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fixbibtex.py
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fixbibtex.py
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#!/usr/bin/env python
"""
BibTeX fixer
------------
Fix your .bib BibTex files automatically
This script will connect to Crossref's API and retrieve
missing details in your bib files.
Set CROSSREF_MAILTO env var to your mail address to
gain access to a priority queue.
It requires `pybtex`, `habanero`, and `tqdm`:
pip install pybtex habanero tqdm
TODO
.....
- String distance comparison to see if the entry matched
in Crossref is not correct
"""
from __future__ import print_function
import os
import sys
if sys.version_info < (3, 5):
raise RuntimeError('fixbibtex requires Python 3.5+')
from copy import copy, deepcopy
from time import sleep
from distutils.spawn import find_executable
import argparse
import asyncio
import concurrent.futures
from difflib import SequenceMatcher
from tqdm import tqdm
from pybtex.errors import set_strict_mode
from pybtex.database import parse_file as parse_bibfile, Person
from habanero import Crossref
cr = Crossref(mailto=os.environ.get('CROSSREF_MAILTO'))
MAX_POOL_WORKERS = int(os.environ.get('FIXBIBTEX_WORKERS', '5'))
COLORS = {
'END': '\33[0m',
'BOLD': '\33[1m',
'ITALIC': '\33[3m',
'URL': '\33[4m',
'BLINK': '\33[5m',
'BLINK2': '\33[6m',
'SELECTED': '\33[7m',
'BLACK': '\33[30m',
'RED': '\33[31m',
'GREEN': '\33[32m',
'YELLOW': '\33[33m',
'BLUE': '\33[34m',
'VIOLET': '\33[35m',
'BEIGE': '\33[36m',
'WHITE': '\33[37m',
'BLACKBG': '\33[40m',
'REDBG': '\33[41m',
'GREENBG': '\33[42m',
'YELLOWBG': '\33[43m',
'BLUEBG': '\33[44m',
'VIOLETBG': '\33[45m',
'BEIGEBG': '\33[46m',
'WHITEBG': '\33[47m',
'GREY': '\33[90m',
'RED2': '\33[91m',
'GREEN2': '\33[92m',
'YELLOW2': '\33[93m',
'BLUE2': '\33[94m',
'VIOLET2': '\33[95m',
'BEIGE2': '\33[96m',
'WHITE2': '\33[97m',
'GREYBG': '\33[100m',
'REDBG2': '\33[101m',
'GREENBG2': '\33[102m',
'YELLOWBG2': '\33[103m',
'BLUEBG2': '\33[104m',
'VIOLETBG2': '\33[105m',
'BEIGEBG2': '\33[106m',
'WHITEBG2': '\33[107m',
}
def cprint(*args, color=None, **kwargs):
if color and color.upper() in COLORS:
print(COLORS[color.upper()], end='')
end = kwargs.pop('end', '\n')
print(*args, end='', **kwargs)
print(COLORS['END'], end=end)
else:
print(*args, **kwargs)
async def fix_bibtex(path):
bib = parse_bibfile(path)
futures = []
loop = asyncio.get_event_loop()
non_article_keys = []
pbar = tqdm(leave=False)
with concurrent.futures.ThreadPoolExecutor(max_workers=MAX_POOL_WORKERS) as executor:
for key, entry in bib.entries.items():
if entry.type != 'article' or 'rxiv.org' in entry.fields.get('url', '') : # skip books, chapters, etc (for now)
non_article_keys.append(key)
continue
futures.append(loop.run_in_executor(executor, find_crossref, (entry, key, pbar)))
pbar.total = len(futures)
for result in await asyncio.gather(*futures):
if result is None:
continue
key, entry, ref = result
if not ref:
continue
doi_in_bibtex = entry.fields.get('doi', '')
title_in_bibtex = entry.fields.get('title', '')
new_entry = update_entry_from_crossref(ref, entry)
if getattr(new_entry, 'similarity', 0) < 0.75: # Fallback with DOI
print('\n! `{}` has low similarity ({:.2f})...'.format(key, new_entry.similarity))
if doi_in_bibtex:
print(' Searching for DOI `{}`...'.format(doi_in_bibtex))
fb_ref = find_crossref_doi(doi_in_bibtex)
if fb_ref:
new_entry_fb = update_entry_from_crossref(fb_ref, entry)
similarity = similar(title_in_bibtex, new_entry_fb.fields['title'])
if similarity < 0.75:
cprint(' Not fixed... :( Similarity with DOI: {:.2f}'.format(similarity), color='red')
else:
