lelouchlamperougevi / pmcbib

Validate bibtex files against PubMed database

pmcbib

If you're anything like me, then you probably use a citation manager such as Mendeley or Zotero, and use the browser plugin to conveniently add citations to your library. Everything is rainbows and unicorns until it's time for dissemination 😱. Enter pmcbib, a friendly utility written in python that checks your .bib file against the PubMed database to find all the fudge-ups.

version 0.0.2.dev1 added support for aliasing and makes use of stdout/stderr (see example use case)

Dependencies

• python 3.7
• metapub
• bibtexparser
• python-Levenshtein
• internet connection (duh!)

Installation

pip install git+https://github.com/LelouchLamperougeVI/pmcbib.git

Usage

pmcbib [-h] [-c config.json] [-o] [-r report.md] [-v] [-w L] file.bib

positional arguments:
  file.bib              ye olde bibtex file

optional arguments:
  -h, --help            show this help message and exit
  -c config.json, --config config.json
                        config file
  -o, --output          output automatically corrected bibtex entries on
                        STDOUT
  -r report.md, --report report.md
                        report outputted as a MarkDown file (default no
                        output)
  -v, --verbose         turn on verbose (overwrites -w)
  -w L, --warn L        minimum warning level to report on console (STDERR)

Examples

Generate a report for a given bibtex file

pmcbib -r report.md example.bib

to suppress warning messages:
pmcbib -r report.md -w 4 example.bib
or
pmcbib -r report.md example.bib 2> /dev/null

Automatically correct bibtex file and save as separate file

pmcbib -o example.bib > corrected.bib

pmcbib will automatically try to fix identified issues. However, it is strongly recommended for the user to go over the report before committing to the output.

Use custom configuration file

pmcbib -c ~/.config/pmcbib/config.json example.bib