Clean a bit the code
This commit is contained in:
parent
97b90ee610
commit
51df30918a
1
.gitignore
vendored
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1
.gitignore
vendored
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__pycache__
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50
arxiv.py
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50
arxiv.py
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import bbl
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import io
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import requests
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import tarfile
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def sources_from_arxiv(eprint):
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"""
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Download sources on arXiv for a given preprint.
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Params:
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- eprint is the arXiv id (e.g. 1401.2910 or 1401.2910v1).
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Returns a TarFile object of the sources of the arXiv preprint.
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"""
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r = requests.get("http://arxiv.org/e-print/%s" % (eprint,))
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file_object = io.BytesIO(r.content)
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return tarfile.open(fileobj=file_object)
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def bbl_from_arxiv(eprint):
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"""
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Get the .bbl files (if any) of a given preprint.
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Params:
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- eprint is the arXiv id (e.g. 1401.2910 or 1401.2910v1).
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Returns a list of the .bbl files as text (if any) or None.
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"""
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tf = sources_from_arxiv(eprint)
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bbl_files = [i for i in tf.getmembers() if i.name.endswith(".bbl")]
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bbl_files = [tf.extractfile(member).read().decode(tarfile.ENCODING)
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for member in bbl_files]
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return bbl_files
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def get_dois(eprint):
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"""
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Get the .bbl files (if any) of a given preprint.
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Params:
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- eprint is the arXiv id (e.g. 1401.2910 or 1401.2910v1).
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Returns a dict of cleaned plaintext citations and their associated doi.
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"""
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bbl_files = bbl_from_arxiv(eprint)
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dois = {}
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for bbl_file in bbl_files:
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dois.update(bbl.get_dois(bbl_file))
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return dois
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124
bbl.py
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124
bbl.py
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import doi
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import math
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import os
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import requests
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import subprocess
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import regex
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import tools
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def clean_bibitem(bibitem):
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"""
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Return a plaintext representation of the bibitem from the bbl file.
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Params:
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- bibitem is the text content of the bibitem.
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Returns a cleaned plaintext citation from the bibitem.
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"""
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script_dir = os.path.dirname(os.path.abspath(__file__))
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output = subprocess.check_output(["%s/opendetex/delatex" % (script_dir,),
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"-s"],
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input=bibitem.encode("utf-8"))
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output = output.decode("utf-8")
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output = tools.clean_whitespaces(output)
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return output
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def parse(bbl):
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"""
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Parse a *.bbl file to get a clean list of plaintext citations.
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Params:
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- bbl is either the path to the .bbl file or the content of a bbl file.
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Returns a list of cleaned plaintext citations.
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"""
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# Handle path or content
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if os.path.isfile(bbl):
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with open(bbl, 'r') as fh:
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bbl_content = fh.read()
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else:
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bbl_content = bbl
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# Get a list of bibitems
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bibitems = regex.bibitems.split(bbl_content)[1:]
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bibitems = [regex.endthebibliography.sub("",
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i).strip() for i in bibitems]
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cleaned_bbl = []
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# Clean every bibitem
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for bibitem in bibitems:
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cleaned_bbl.append(clean_bibitem(bibitem))
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return cleaned_bbl
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def get_dois(bbl_input):
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"""
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Get the papers cited by the paper identified by the given DOI.
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Params:
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- bbl_input is either the path to the .bbl file or the content of a bbl
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file.
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Returns a dict of cleaned plaintext citations and their associated doi.
