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 

import sys, os, re

try:    bibtexdb = open(sys.argv[1]).read()
except: print("Error: specify the file to be processed!")

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

for rule in rulesfile.readlines()[::-1]:           ## reversed alphabetical order matches extended journal names first
    pattern1, pattern2 = rule.strip().split(" = ")
    if pattern1 != pattern1.upper() and (' ' in pattern1):        ## avoid mere abbreviations
        #bibtexdb = bibtexdb.replace(pattern1.strip(), pattern2.strip())    ## problem - this is case sensitive
        repl = re.compile(re.escape(pattern1), re.IGNORECASE)               ## this is more robust, although ca. 10x slower
        (bibtexdb, num_subs) = repl.subn(pattern2, bibtexdb)
        if num_subs > 0:
            print "Replacing '%s' FOR '%s'" % (pattern1, pattern2)

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

Check out my latest revision: https://gist.github.com/peci1/4e67f3d0521ce014fc952bcca664b37d/revisions

The text "Replacing..." is only printed when there is at least one successful match for the pattern.

You need to add: import re
Also, to be used in Python 3.0. your print statement should have ().

Thank you all. 👍

Lines 23 and 27 still use print as a statement, but should use it like a function with parantheses.
Also have a look at this awesome resource:
https://pyformat.info/
I highliy recommend the "new" format syntax.

When I using this script in my windows laptop. It gives an error like this:
for rule in rulesfile.readlines()[::-1]: ## reversed alphabetical order matches extended journal names first
UnicodeDecodeError: 'gbk' codec can't decode byte 0x99 in position 7474: illegal multibyte sequence

So what happens ? Thanks.

It seems there is no https://raw.githubusercontent.com/JabRef/jabref/master/src/main/resources/journals/journalList.txt any more. I obtain

6b6b>./Abbreviate\ Journal\ Names\ in\ Bibtex\ Database.py bib.bib
Traceback (most recent call last):
File "./Abbreviate Journal Names in Bibtex Database.py", line 17, in
pattern1, pattern2 = rule.strip().split(" = ")
ValueError: need more than 1 value to unpack

@bergerrjf, you are right, the file has disappeared. I can look for a cached version in my computer, though.

That would be cool!

Is this the missing file?
https://github.com/JabRef/jabref/blob/master/src/main/resources/journals/journalList.csv

https://raw.githubusercontent.com/JabRef/jabref/master/src/main/resources/journals/journalList.csv

Yes it seems so! Though its in csv and not txt.

csv is a txt file. Nothing to worry about.

However, there are changes that make the script useless. I had to change ";" to " = ", remove the ";;" at the end of each line, and remove some odd lines with more than one "=" symbol. Besides that, the script works fine just for one thing: If the journal is also the title of a paper (What is systems biology? -> What is Syst. Biol.?)

I thank you, @FilipDominec for your wonderful work.

For anybody having trouble with the new script referenced by @glucksfall, I attach the good old journalList.txt: https://gist.github.com/FilipDominec/6df14b3424e335c4a47a96640f7f0df9

This was of great help, thanks @FilipDominec !
I updated it to directly process the JabRef CSV and solve the issue mentioned by @glucksfall as well as another one I had, where a subset of the journal name was matched to another journal and then only part of it was abbreviated ("Journal of Medicine" being alphabetically before "New England Journal of Medicine").
I basically updated the regex to find and replace Journal = {pattern}.

I am happy that you find this little script useful. Perhaps should I somehow sync all the improvements in at least 4 modified forks?

I am glad you found it useful. Should I review your changes and possibly sync them with the original script?

…

On Thu, 28 Jan 2021 at 08:47, Shun Arahata ***@***.***> wrote: ***@***.**** commented on this gist. ------------------------------ This tool is really useful. I fix some parts of the code in order to run my Python 3 environment. https://gist.github.com/arahatashun/2d27d5e2694c3f1f25aa5cd624defe5f — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://gist.github.com/9ff081952dbc4aae1df657a56c3db4ea#gistcomment-3610691>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAD47TTZ3VPD2WU4GU6UYHLS4EJAHANCNFSM4KIYT7JQ> .

I found @trevismd's python3 version of code after I posted my code so I deleted mine.

Anyway, providing python3 code explicitly will be helpful for people who come up with this gist.

By the way, what is journalList.txt based on? A journal I try to submit to requires to follow ISSN List of Title Word Abbreviations so I want to know that.
It seems the list is based on JabRef.

@FilipDominec, feel free to reuse any part of my contribution.