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Save FilipDominec/9ff081952dbc4aae1df657a56c3db4ea to your computer and use it in GitHub Desktop.
| #!/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'" |
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
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 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.
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.
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.