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"""
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cleaned_citations_with_URLs = parse(bbl_input)
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dois = {}
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cleaned_citations = []
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# Try to get the DOI directly from the citation
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for citation in cleaned_citations_with_URLs[:]:
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# Get all the urls in the citation
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raw_urls = regex.urls.findall(citation)
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urls = [u.lower() for u in raw_urls]
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# Remove URLs in citation
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for url in raw_urls:
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citation = citation.replace(url, "")
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citation = tools.clean_whitespaces(citation)
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# Try to find an arXiv link
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arxiv_url = doi.extract_arxiv_links(urls)
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if arxiv_url:
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dois[citation] = arxiv_url
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# Try to find a DOI link
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doi_url = doi.extract_doi_links(urls)
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if doi_url:
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dois[citation] = doi_url
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# Try to find a direct match using a regex if links search failed
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if not doi_url and not arxiv_url:
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regex.match = doi.match_doi_or_arxiv(citation)
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if regex.match:
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print(regex.match)
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citation = citation.replace(regex.match[1], "")
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if regex.match[0] == "DOI":
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dois[citation] = "http://dx.doi.org/%s" % (regex.match[1],)
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else:
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dois[citation] = (
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"http://arxiv.org/abs/%s" %
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(regex.match[1].replace("arxiv:", ""),)
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)
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# If no match found, stack it for next step
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if citation not in dois:
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cleaned_citations.append(citation)
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# Do batch of 10 papers, to prevent from the timeout of crossref
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for i in range(math.ceil(len(cleaned_citations) / 10)):
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lower_bound = 10 * i
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upper_bound = min(10 * (i + 1), len(cleaned_citations))
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r = requests.post("http://search.crossref.org/links",
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json=cleaned_citations[lower_bound:upper_bound])
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for result in r.json()["results"]:
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if "doi" not in result:
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# If DOI is not found, try a direct query to get a DOI
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# r = requests.get("http://search.crossref.org/dois",
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# params={
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# 'q': result["text"],
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# "sort": "score",
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# "rows": 1
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# })
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# doi_result = r.json()
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# if len(doi_result) > 0:
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# dois[result["text"]] = doi_result[0]["doi"]
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# else:
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# dois[result["text"]] = None
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dois[result["text"]] = None
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else:
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dois[result["text"]] = result["doi"]
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return dois
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77
doi.py
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77
doi.py
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import regex
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import tools
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def extract_doi_links(urls):
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"""
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Try to find a DOI from a given list of URLs.
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"""
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doi_urls = [url for url in urls if "/doi/" in url]
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if len(doi_urls) > 0:
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return ("http://dx.doi.org" +
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doi_urls[0][doi_urls[0].find("/doi/") + 4:])
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else:
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return None
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def extract_arxiv_links(urls):
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"""
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Try to find an arXiv link from a given list of URLs.
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"""
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arxiv_urls = [url for url in urls if "://arxiv.org" in url]
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if len(arxiv_urls) > 0:
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return arxiv_urls[0]
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else:
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return None
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def match_doi_or_arxiv(text, only=["DOI", "arXiv"]):
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"""
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Search for a valid article ID (DOI or ArXiv) in the given text
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(regex-based).
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Returns a tuple (type, first matching ID) or None if not found.
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From : http://en.dogeno.us/2010/02/release-a-python-script-for-organizing-scientific-papers-pyrenamepdf-py/
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and https://github.com/minad/bibsync/blob/3fdf121016f6187a2fffc66a73cd33b45a20e55d/lib/bibsync/utils.rb
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"""
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text = text.lower()
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# Try to extract DOI
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if "DOI" in only:
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extractID = regex.doi.search(text.replace('Œ', '-'))
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if not extractID:
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# PNAS fix
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extractID = regex.doi_pnas.search(text.
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replace('pnas', '/pnas'))
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if not extractID:
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# JSB fix
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extractID = regex.doi_jsb.search(text)
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if extractID:
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# If DOI extracted, clean it and return it
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cleanDOI = False
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cleanDOI = extractID.group(0).replace(':', '').replace(' ', '')
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if regex.clean_doi.search(cleanDOI):
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cleanDOI = cleanDOI[1:]
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# FABSE J fix
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if regex.clean_doi_fabse.search(cleanDOI):
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cleanDOI = cleanDOI[:20]
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# Second JCB fix
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if regex.clean_doi_jcb.search(cleanDOI):
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cleanDOI = cleanDOI[:21]
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if len(cleanDOI) > 40:
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cleanDOItemp = regex.clean_doi_len.sub('000', cleanDOI)
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reps = {'.': 'A', '-': '0'}
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cleanDOItemp = tools.replaceAll(cleanDOItemp[8:], reps)
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digitStart = 0
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for i in range(len(cleanDOItemp)):
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if cleanDOItemp[i].isdigit():
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digitStart = 1
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if cleanDOItemp[i].isalpha() and digitStart:
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break
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cleanDOI = cleanDOI[0:(8+i)]
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return ("DOI", cleanDOI)
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# Else, try to extract arXiv
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if "arXiv" in only:
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extractID = regex.arXiv.search(text)
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if extractID:
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return ("arXiv", extractID.group(1))
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return None
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276
main.py
276
main.py
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#!/usr/bin/env python3
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import io
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import math
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import os
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import re
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import requests
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import subprocess
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import sys
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import tarfile
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regex_urls = re.compile(r"http[s]?://(?:[a-zA-Z]|[0-9]|[$-_@.&+]|[!*\(\),]|(?:%[0-9a-fA-F][0-9a-fA-F]))+")
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regex_bibitems = re.compile(r"\\bibitem\{.+?\}")
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regex_endthebibliography = re.compile(r"\\end\{thebibliography}")
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regex_doi = re.compile('(?<=doi)/?:?\s?[0-9\.]{7}/\S*[0-9]', re.IGNORECASE)
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regex_doi_pnas = re.compile('(?<=doi).?10.1073/pnas\.\d+', re.IGNORECASE)
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regex_doi_jsb = re.compile('10\.1083/jcb\.\d{9}', re.IGNORECASE)
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regex_clean_doi = re.compile('^/')
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regex_clean_doi_fabse = re.compile('^10.1096')
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regex_clean_doi_jcb = re.compile('^10.1083')
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regex_clean_doi_len = re.compile(r'\d\.\d')
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regex_arXiv = re.compile(r'arXiv:\s*([\w\.\/\-]+)', re.IGNORECASE)
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def replaceAll(text, dic):
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"""Replace all the dic keys by the associated item in text"""
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for i, j in dic.items():
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text = text.replace(i, j)
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return text
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def clean_whitespaces(text):
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"""
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Remove double whitespaces and trailing . and , from text.
