Beginning of refactor
This commit is contained in:
Phyks
parent
613f082471
commit
cce4fd50bb
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@ -115,6 +115,8 @@ A list of ideas and TODO. Don't hesitate to give feedback on the ones you really
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* Split main.py
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* Categories
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* Edit an entry instead of deleting it and adding it again
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* Doc / Man
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* No DOI for arXiv / HAL
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## Issues ?
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@ -1,30 +1,26 @@
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#!/usr/bin/python2 -u
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#!/usr/bin/env python2
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# coding=utf8
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"""
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Fetches papers.
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"""
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from __future__ import print_function
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import sys
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import requesocks as requests
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import isbntools
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import re
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import requesocks as requests # Requesocks is requests with SOCKS support
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import subprocess
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import tools
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import params
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def warning(*objs):
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"""
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Write to stderr
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"""
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print("WARNING: ", *objs, file=sys.stderr)
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def download(url):
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"""Download url tofile
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def download_url(url):
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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 params.proxies:
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r_proxy = {
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"http": proxy,
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"https": proxy,
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}
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try:
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r = requests.get(url, proxies=r_proxy)
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contenttype = False
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@ -37,8 +33,122 @@ def download_url(url):
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continue
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return r.content, contenttype
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# TODO : except trop large
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except:
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warning("Proxy "+proxy+" not available.")
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tools.warning("Proxy "+proxy+" not available.")
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continue
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return False
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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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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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extractfull = totext.communicate()
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# TODO : ^ Return result before processing the whole book ?
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if extractfull[1] is not "":
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# Error happened
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tools.warning(extractfull[1])
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return False
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extractfull = extractfull[0]
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extractISBN = re.search(r"isbn (([0-9]{3}[ -])?[0-9][ -][0-9]{2}[ -][0-9]{6}[ -][0-9])",
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extractfull.lower().replace('Œ', '-'))
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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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"""Try to get bibtex entry from an ISBN number"""
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try:
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# Default merges results from worldcat.org and google books
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return isbntools.dev.fmt.fmtbib('bibtex',
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isbntools.meta(isbn, 'default'))
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except:
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return ''
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def findDOI(src):
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"""Search for a valid DOI in src.
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Returns the DOI or False if not found 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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"""
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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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extractfull = totext.communicate()
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# TODO : ^ Return result before full conversion ?
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if extractfull[1] is not "":
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# Error happened
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tools.warning(extractfull[1])
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return False
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extractfull = extractfull[0]
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extractDOI = re.search('(?<=doi)/?:?\s?[0-9\.]{7}/\S*[0-9]',
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extractfull.lower().replace('Œ', '-'))
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if not extractDOI:
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# PNAS fix
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extractDOI = re.search('(?<=doi).?10.1073/pnas\.\d+',
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extractfull.lower().replace('pnas', '/pnas'))
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if not extractDOI:
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# JSB fix
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extractDOI = re.search('10\.1083/jcb\.\d{9}', extractfull.lower())
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cleanDOI = False
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if extractDOI:
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cleanDOI = extractDOI.group(0).replace(':', '').replace(' ', '')
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if re.search('^/', cleanDOI):
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cleanDOI = cleanDOI[1:]
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# FABSE J fix
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if re.search('^10.1096', cleanDOI):
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cleanDOI = cleanDOI[:20]
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# Second JCB fix
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if re.search('^10.1083', cleanDOI):
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cleanDOI = cleanDOI[:21]
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if len(cleanDOI) > 40:
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cleanDOItemp = re.sub(r'\d\.\d', '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 cleanDOI
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def doi2Bib(doi):
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"""Return 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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try:
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r = requests.get(url, headers=headers)
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if r.headers['content-type'] == 'application/x-bibtex':
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return r.text
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else:
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return ''
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except requests.exceptions.ConnectionError:
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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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227
main.py
227
main.py
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@ -1,44 +1,22 @@
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#!/usr/bin/env python2
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# -*- coding: utf8 -*-
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from __future__ import print_function
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import tools
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import fetcher
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import backend
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import tearpages
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import sys
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import shutil
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import tempfile
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import requests
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import subprocess
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import re
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import os
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from isbntools import meta
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from isbntools.dev.fmt import fmtbib
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try:
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from cStringIO import StringIO
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except:
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from StringIO import StringIO
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from bibtexparser.bparser import BibTexParser
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from bibtexparser.customization import homogeneize_latex_encoding
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from bibtexparser.bwriter import bibtex as bibTexWriter
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from termios import tcflush, TCIOFLUSH
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import params
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EDITOR = os.environ.get('EDITOR') if os.environ.get('EDITOR') else 'vim'
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def rawInput(string):
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tcflush(sys.stdin, TCIOFLUSH)
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return raw_input(string)
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def warning(*objs):
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"""
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Write to stderr
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"""
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print("WARNING: ", *objs, file=sys.stderr)
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def parsed2Bibtex(parsed):
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"""
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Convert a single bibtex entry dict to bibtex string
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@ -51,165 +29,6 @@ def parsed2Bibtex(parsed):
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return bibtex
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def bibtexAppend(data):
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"""
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Append data to the main bibtex file
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data is a dict for one entry in bibtex, as the one from bibtexparser output
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"""
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with open(params.folder+'index.bib', 'a') as fh:
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fh.write(parsed2Bibtex(data)+"\n")
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def bibtexRewrite(data):
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"""
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Rewrite the bibtex index file.
