How to automatically turn BibTex citation into something parseable by Zotero? - ruby

Question

I have a citation system which publishes users notes to a wiki (Researchr). Programmatically, I have access to the full BibTeX record of each entry, and I also display this on the individual pages (for example - click on BibTeX). This is in the interest of making it easy for users of other citation manager to automatically import the citation of a paper that interests them. I would also like other citation managers, especially Zotero, to be able to automatically detect and import a citation.
Zotero lists a number of ways of exposing metadata that it will understand, including meta tags with RDF, COiNS, Dublin Core and unAPI. Is there a Ruby library for converting BibTeX to any of these standards automatically - or a Javascript library? I could probably create something, but if something existed, it would be far more robust (BibTeX has so many publication types and fields etc).

Answer 1

There's a BibTeX2RDF convertor available here, might be what you're after.

Answer 2

unAPI is not a data standard - it's a way to serve data (to Zotero and other programs). Zotero imports Bibtex, so serving Bibtex via unAPI works just fine. Inspire is an example of a site that does that:
http://inspirehep.net/

Answer 3

By now one can simply import bibtex files of type .bib directly in Zotero. However, I noticed my bibtex files were often less complete than Zotero (in particular they often missed a DOI), and I did not find an "auto-complete" function (based on the data in the bibtex entries) in Zotero.
So I import the .bib file with Zotero, to ensure they are all in there. Then I run a python script that gets all the missing DOI's it can find for the entries in that .bib file, and exports them to a space separated .txt file.:
# pip install habanero
from habanero import Crossref
import re
def titletodoi(keyword):
cr = Crossref()
result = cr.works(query=keyword)
items = result["message"]["items"]
item_title = items[0]["title"]
tmp = ""
for it in item_title:
tmp += it
title = keyword.replace(" ", "").lower()
title = re.sub(r"\W", "", title)
# print('title: ' + title)
tmp = tmp.replace(" ", "").lower()
tmp = re.sub(r"\W", "", tmp)
# print('tmp: ' + tmp)
if title == tmp:
doi = items[0]["DOI"]
return doi
else:
return None
def get_dois(titles):
dois = []
for title in titles:
try:
doi = titletodoi(title)
print(f"doi={doi}, title={title}")
if not doi is None:
dois.append(doi)
except:
pass
# print("An exception occurred")
print(f"dois={dois}")
return dois
def read_titles_from_file(filepath):
with open(filepath) as f:
lines = f.read().splitlines()
split_lines = splits_lines(lines)
return split_lines
def splits_lines(lines):
split_lines = []
for line in lines:
new_lines = line.split(";")
for new_line in new_lines:
split_lines.append(new_line)
return split_lines
def write_dois_to_file(dois, filename, separation_char):
textfile = open(filename, "w")
for doi in dois:
textfile.write(doi + separation_char)
textfile.close()
filepath = "list_of_titles.txt"
titles = read_titles_from_file(filepath)
dois = get_dois(titles)
write_dois_to_file(dois, "dois_space.txt", " ")
write_dois_to_file(dois, "dois_per_line.txt", "\n")
The DOIs of the .txt are fed into magic wand of Zotero. Next, I (manually) remove the duplicates by choosing the latest added entry (because that comes from the magic wand with the most data).
After that, I run another script to update all the reference id's in my .tex and .bib files to those generated by Zotero:
# Importing library
import bibtexparser
from bibtexparser.bparser import BibTexParser
from bibtexparser.customization import *
import os, fnmatch
import Levenshtein as lev
# Let's define a function to customize our entries.
# It takes a record and return this record.
def customizations(record):
"""Use some functions delivered by the library
:param record: a record
:returns: -- customized record
"""
record = type(record)
record = author(record)
record = editor(record)
record = journal(record)
record = keyword(record)
record = link(record)
record = page_double_hyphen(record)
record = doi(record)
return record
def get_references(filepath):
with open(filepath) as bibtex_file:
parser = BibTexParser()
parser.customization = customizations
bib_database = bibtexparser.load(bibtex_file, parser=parser)
# print(bib_database.entries)
return bib_database
def get_reference_mapping(main_filepath, sub_filepath):
found_sub = []
found_main = []
main_into_sub = []
main_references = get_references(main_filepath)
sub_references = get_references(sub_filepath)
for main_entry in main_references.entries:
for sub_entry in sub_references.entries:
# Match the reference ID if 85% similair titles are detected
lev_ratio = lev.ratio(
remove_curly_braces(main_entry["title"]).lower(),
remove_curly_braces(sub_entry["title"]).lower(),
)
if lev_ratio > 0.85:
print(f"lev_ratio={lev_ratio}")
if main_entry["ID"] != sub_entry["ID"]:
print(f'replace: {sub_entry["ID"]} with: {main_entry["ID"]}')
main_into_sub.append([main_entry, sub_entry])
# Keep track of which entries have been found
found_sub.append(sub_entry)
found_main.append(main_entry)
return (
main_into_sub,
found_main,
found_sub,
main_references.entries,
sub_references.entries,
)
def remove_curly_braces(string):
left = string.replace("{", "")
right = left.replace("{", "")
return right
def replace_references(main_into_sub, directory):
for pair in main_into_sub:
main = pair[0]["ID"]
sub = pair[1]["ID"]
print(f"replace: {sub} with: {main}")
# UNCOMMENT IF YOU WANT TO ACTUALLY DO THE PRINTED REPLACEMENT
# findReplace(latex_root_dir, sub, main, "*.tex")
# findReplace(latex_root_dir, sub, main, "*.bib")
def findReplace(directory, find, replace, filePattern):
for path, dirs, files in os.walk(os.path.abspath(directory)):
for filename in fnmatch.filter(files, filePattern):
filepath = os.path.join(path, filename)
with open(filepath) as f:
s = f.read()
s = s.replace(find, replace)
with open(filepath, "w") as f:
f.write(s)
def list_missing(main_references, sub_references):
for sub in sub_references:
if not sub["ID"] in list(map(lambda x: x["ID"], main_references)):
print(f'the following reference has a changed title:{sub["ID"]}')
latex_root_dir = "some_path/"
main_filepath = f"{latex_root_dir}latex/Literature_study/zotero.bib"
sub_filepath = f"{latex_root_dir}latex/Literature_study/references.bib"
(
main_into_sub,
found_main,
found_sub,
main_references,
sub_references,
) = get_reference_mapping(main_filepath, sub_filepath)
replace_references(main_into_sub, latex_root_dir)
list_missing(main_references, sub_references)
# For those references which have levenshtein ratio below 85 you can specify a manual swap:
manual_swap = [] # main into sub
# manual_swap.append(["cantley_impact_2021","cantley2021impact"])
# manual_swap.append(["widemann_envision_2021","widemann2020envision"])
for pair in manual_swap:
main = pair[0]
sub = pair[1]
print(f"replace: {sub} with: {main}")
# UNCOMMENT IF YOU WANT TO ACTUALLY DO THE PRINTED REPLACEMENT
# findReplace(latex_root_dir, sub, main, "*.tex")
# findReplace(latex_root_dir, sub, main, "*.bib")