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This is a little tool to find freely available, open-access PDFs for articles in a Bibtex file, and to alter the Bibtex file so that it points to these PDF files.

The tool is quite specific to the use-case I had, but the included functions might be useful in other contexts.

It requires an installation of requests (https://github.com/kennethreitz/requests/) and bibtexparser (https://github.com/sciunto-org/python-bibtexparser)

Here's what it does when executed as a script (change SOURCE_FILENAME and TARGET_FILENAME in the source code directly to adapt to your system):

  1. Go through the Bibtex file and check for each entry whether it has an URL with a Pubmed link (http://www.ncbi.nlm.nih.gov/pubmed/...)
  2. Check whether PubMedCentral has a PDF for this article (following up redirections if necessary)
  3. If yes, replace the URL in the Bibtex file with the URL to the PDF; if no, delete the URL (if we have a link to the article via the DOI field)

Please note that I am not particularly interested in extending this into a fully-featured package that does a lot more than that. This was mostly a one-use script that I am sharing just in case it is useful to anyone.