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data is a dict of bibtex entry dict.
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"""
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bibtex = ''
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for entry in data.keys():
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bibtex += parsed2Bibtex(data[entry])+"\n"
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with open(params.folder+'index.bib', 'w') as fh:
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fh.write(bibtex)
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def replaceAll(text, dic):
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for i, j in dic.iteritems():
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text = text.replace(i, j)
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return text
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def findISBN(src):
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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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extractfull = totext.communicate()
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if extractfull[1] is not "":
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return False
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extractfull = extractfull[0]
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extractISBN = re.search(r"isbn (([0-9]{3}[ -])?[0-9][ -][0-9]{2}[ -][0-9]{6}[ -][0-9])",
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extractfull.lower().replace('Œ', '-'))
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cleanISBN = False
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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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try:
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return fmtbib('bibtex', meta(isbn, 'default'))
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except:
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return ''
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def findDOI(src):
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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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extractfull = totext.communicate()
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if extractfull[1] is not "":
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return False
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extractfull = extractfull[0]
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extractDOI = re.search('(?<=doi)/?:?\s?[0-9\.]{7}/\S*[0-9]',
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extractfull.lower().replace('Œ', '-'))
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if not extractDOI:
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# PNAS fix
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extractDOI = re.search('(?<=doi).?10.1073/pnas\.\d+',
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extractfull.lower().replace('pnas', '/pnas'))
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if not extractDOI:
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# JSB fix
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extractDOI = re.search('10\.1083/jcb\.\d{9}', extractfull.lower())
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cleanDOI = False
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if extractDOI:
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cleanDOI = extractDOI.group(0).replace(':', '').replace(' ', '')
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if re.search('^/', cleanDOI):
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cleanDOI = cleanDOI[1:]
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# FABSE J fix
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if re.search('^10.1096', cleanDOI):
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cleanDOI = cleanDOI[:20]
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# Second JCB fix
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if re.search('^10.1083', cleanDOI):
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cleanDOI = cleanDOI[:21]
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if len(cleanDOI) > 40:
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cleanDOItemp = re.sub(r'\d\.\d', '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 cleanDOI
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def doi2Bib(doi):
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"""
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Return 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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try:
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r = requests.get(url, headers=headers)
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if r.headers['content-type'] == 'application/x-bibtex':
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return r.text
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else:
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return ''
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except requests.exceptions.ConnectionError:
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warning('Unable to contact remote server to get the bibtex entry ' +
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'for doi '+doi)
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return ''
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_slugify_strip_re = re.compile(r'[^\w\s-]')
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_slugify_hyphenate_re = re.compile(r'[\s]+')
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def _slugify(value):
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"""
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Normalizes string, converts to lowercase, removes non-alpha characters,
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and converts spaces to hyphens.
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From Django's "django/template/defaultfilters.py".
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"""
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import unicodedata
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if not isinstance(value, unicode):
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value = unicode(value)
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value = unicodedata.normalize('NFKD', value).encode('ascii', 'ignore')
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value = unicode(_slugify_strip_re.sub('', value).strip())
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return _slugify_hyphenate_re.sub('_', value)
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def getExtension(filename):
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"""
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Get the extension of the filename
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"""
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return filename[filename.rfind('.'):]
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def checkBibtex(filename, bibtex):
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print("The bibtex entry found for "+filename+" is :")
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@ -222,7 +41,7 @@ def checkBibtex(filename, bibtex):
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else:
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bibtex_string = ''
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print(bibtex_string)
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check = rawInput("Is it correct ? [Y/n] ")
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check = tools.rawInput("Is it correct ? [Y/n] ")
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while check.lower() == 'n':
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with tempfile.NamedTemporaryFile(suffix=".tmp") as tmpfile:
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@ -240,7 +59,7 @@ def checkBibtex(filename, bibtex):
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bibtex_string = ''
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print("\nThe bibtex entry for "+filename+" is :")
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print(bibtex_string)
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check = rawInput("Is it correct ? [Y/n] ")
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check = tools.rawInput("Is it correct ? [Y/n] ")
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return bibtex
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@ -256,23 +75,23 @@ def addFile(src, filetype):
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if doi is False and isbn is False:
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if filetype is None:
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warning("Could not determine the DOI or the ISBN for "+src+"." +
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tools.warning("Could not determine the DOI or the ISBN for "+src+"." +
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"Switching to manual entry.")
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doi_isbn = ''
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while doi_isbn not in ['doi', 'isbn']:
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doi_isbn = rawInput("DOI / ISBN ? ").lower()
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doi_isbn = tools.rawInput("DOI / ISBN ? ").lower()
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if doi_isbn == 'doi':
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doi = rawInput('DOI ? ')
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doi = tools.rawInput('DOI ? ')
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else:
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isbn = rawInput('ISBN ? ')
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isbn = tools.rawInput('ISBN ? ')
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elif filetype == 'article':
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warning("Could not determine the DOI for "+src +
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tools.warning("Could not determine the DOI for "+src +
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", switching to manual entry.")
