357 lines
12 KiB
Python
357 lines
12 KiB
Python
# -*- coding: utf8 -*-
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# -----------------------------------------------------------------------------
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# "THE NO-ALCOHOL BEER-WARE LICENSE" (Revision 42):
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# Phyks (webmaster@phyks.me) wrote this file. As long as you retain this notice
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# you can do whatever you want with this stuff (and you can also do whatever
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# you want with this stuff without retaining it, but that's not cool...). If we
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# meet some day, and you think this stuff is worth it, you can buy me a
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# <del>beer</del> soda in return.
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# Phyks
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# -----------------------------------------------------------------------------
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import isbnlib
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import re
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import socket
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import socks
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import subprocess
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import sys
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try:
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# For Python 3.0 and later
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from urllib.request import urlopen, Request
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from urllib.error import URLError
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except ImportError:
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# Fall back to Python 2's urllib2
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from urllib2 import urlopen, Request, URLError
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import arxiv2bib as arxiv_metadata
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import libbmc.tools as tools
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from bibtexparser.bparser import BibTexParser
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from libbmc.config import Config
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config = Config()
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default_socket = socket.socket
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try:
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stdout_encoding = sys.stdout.encoding
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assert(stdout_encoding is not None)
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except (AttributeError, AssertionError):
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stdout_encoding = 'UTF-8'
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def download(url):
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"""Download url tofile
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Check that it is a valid pdf or djvu file. Tries all the
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available proxies sequentially. Returns the raw content of the file, or
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false if it could not be downloaded.
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"""
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for proxy in config.get("proxies"):
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if proxy.startswith('socks'):
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if proxy[5] == '4':
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proxy_type = socks.SOCKS4
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else:
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proxy_type = socks.SOCKS5
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proxy = proxy[proxy.find('://')+3:]
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try:
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proxy, port = proxy.split(':')
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except ValueError:
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port = None
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socks.set_default_proxy(proxy_type, proxy, port)
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socket.socket = socks.socksocket
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elif proxy == '':
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socket.socket = default_socket
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else:
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try:
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proxy, port = proxy.split(':')
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except ValueError:
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port = None
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socks.set_default_proxy(socks.HTTP, proxy, port)
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socket.socket = socks.socksocket
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try:
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r = urlopen(url)
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try:
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size = int(dict(r.info())['content-length'].strip())
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except KeyError:
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try:
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size = int(dict(r.info())['Content-Length'].strip())
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except KeyError:
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size = 0
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dl = b""
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dl_size = 0
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while True:
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buf = r.read(1024)
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if buf:
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dl += buf
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dl_size += len(buf)
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if size != 0:
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done = int(50 * dl_size / size)
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sys.stdout.write("\r[%s%s]" % ('='*done, ' '*(50-done)))
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sys.stdout.write(" "+str(int(float(done)/52*100))+"%")
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sys.stdout.flush()
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else:
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break
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contenttype = False
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contenttype_req = None
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try:
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contenttype_req = dict(r.info())['content-type']
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except KeyError:
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try:
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contenttype_req = dict(r.info())['Content-Type']
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except KeyError:
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continue
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try:
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if 'pdf' in contenttype_req:
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contenttype = 'pdf'
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elif 'djvu' in contenttype_req:
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contenttype = 'djvu'
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except KeyError:
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pass
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if r.getcode() != 200 or contenttype is False:
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continue
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return dl, contenttype
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except ValueError:
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tools.warning("Invalid URL")
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return False, None
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except URLError:
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tools.warning("Unable to get "+url+" using proxy "+proxy+". It " +
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"may not be available.")
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continue
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return False, None
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isbn_re = re.compile(r'isbn[\s]?:?[\s]?((?:[0-9]{3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[- ]?[0-9])',
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re.IGNORECASE)
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def findISBN(src):
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"""Search for a valid ISBN in src.
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Returns the ISBN or false if not found or an error occurred."""
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if src.endswith(".pdf"):
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totext = subprocess.Popen(["pdftotext", src, "-"],
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stdout=subprocess.PIPE,
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stderr=subprocess.PIPE,
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bufsize=1)
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elif src.endswith(".djvu"):
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totext = subprocess.Popen(["djvutxt", src],
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stdout=subprocess.PIPE,
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stderr=subprocess.PIPE,
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bufsize=1)
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else:
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return False
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while totext.poll() is None:
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extractfull = ' '.join([i.decode(stdout_encoding).strip() for i in totext.stdout.readlines()])
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extractISBN = isbn_re.search(extractfull.lower().replace('Œ',
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'-'))
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if extractISBN:
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totext.terminate()
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break
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err = totext.communicate()[1]
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if totext.returncode > 0:
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# Error happened
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tools.warning(err)
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return False
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cleanISBN = False
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# Clean ISBN is the ISBN number without separators
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if extractISBN:
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cleanISBN = extractISBN.group(1).replace('-', '').replace(' ', '')
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return cleanISBN
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def isbn2Bib(isbn):
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"""Tries to get bibtex entry from an ISBN number"""
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# Default merges results from worldcat.org and google books
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try:
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return isbnlib.registry.bibformatters['bibtex'](isbnlib.meta(isbn,
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'default'))
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except (isbnlib.ISBNLibException, isbnlib.ISBNToolsException, TypeError):
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return ''
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doi_re = re.compile('(?<=doi)/?:?\s?[0-9\.]{7}/\S*[0-9]', re.IGNORECASE)
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doi_pnas_re = re.compile('(?<=doi).?10.1073/pnas\.\d+', re.IGNORECASE)
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doi_jsb_re = re.compile('10\.1083/jcb\.\d{9}', re.IGNORECASE)
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clean_doi_re = re.compile('^/')
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clean_doi_fabse_re = re.compile('^10.1096')
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clean_doi_jcb_re = re.compile('^10.1083')
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clean_doi_len_re = re.compile(r'\d\.\d')
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arXiv_re = re.compile(r'arXiv:\s*([\w\.\/\-]+)', re.IGNORECASE)
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def findArticleID(src, only=["DOI", "arXiv"]):
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"""Search for a valid article ID (DOI or ArXiv) in src.
