid service only. It should work but I don't have a service to verify this
- Citations can now be generated as plain text without tags on journals, etc. It defaults to true here but will default to false in a future release.
- Removed some unused parameters from citation functions
- Cleaned up unit tests
- Fixed issue with eCollection dates in citations
- Refactor and reformat for pep8
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