cprint(' Fixed! Similarity with DOI: {:.2f}'.format(similarity), color='green')
new_entry = new_entry_fb
else:
cprint(' Wrong DOI!', color='red')
else:
cprint(' No DOI available for fallback search.', color='red')
bib.entries[key] = new_entry
pbar.close()
if len(bib.entries) != len(futures):
print('\n! Skipped', len(bib.entries) - len(futures),
'non-article pieces (book chapters, pre-prints...):\n ',
'\n '.join(non_article_keys))
return bib
def find_crossref(args):
sleep(0.1)
entry, key, pbar = args
query = entry.fields['title']
filters = {}
if 'issn' in entry.fields:
filters['issn'] = entry.fields['issn']
if 'year' in entry.fields:
filters['from-pub-date'] = entry.fields['year']
if 'author' in entry.persons: # add last author to query
query += ' ' + str(entry.persons['author'][-1])
try:
ref = cr.works(query=query, filter=filters)
pbar.update()
except Exception as e:
print('! Could not fetch', key, 'due to error:', e)
pbar.update()
return None, None, None
if ref['message']['items']:
first = ref['message']['items'][0]
return key, entry, first
def find_crossref_doi(doi):
sleep(0.1)
if not doi:
return
try:
ref = cr.works(ids=doi)
except Exception as e:
return
else:
if ref['status'] == 'ok' and ref['message']:
return ref['message']
def update_entry_from_crossref(ref, entry):
entry = copy(entry)
if 'container-title' in ref:
entry.fields['journal'] = ref['container-title'][0]
if 'issue' in ref:
entry.fields['number'] = str(ref['issue'])
if 'page' in ref:
entry.fields['pages'] = str(ref['page']).replace('-', '--')
if 'title' in ref and ref['title']:
entry.similarity = similar(entry.fields['title'], ref['title'][0])
entry.fields['title'] = ref['title'][0]
if 'URL' in ref:
entry.fields['url'] = ref['URL']
if 'volume' in ref:
entry.fields['volume'] = str(ref['volume'])
if 'published-print' in ref: # prioritize print vs online
entry.fields['year'] = str(ref['published-print']['date-parts'][0][0])
elif 'published-online' in ref:
entry.fields['year'] = str(ref['published-online']['date-parts'][0][0])
if 'DOI' in ref:
entry.fields['doi'] = ref['DOI']
if 'ISSN' in ref:
entry.fields['issn'] = ref['ISSN'][0]
if 'author' in ref:
persons = {'author': []}
for author in ref['author']:
if 'family' in author:
authorname = author['family']
if 'given' in author:
authorname += ', ' + author['given']
person = Person(authorname)
else:
# Author is not a person but an organization or similar
person = Person(author['name'])
persons['author'].append(person)
if len(entry.persons.get('author', [])) <= len(persons['author']):
entry.persons = persons
entry.relevance = ref.get('score', 100)
return entry
def similar(a, b):
return SequenceMatcher(None, a.lower(), b.lower()).ratio()
def _difftool():
for tool in 'code --diff', 'colordiff', 'diff':
if find_executable(tool.split()[0]):
return tool
return '<difftool>'
def main(path, strict=False):
set_strict_mode(strict)
loop = asyncio.get_event_loop()
newbib = loop.run_until_complete(fix_bibtex(path))
basename, ext = os.path.splitext(path)
newbib_path = '{}.new{}'.format(basename, ext)
newbib.to_file(newbib_path)
oldbib_path = '{}.old{}'.format(basename, ext)
parse_bibfile(path).to_file(oldbib_path)
print('\nPatched file:', newbib_path)
print('Original file:', oldbib_path)
print('Use a diff tool to see changes:')
print(' ', _difftool(), oldbib_path, newbib_path)
def cli():
parser = argparse.ArgumentParser()
parser.add_argument('path', metavar='FILE', help="BibTex file")
parser.add_argument('--strict', action='store_true', default=False,
help='Transforms warnings into errors (off by default).')
args = parser.parse_args()
main(args.path, args.strict)
if __name__ == '__main__':
cli()