Plug arXiv

This commit is contained in:
Lucas Verney 2015-12-23 22:18:52 +01:00
parent a299cc7816
commit 985304446c
2 changed files with 161 additions and 16 deletions

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@ -13,4 +13,5 @@ For building `opendetex` (which is a necessary dependency), you will need
## Usage
`./main.py some_file.bbl` to get a list of DOIs associated to each `\bibitem`.
* `./main.py some_file.bbl` to get a list of DOIs associated to each `\bibitem`.
* `./main.py arxiv_eprint_id` to get a list of DOIs associated to each reference from the provided arXiv eprint.

168
main.py
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@ -1,10 +1,24 @@
#!/usr/bin/env python3
import io
import math
import os
import re
import requests
import subprocess
import sys
import tarfile
regex_urls = re.compile(r"http[s]?://(?:[a-zA-Z]|[0-9]|[$-_@.&+]|[!*\(\),]|(?:%[0-9a-fA-F][0-9a-fA-F]))+")
regex_bibitems = re.compile(r"\\bibitem\{.+?\}")
regex_endthebibliography = re.compile(r"\\end\{thebibliography}")
def clean_whitespaces(text):
"""
Remove double whitespaces and trailing . and , from text.
"""
return ' '.join(text.strip().rstrip(".,").split())
def oa_from_doi(doi):
@ -18,34 +32,103 @@ def oa_from_doi(doi):
def clean_bibitem(bibitem):
"""
Return a plaintext representation of the bibitem from the bbl file.
Params:
- bibitem is the text content of the bibitem.
Returns a cleaned plaintext citation from the bibitem.
"""
script_dir = os.path.dirname(os.path.abspath(__file__))
output = subprocess.check_output([script_dir + "/opendetex/delatex", "-s"],
output = subprocess.check_output(["%s/opendetex/delatex" % (script_dir,),
"-s"],
input=bibitem.encode("utf-8"))
output = output.decode("utf-8")
output = ' '.join(output.strip().rstrip(".,").split())
output = clean_whitespaces(output)
return output
def parse_bbl(bbl_file):
with open(bbl_file, 'r') as fh:
def parse_bbl(bbl):
"""
Parse a *.bbl file to get a clean list of plaintext citations.
Params:
- bbl is either the path to the .bbl file or the content of a bbl file.
Returns a list of cleaned plaintext citations.
"""
# Handle path or content
if os.path.isfile(bbl):
with open(bbl, 'r') as fh:
bbl_content = fh.read()
bibitems = re.split(r"\\bibitem\{.+?\}", bbl_content)[1:]
bibitems = [re.sub(r"\\end\{thebibliography}",
"",
else:
bbl_content = bbl
# Get a list of bibitems
bibitems = regex_bibitems.split(bbl_content)[1:]
bibitems = [regex_endthebibliography.sub("",
i).strip() for i in bibitems]
cleaned_bbl = []
# Clean every bibitem
for bibitem in bibitems:
cleaned_bbl.append(clean_bibitem(bibitem))
return cleaned_bbl
def dois_from_bbl(bbl_file):
def extract_doi_links(urls):
"""
Try to find a DOI from a given list of URLs.
"""
doi_urls = [url for url in urls if "/doi/" in url]
if len(doi_urls) > 0:
return ("http://dx.doi.org" +
doi_urls[0][doi_urls[0].find("/doi/") + 4:])
else:
return None
def extract_arxiv_links(urls):
"""
Try to find an arXiv link from a given list of URLs.
"""
arxiv_urls = [url for url in urls if "://arxiv.org" in url]
if len(arxiv_urls) > 0:
return arxiv_urls[0]
else:
return None
def dois_from_bbl(bbl):
"""
Get the papers cited by the paper identified by the given DOI.
Params:
- bbl is either the path to the .bbl file or the content of a bbl file.
Returns a dict of cleaned plaintext citations and their associated doi.
"""
cleaned_citations = parse_bbl(bbl_file)
cleaned_citations_with_URLs = parse_bbl(bbl)
dois = {}
cleaned_citations = []
# Try to get the DOI directly from the citation
for citation in cleaned_citations_with_URLs[:]:
# Get all the urls in the citation
raw_urls = regex_urls.findall(citation)
urls = [u.lower() for u in raw_urls]
# Remove URLs in citation
for url in raw_urls:
citation = citation.replace(url, "")
citation = clean_whitespaces(citation)
# Try to find an arXiv link
arxiv_url = extract_arxiv_links(urls)
if arxiv_url:
dois[citation] = arxiv_url
# Try to find a DOI link
doi_url = extract_doi_links(urls)
if doi_url:
dois[citation] = doi_url
# If no match found, stack it for next step
if citation not in dois:
cleaned_citations.append(citation)
# Do batch of 10 papers, to prevent from the timeout of crossref
for i in range(math.ceil(len(cleaned_citations) / 10)):
lower_bound = 10 * i
upper_bound = min(10 * (i + 1), len(cleaned_citations))
@ -53,15 +136,76 @@ def dois_from_bbl(bbl_file):
json=cleaned_citations[lower_bound:upper_bound])
for result in r.json()["results"]:
if "doi" not in result:
# If DOI is not found, try a direct query to get a DOI
# r = requests.get("http://search.crossref.org/dois",
# params={
# 'q': result["text"],
# "sort": "score",
# "rows": 1
# })
# doi_result = r.json()
# if len(doi_result) > 0:
# dois[result["text"]] = doi_result[0]["doi"]
# else:
# dois[result["text"]] = None
dois[result["text"]] = None
else:
dois[result["text"]] = result["doi"]
return dois
if __name__ == "__main__":
if len(sys.argv) < 2:
sys.exit("Usage: " + sys.argv[0] + " BBL_FILE.")
def sources_from_arxiv(eprint):
"""
Download sources on arXiv for a given preprint.
Params:
- eprint is the arXiv id (e.g. 1401.2910 or 1401.2910v1).
Returns a TarFile object of the sources of the arXiv preprint.
"""
r = requests.get("http://arxiv.org/e-print/%s" % (eprint,))
file_object = io.BytesIO(r.content)
return tarfile.open(fileobj=file_object)
def bbl_from_arxiv(eprint):
"""
Get the .bbl files (if any) of a given preprint.
Params:
- eprint is the arXiv id (e.g. 1401.2910 or 1401.2910v1).
Returns a list of the .bbl files as text (if any) or None.
"""
tf = sources_from_arxiv(eprint)
bbl_files = [i for i in tf.getmembers() if i.name.endswith(".bbl")]
bbl_files = [tf.extractfile(member).read().decode(tarfile.ENCODING)
for member in bbl_files]
return bbl_files
def dois_from_arxiv(eprint):
"""
Get the .bbl files (if any) of a given preprint.
Params:
- eprint is the arXiv id (e.g. 1401.2910 or 1401.2910v1).
Returns a dict of cleaned plaintext citations and their associated doi.
"""
bbl_files = bbl_from_arxiv(eprint)
dois = {}
for bbl in bbl_files:
dois.update(dois_from_bbl(bbl))
return dois
if __name__ == "__main__":
import pprint
if len(sys.argv) < 2:
sys.exit("Usage: " + sys.argv[0] + " BBL_FILE|ARXIV_EPRINT.")
if os.path.isfile(sys.argv[1]):
pprint.pprint(dois_from_bbl(sys.argv[1]))
else:
pprint.pprint(dois_from_arxiv(sys.argv[1]))