Using the translation table from the Jabref program, finds and replaces all scientific journal names to their standardized abbreviated form. First argument is the file to be processed; outputs safely to 'abbreviated.bib'

Abbreviate Journal Names in Bibtex Database.py

#!/usr/bin/env python
#-*- coding: utf-8 -*-
# Supporting Python 3 and JabRef csv file

import os
import re
import sys

try:
    bibtexdb = open(sys.argv[1]).read()
except IndexError:
    print("Error: specify the file to be processed!")
    exit(1)
except FileNotFoundError:
    print("Error: Provided filename could not be loaded!")
    exit(1)

if not os.path.isfile('journalList.csv'):
    import urllib.request
    urllib.request.urlretrieve(
        "https://raw.githubusercontent.com/JabRef/jabref/master/src/main/"
        "resources/journals/journalList.csv",
        filename="journalList.csv")

rulesfile = open('journalList.csv')

for rule in rulesfile.readlines():
    patterns = rule.split(";")[:2]
    pattern1, pattern2 = map(lambda pattern: "Journal = {%s}" % pattern,
                             patterns)
    # avoid mere abbreviations
    if pattern1 != pattern1.upper() and (' ' in pattern1):
        repl = re.compile(re.escape(pattern1), re.IGNORECASE)
        (bibtexdb, num_subs) = repl.subn(pattern2, bibtexdb)

        if num_subs > 0:
            print("Replaced (%ix) '%s' FOR '%s'" % (num_subs, *patterns))

with open('abbreviated.bib', 'w') as outfile:
    outfile.write(bibtexdb)
    print("Bibtex database with abbreviated files saved into 'abbreviated.bib'")