Parse URLs for DOIs, PubMed identifiers, PMC identifiers, arXiv identifiers, etc.
This module has a single parse() function that takes in a URL and gives back
a parse status (success, unknown, or irreconcilable), a prefix, and
an identifier. If the status is unknown or irreconcilable, the prefix will
be left as None and the identifier will match the input:
>>> from citation_url import parse, Status
>>> parse("https://joss.theoj.org/papers/10.21105/joss.01708")
(Status.success, 'doi', '10.21105/joss.01708')
>>> parse("http://www.ncbi.nlm.nih.gov/pubmed/34739845")
(Status.success, 'pubmed', '34739845')
>>> parse("https://example.com/true-garbage")
(Status.unknown, None, 'https://example.com/true-garbage')
>>> parse("https://example.com/true-garbage")
(Status.unknown, None, 'https://example.com/true-garbage')
>>> parse("http://msb.embopress.org/content/13/11/954.full.pdf")
(Status.irreconcilable, None, 'http://msb.embopress.org/content/13/11/954.full.pdf')I wanted to be able to curate a list of papers in
Zotero, Mendeley, or any
other modern citation manager, make an XML export in the EndNote format, extract
and normalize the messy contents in the electronic-resource-num, text-urls,
and pdf-urls fields, then ensure that there are corresponding entries
on Wikidata using the Su Lab's
Wikidata Integrator.
Reuse this functionality with:
$ python -m citation_url.endnote --helpThe most recent release can be installed from PyPI with:
$ pip install citation_urlThe most recent code and data can be installed directly from GitHub with:
$ pip install git+https://github.com/cthoyt/citation-url.gitContributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.
The code in this package is licensed under the MIT License.
This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.
See developer instrutions
The final section of the README is for if you want to get involved by making a code contribution.
To install in development mode, use the following:
$ git clone git+https://github.com/cthoyt/citation-url.git
$ cd citation-url
$ pip install -e .After cloning the repository and installing tox with pip install tox, the unit tests in the tests/ folder can be
run reproducibly with:
$ toxAdditionally, these tests are automatically re-run with each commit in a GitHub Action.
$ tox -e docsAfter installing the package in development mode and installing
tox with pip install tox, the commands for making a new release are contained within the finish environment
in tox.ini. Run the following from the shell:
$ tox -e finishThis script does the following:
- Uses Bump2Version to switch the version number in the
setup.cfgandsrc/citation_url/version.pyto not have the-devsuffix - Packages the code in both a tar archive and a wheel
- Uploads to PyPI using
twine. Be sure to have a.pypircfile configured to avoid the need for manual input at this step - Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
- Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can
use
tox -e bumpversion minorafter.