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"""
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return ' '.join(text.strip().rstrip(".,").split())
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# Local import
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import arxiv
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import bbl
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def oa_from_doi(doi):
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@ -45,248 +15,12 @@ def oa_from_doi(doi):
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pass
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def clean_bibitem(bibitem):
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"""
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Return a plaintext representation of the bibitem from the bbl file.
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Params:
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- bibitem is the text content of the bibitem.
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Returns a cleaned plaintext citation from the bibitem.
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"""
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script_dir = os.path.dirname(os.path.abspath(__file__))
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output = subprocess.check_output(["%s/opendetex/delatex" % (script_dir,),
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"-s"],
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input=bibitem.encode("utf-8"))
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output = output.decode("utf-8")
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output = clean_whitespaces(output)
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return output
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def parse_bbl(bbl):
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"""
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Parse a *.bbl file to get a clean list of plaintext citations.
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Params:
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- bbl is either the path to the .bbl file or the content of a bbl file.
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Returns a list of cleaned plaintext citations.
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"""
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# Handle path or content
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if os.path.isfile(bbl):
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with open(bbl, 'r') as fh:
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bbl_content = fh.read()
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else:
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bbl_content = bbl
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# Get a list of bibitems
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bibitems = regex_bibitems.split(bbl_content)[1:]
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bibitems = [regex_endthebibliography.sub("",
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i).strip() for i in bibitems]
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cleaned_bbl = []
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# Clean every bibitem
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for bibitem in bibitems:
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cleaned_bbl.append(clean_bibitem(bibitem))
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return cleaned_bbl
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def extract_doi_links(urls):
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"""
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Try to find a DOI from a given list of URLs.
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"""
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doi_urls = [url for url in urls if "/doi/" in url]
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if len(doi_urls) > 0:
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return ("http://dx.doi.org" +
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doi_urls[0][doi_urls[0].find("/doi/") + 4:])
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else:
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return None
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def extract_arxiv_links(urls):
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"""
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Try to find an arXiv link from a given list of URLs.
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"""
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arxiv_urls = [url for url in urls if "://arxiv.org" in url]
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if len(arxiv_urls) > 0:
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return arxiv_urls[0]
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else:
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return None
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def match_doi_or_arxiv(text, only=["DOI", "arXiv"]):
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"""
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Search for a valid article ID (DOI or ArXiv) in the given text
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(regex-based).
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Returns a tuple (type, first matching ID) or None if not found.
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From : http://en.dogeno.us/2010/02/release-a-python-script-for-organizing-scientific-papers-pyrenamepdf-py/
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and https://github.com/minad/bibsync/blob/3fdf121016f6187a2fffc66a73cd33b45a20e55d/lib/bibsync/utils.rb
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"""
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text = text.lower()
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# Try to extract DOI
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if "DOI" in only:
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extractID = regex_doi.search(text.replace('Œ', '-'))
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if not extractID:
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# PNAS fix
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extractID = regex_doi_pnas.search(text.
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replace('pnas', '/pnas'))
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if not extractID:
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# JSB fix
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extractID = regex_doi_jsb.search(text)
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if extractID:
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# If DOI extracted, clean it and return it
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cleanDOI = False
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cleanDOI = extractID.group(0).replace(':', '').replace(' ', '')
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if regex_clean_doi.search(cleanDOI):
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cleanDOI = cleanDOI[1:]
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# FABSE J fix
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if regex_clean_doi_fabse.search(cleanDOI):
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cleanDOI = cleanDOI[:20]
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# Second JCB fix
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if regex_clean_doi_jcb.search(cleanDOI):
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cleanDOI = cleanDOI[:21]
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if len(cleanDOI) > 40:
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cleanDOItemp = regex_clean_doi_len.sub('000', cleanDOI)
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reps = {'.': 'A', '-': '0'}
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cleanDOItemp = replaceAll(cleanDOItemp[8:], reps)
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digitStart = 0
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for i in range(len(cleanDOItemp)):
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if cleanDOItemp[i].isdigit():
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digitStart = 1
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if cleanDOItemp[i].isalpha() and digitStart:
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break
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cleanDOI = cleanDOI[0:(8+i)]
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return ("DOI", cleanDOI)
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# Else, try to extract arXiv
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if "arXiv" in only:
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extractID = regex_arXiv.search(text)
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if extractID:
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return ("arXiv", extractID.group(1))
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return None
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def dois_from_bbl(bbl):
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"""
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Get the papers cited by the paper identified by the given DOI.
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Params:
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- bbl is either the path to the .bbl file or the content of a bbl file.
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Returns a dict of cleaned plaintext citations and their associated doi.
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"""
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cleaned_citations_with_URLs = parse_bbl(bbl)
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dois = {}
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cleaned_citations = []
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# Try to get the DOI directly from the citation
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for citation in cleaned_citations_with_URLs[:]:
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# Get all the urls in the citation
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raw_urls = regex_urls.findall(citation)
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urls = [u.lower() for u in raw_urls]
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# Remove URLs in citation
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for url in raw_urls:
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citation = citation.replace(url, "")
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citation = clean_whitespaces(citation)
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# Try to find an arXiv link
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arxiv_url = extract_arxiv_links(urls)
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if arxiv_url:
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dois[citation] = arxiv_url
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# Try to find a DOI link
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doi_url = extract_doi_links(urls)
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if doi_url:
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dois[citation] = doi_url
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# Try to find a direct match using a regex if links search failed
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if not doi_url and not arxiv_url:
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regex_match = match_doi_or_arxiv(citation)
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if regex_match:
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print(regex_match)
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citation = citation.replace(regex_match[1], "")
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||||
if regex_match[0] == "DOI":
|
||||
dois[citation] = "http://dx.doi.org/%s" % (regex_match[1],)
|
||||
else:
|
||||
dois[citation] = (
|
||||
"http://arxiv.org/abs/%s" %
|
||||
(regex_match[1].replace("arxiv:", ""),)
|
||||
)
|
||||
# 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))
|
||||
r = requests.post("http://search.crossref.org/links",
|
||||
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
|
||||
|
||||
|
||||
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]))
|
||||
pprint.pprint(bbl.get_dois(sys.argv[1]))
|
||||
else:
|
||||
pprint.pprint(dois_from_arxiv(sys.argv[1]))
|
||||
pprint.pprint(arxiv.get_dois(sys.argv[1]))
|
||||
|
||||
14
regex.py
Normal file
14
regex.py
Normal file
@ -0,0 +1,14 @@
|
||||
import re
|
||||
|
||||
urls = re.compile(r"http[s]?://(?:[a-zA-Z]|[0-9]|[$-_@.&+]|[!*\(\),]|(?:%[0-9a-fA-F][0-9a-fA-F]))+")
|
||||
bibitems = re.compile(r"\\bibitem\{.+?\}")
|
||||
endthebibliography = re.compile(r"\\end\{thebibliography}")
|
||||
|
||||
doi = re.compile('(?<=doi)/?:?\s?[0-9\.]{7}/\S*[0-9]', re.IGNORECASE)
|
||||
doi_pnas = re.compile('(?<=doi).?10.1073/pnas\.\d+', re.IGNORECASE)
|
||||
doi_jsb = re.compile('10\.1083/jcb\.\d{9}', re.IGNORECASE)
|
||||
clean_doi = re.compile('^/')
|
||||
clean_doi_fabse = re.compile('^10.1096')
|
||||
clean_doi_jcb = re.compile('^10.1083')
|
||||
clean_doi_len = re.compile(r'\d\.\d')
|
||||
arXiv = re.compile(r'arXiv:\s*([\w\.\/\-]+)', re.IGNORECASE)
|
||||
12
tools.py
Normal file
12
tools.py
Normal file
@ -0,0 +1,12 @@
|
||||
def replaceAll(text, dic):
|
||||
"""Replace all the dic keys by the associated item in text"""
|
||||
for i, j in dic.items():
|
||||
text = text.replace(i, j)
|
||||
return text
|
||||
|
||||
|
||||
def clean_whitespaces(text):
|
||||
"""
|
||||
Remove double whitespaces and trailing . and , from text.
|
||||
"""
|
||||
return ' '.join(text.strip().rstrip(".,").split())
|
||||
Loading…
Reference in New Issue
Block a user