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Returns a tuple (type, first matching ID) or False if not found
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or an error occurred.
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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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if src.endswith(".pdf"):
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totext = subprocess.Popen(["pdftotext", src, "-"],
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stdout=subprocess.PIPE,
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stderr=subprocess.PIPE)
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elif src.endswith(".djvu"):
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totext = subprocess.Popen(["djvutxt", src],
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stdout=subprocess.PIPE,
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stderr=subprocess.PIPE)
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else:
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return (False, False)
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extractfull = ''
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extract_type = False
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extractID = None
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while totext.poll() is None:
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extractfull += ' '.join([i.decode(stdout_encoding).strip() for i in totext.stdout.readlines()])
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# Try to extract DOI
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if "DOI" in only:
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extractID = doi_re.search(extractfull.lower().replace('Œ', '-'))
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if not extractID:
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# PNAS fix
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extractID = doi_pnas_re.search(extractfull.
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lower().
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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 = doi_jsb_re.search(extractfull.lower())
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if extractID:
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extract_type = "DOI"
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totext.terminate()
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# Try to extract arXiv
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if "arXiv" in only:
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tmp_extractID = arXiv_re.search(extractfull)
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if tmp_extractID:
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if not extractID or extractID.start(0) > tmp_extractID.start(1):
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# Only use arXiv id if it is before the DOI in the pdf
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extractID = tmp_extractID
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extract_type = "arXiv"
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totext.terminate()
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if extract_type is not False:
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break
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err = totext.communicate()[1]
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if totext.returncode > 0:
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# Error happened
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tools.warning(err)
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return (False, False)
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if extractID is not None and extract_type == "DOI":
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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 clean_doi_re.search(cleanDOI):
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cleanDOI = cleanDOI[1:]
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# FABSE J fix
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if clean_doi_fabse_re.search(cleanDOI):
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cleanDOI = cleanDOI[:20]
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# Second JCB fix
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if clean_doi_jcb_re.search(cleanDOI):
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cleanDOI = cleanDOI[:21]
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if len(cleanDOI) > 40:
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cleanDOItemp = clean_doi_len_re.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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elif extractID is not None and extract_type == "arXiv":
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# If arXiv id is extracted, return it
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return ("arXiv", extractID.group(1))
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return (False, False)
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def doi2Bib(doi):
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"""Returns a bibTeX string of metadata for a given DOI.
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From : https://gist.github.com/jrsmith3/5513926
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"""
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url = "http://dx.doi.org/" + doi
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headers = {"accept": "application/x-bibtex"}
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req = Request(url, headers=headers)
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try:
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r = urlopen(req)
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try:
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if dict(r.info())['content-type'] == 'application/x-bibtex':
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return r.read().decode('utf-8')
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else:
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return ''
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except KeyError:
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try:
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if dict(r.info())['Content-Type'] == 'application/x-bibtex':
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return r.read().decode('utf-8')
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else:
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return ''
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except KeyError:
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return ''
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except URLError:
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tools.warning('Unable to contact remote server to get the bibtex ' +
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'entry for doi '+doi)
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return ''
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def arXiv2Bib(arxiv):
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"""Returns bibTeX string of metadata for a given arXiv id
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arxiv is an arxiv id
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"""
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bibtex = arxiv_metadata.arxiv2bib([arxiv])
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for bib in bibtex:
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if isinstance(bib, arxiv_metadata.ReferenceErrorInfo):
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continue
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else:
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fetched_bibtex = BibTexParser(bib.bibtex())
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fetched_bibtex = fetched_bibtex.get_entry_dict()
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fetched_bibtex = fetched_bibtex[list(fetched_bibtex.keys())[0]]
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try:
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del(fetched_bibtex['file'])
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except KeyError:
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pass
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return tools.parsed2Bibtex(fetched_bibtex)
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return ''
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HAL_re = re.compile(r'(hal-\d{8}), version (\d+)')
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def findHALId(src):
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"""Searches for a valid HAL id in src
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Returns a tuple of the HAL id and the version
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or False if not found or an error occurred.
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"""
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if src.endswith(".pdf"):
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totext = subprocess.Popen(["pdftotext", src, "-"],
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stdout=subprocess.PIPE,
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stderr=subprocess.PIPE)
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elif src.endswith(".djvu"):
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totext = subprocess.Popen(["djvutxt", src],
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stdout=subprocess.PIPE,
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stderr=subprocess.PIPE)
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else:
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return False
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while totext.poll() is None:
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extractfull = ' '.join([i.decode(stdout_encoding).strip() for i in totext.stdout.readlines()])
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extractID = HAL_re.search(extractfull)
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if extractID:
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totext.terminate()
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break
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err = totext.communicate()[1]
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if totext.returncode > 0:
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# Error happened
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tools.warning(err)
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return False
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else:
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return extractID.group(1), extractID.group(2)
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