Skip to content

Instantly share code, notes, and snippets.

  • Star 14 You must be signed in to star a gist
  • Fork 11 You must be signed in to fork a gist
Star You must be signed in to star a gist
Save FilipDominec/9ff081952dbc4aae1df657a56c3db4ea to your computer and use it in GitHub Desktop.
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'
#!/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'"
@peci1
Copy link

peci1 commented May 10, 2016

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.

@jskDr
Copy link

jskDr commented Oct 17, 2016

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

@FilipDominec
Copy link
Author

Thank you all. 👍

@thorade
Copy link

thorade commented Feb 16, 2017

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.

@kuangyia
Copy link

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.

@bergerrjf
Copy link

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

@FilipDominec
Copy link
Author

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

@bergerrjf
Copy link

That would be cool!

@glucksfall
Copy link

@bergerrjf
Copy link

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

@glucksfall
Copy link

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.

@FilipDominec
Copy link
Author

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

@trevismd
Copy link

trevismd commented Jun 4, 2020

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}.

@FilipDominec
Copy link
Author

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

@FilipDominec
Copy link
Author

FilipDominec commented Jan 28, 2021 via email

@arahatashun
Copy link

arahatashun commented Jan 28, 2021

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.

@trevismd
Copy link

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

@GuusAvis
Copy link

For my own use, I took the code posted by @arahatashun and updated it to pull the latest version of the JabRef lists, which have moved to abbrv.jabref.org and switched to CSV files. It can be found here, in case anyone is interested.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment