bmc/fetcher.py
Phyks b4f0e7c0eb Import / Download / Delete working
All bug should be fixed for the import / download / delete functions.

* Some problems with utf-8 and homogeneize_latex_encoding in
python-bbtexparser are bypassed and will be cleaned in a better way when
the latest version will be available in pip.
* Tweaked regex for isbn, which was not cas insensitive and forgot about
spaces separated numbers.
* File entry in arXiv bibtex is now deleted to avoid confusion.
2014-05-11 19:29:42 +02:00

278 lines
8.9 KiB
Python

#!/usr/bin/env python2
# coding=utf8
import isbntools
import re
import requesocks as requests # Requesocks is requests with SOCKS support
import subprocess
import arxiv2bib as arxiv_metadata
import tools
import params
from bibtexparser.bparser import BibTexParser
from isbntools.dev.fmt import fmtbib
def download(url):
"""Download url tofile
Check that it is a valid pdf or djvu file. Tries all the
available proxies sequentially. Returns the raw content of the file, or
false if it could not be downloaded.
"""
for proxy in params.proxies:
r_proxy = {
"http": proxy,
"https": proxy,
}
try:
r = requests.get(url, proxies=r_proxy)
contenttype = False
if 'pdf' in r.headers['content-type']:
contenttype = 'pdf'
elif 'djvu' in r.headers['content-type']:
contenttype = 'djvu'
if r.status_code != 200 or contenttype is False:
continue
return r.content, contenttype
except requests.exceptions.RequestException:
tools.warning("Unable to get "+url+" using proxy "+proxy+". It " +
"may not be available.")
continue
return False
isbn_re = re.compile(r"isbn (([0-9]{3}[ -])?[0-9][ -][0-9]{2}[ -][0-9]{6}[ -][0-9])",
re.IGNORECASE)
def findISBN(src):
"""Search for a valid ISBN in src.
Returns the ISBN or false if not found or an error occurred."""
if src.endswith(".pdf"):
totext = subprocess.Popen(["pdftotext", src, "-"],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
bufsize=1)
elif src.endswith(".djvu"):
totext = subprocess.Popen(["djvutxt", src],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
bufsize=1)
else:
return False
while totext.poll() is None:
extractfull = totext.stdout.readline()
extractISBN = isbn_re.search(extractfull.lower().replace('Œ',
'-'))
if extractISBN:
totext.terminate()
break
err = totext.communicate()[1]
if totext.returncode > 0:
# Error happened
tools.warning(err)
return False
cleanISBN = False
# Clean ISBN is the ISBN number without separators
if extractISBN:
cleanISBN = extractISBN.group(1).replace('-', '').replace(' ', '')
return cleanISBN
def isbn2Bib(isbn):
"""Tries to get bibtex entry from an ISBN number"""
# Default merges results from worldcat.org and google books
return fmtbib('bibtex', isbntools.meta(isbn, 'default'))
doi_re = re.compile('(?<=doi)/?:?\s?[0-9\.]{7}/\S*[0-9]', re.IGNORECASE)
doi_pnas_re = re.compile('(?<=doi).?10.1073/pnas\.\d+', re.IGNORECASE)
doi_jsb_re = re.compile('10\.1083/jcb\.\d{9}', re.IGNORECASE)
clean_doi_re = re.compile('^/')
clean_doi_fabse_re = re.compile('^10.1096')
clean_doi_jcb_re = re.compile('^10.1083')
clean_doi_len_re = re.compile(r'\d\.\d')
def findDOI(src):
"""Search for a valid DOI in src.
Returns the DOI or False if not found or an error occurred.
From : http://en.dogeno.us/2010/02/release-a-python-script-for-organizing-scientific-papers-pyrenamepdf-py/
"""
if src.endswith(".pdf"):
totext = subprocess.Popen(["pdftotext", src, "-"],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
elif src.endswith(".djvu"):
totext = subprocess.Popen(["djvutxt", src],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
else:
return False
while totext.poll() is None:
extractfull = totext.stdout.readline()
extractDOI = doi_re.search(extractfull.lower().replace('&#338;', '-'))
if not extractDOI:
# PNAS fix
extractDOI = doi_pnas_re.search(extractfull.lower().replace('pnas',
'/pnas'))
if not extractDOI:
# JSB fix
extractDOI = doi_jsb_re.search(extractfull.lower())
if extractDOI:
totext.terminate()
break
err = totext.communicate()[1]
if totext.returncode > 0:
# Error happened
tools.warning(err)
return False
cleanDOI = False
if extractDOI:
cleanDOI = extractDOI.group(0).replace(':', '').replace(' ', '')
if clean_doi_re.search(cleanDOI):
cleanDOI = cleanDOI[1:]
# FABSE J fix
if clean_doi_fabse_re.search(cleanDOI):
cleanDOI = cleanDOI[:20]
# Second JCB fix
if clean_doi_jcb_re.search(cleanDOI):
cleanDOI = cleanDOI[:21]
if len(cleanDOI) > 40:
cleanDOItemp = clean_doi_len_re.sub('000', cleanDOI)
reps = {'.': 'A', '-': '0'}
cleanDOItemp = tools.replaceAll(cleanDOItemp[8:], reps)
digitStart = 0
for i in range(len(cleanDOItemp)):
if cleanDOItemp[i].isdigit():
digitStart = 1
if cleanDOItemp[i].isalpha() and digitStart:
break
cleanDOI = cleanDOI[0:(8+i)]
return cleanDOI
def doi2Bib(doi):
"""Returns a bibTeX string of metadata for a given DOI.
From : https://gist.github.com/jrsmith3/5513926
"""
url = "http://dx.doi.org/" + doi
headers = {"accept": "application/x-bibtex"}
try:
r = requests.get(url, headers=headers)
if r.headers['content-type'] == 'application/x-bibtex':
return r.text
else:
return ''
except requests.exceptions.ConnectionError:
tools.warning('Unable to contact remote server to get the bibtex ' +
'entry for doi '+doi)
return ''
arXiv_re = re.compile(r'arXiv:\s*([\w\.\/\-]+)', re.IGNORECASE)
def findArXivId(src):
"""Searches for a valid arXiv id in src.
Returns the arXiv id or False if not found or an error occurred.
From : https://github.com/minad/bibsync/blob/3fdf121016f6187a2fffc66a73cd33b45a20e55d/lib/bibsync/utils.rb
"""
if src.endswith(".pdf"):
totext = subprocess.Popen(["pdftotext", src, "-"],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
elif src.endswith(".djvu"):
totext = subprocess.Popen(["djvutxt", src],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
else:
return False
while totext.poll() is None:
extractfull = totext.stdout.readline()
extractID = arXiv_re.search(extractfull)
if extractID:
totext.terminate()
break
err = totext.communicate()[1]
if totext.returncode > 0:
# Error happened
tools.warning(err)
return False
elif extractID is not None:
return extractID.group(1)
else:
return False
def arXiv2Bib(arxiv):
"""Returns bibTeX string of metadata for a given arXiv id
arxiv is an arxiv id
"""
bibtex = arxiv_metadata.arxiv2bib([arxiv])
for bib in bibtex:
if isinstance(bib, arxiv_metadata.ReferenceErrorInfo):
continue
else:
fetched_bibtex = BibTexParser(bib.bibtex())
fetched_bibtex = fetched_bibtex.get_entry_dict()
fetched_bibtex = fetched_bibtex[fetched_bibtex.keys()[0]]
try:
del(fetched_bibtex['file'])
except:
pass
return tools.parsed2Bibtex(fetched_bibtex)
return False
HAL_re = re.compile(r'(hal-\d{8}), version (\d+)')
def findHALId(src):
"""Searches for a valid HAL id in src
Returns a tuple of the HAL id and the version
or False if not found or an error occurred.
"""
if src.endswith(".pdf"):
totext = subprocess.Popen(["pdftotext", src, "-"],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
elif src.endswith(".djvu"):
totext = subprocess.Popen(["djvutxt", src],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
else:
return False
while totext.poll() is None:
extractfull = totext.stdout.readline()
extractID = HAL_re.search(extractfull)
if extractID:
totext.terminate()
break
err = totext.communicate()[1]
if totext.returncode > 0:
# Error happened
tools.warning(err)
return False
else:
return extractID.group(1), extractID.group(2)