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doi = rawInput('DOI ? ')
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doi = tools.rawInput('DOI ? ')
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elif filetype == 'book':
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warning("Could not determine the ISBN for "+src +
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tools.warning("Could not determine the ISBN for "+src +
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", switching to manual entry.")
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isbn = rawInput('ISBN ? ')
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isbn = tools.rawInput('ISBN ? ')
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elif doi is not False:
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print("DOI for "+src+" is "+doi+".")
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elif isbn is not False:
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@ -310,13 +129,13 @@ def addFile(src, filetype):
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new_name = new_name.replace("%a", ', '.join([i.split(',')[0].strip()
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for i in authors]))
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new_name = params.folder+_slugify(new_name)+getExtension(src)
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new_name = params.folder+tools.slugify(new_name)+tools.getExtension(src)
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while os.path.exists(new_name):
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warning("file "+new_name+" already exists.")
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default_rename = new_name.replace(getExtension(new_name),
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" (2)"+getExtension(new_name))
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rename = rawInput("New name ["+default_rename+"] ? ")
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tools.warning("file "+new_name+" already exists.")
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default_rename = new_name.replace(tools.getExtension(new_name),
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" (2)"+tools.getExtension(new_name))
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rename = tools.rawInput("New name ["+default_rename+"] ? ")
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if rename == '':
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new_name = default_rename
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else:
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@ -351,7 +170,7 @@ def deleteId(ident):
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try:
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os.remove(bibtex[ident]['file'])
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except:
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warning("Unable to delete file associated to id "+ident+" : " +
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tools.warning("Unable to delete file associated to id "+ident+" : " +
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bibtex[ident]['file'])
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del(bibtex[ident])
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bibtexRewrite(bibtex)
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@ -373,7 +192,7 @@ def deleteFile(filename):
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try:
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os.remove(bibtex[key]['file'])
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except:
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warning("Unable to delete file associated to id "+key+" : " +
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tools.warning("Unable to delete file associated to id "+key+" : " +
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bibtex[key]['file'])
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del(bibtex[key])
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if found:
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|
|
@ -382,7 +201,7 @@ def deleteFile(filename):
|
|||
|
||||
|
||||
def downloadFile(url, filetype):
|
||||
dl, contenttype = fetcher.download_url(url)
|
||||
dl, contenttype = fetcher.download(url)
|
||||
|
||||
if dl is not False:
|
||||
tmp = tempfile.NamedTemporaryFile(suffix='.'+contenttype)
|
||||
|
|
@ -393,7 +212,7 @@ def downloadFile(url, filetype):
|
|||
tmp.close()
|
||||
return new_name
|
||||
else:
|
||||
warning("Could not fetch "+url)
|
||||
tools.warning("Could not fetch "+url)
|
||||
return False
|
||||
|
||||
|
||||
|
|
@ -434,13 +253,13 @@ if __name__ == '__main__':
|
|||
if len(sys.argv) < 3:
|
||||
sys.exit("Usage : " + sys.argv[0] + " delete FILE|ID")
|
||||
|
||||
confirm = rawInput("Are you sure you want to delete "+sys.argv[2] +
|
||||
confirm = tools.rawInput("Are you sure you want to delete "+sys.argv[2] +
|
||||
" ? [y/N] ")
|
||||
|
||||
if confirm.lower() == 'y':
|
||||
if not deleteId(sys.argv[2]):
|
||||
if not deleteFile(sys.argv[2]):
|
||||
warning("Unable to delete "+sys.argv[2])
|
||||
tools.warning("Unable to delete "+sys.argv[2])
|
||||
sys.exit(1)
|
||||
|
||||
print(sys.argv[2]+" successfully deleted.")
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
#!/usr/bin/env python
|
||||
#!/usr/bin/env python2
|
||||
# -*- coding: utf-8 -*-
|
||||
# Author: Francois Boulogne
|
||||
# License: GPLv3
|
||||
|
|
@ -30,6 +30,7 @@ def fixPdf(pdfFile, destination):
|
|||
output.close()
|
||||
shutil.copy(tmp.name, destination)
|
||||
|
||||
|
||||
def tearpage(filename):
|
||||
"""
|
||||
Copy filename to a tempfile, write pages 1..N to filename.
|
||||
|
|
@ -60,8 +61,8 @@ def tearpage(filename):
|
|||
|
||||
|
||||
if __name__ == '__main__':
|
||||
parser = argparse.ArgumentParser(description='Remove the first page of a PDF',
|
||||
epilog='')
|
||||
parser = argparse.ArgumentParser(description='Remove the first page ' +
|
||||
'of a PDF', epilog='')
|
||||
parser.add_argument('--version', action='version', version=__version__)
|
||||
parser.add_argument('pdf', metavar='PDF', help='PDF filepath')
|
||||
args = parser.parse_args()
|
||||
|
|
|
|||
Loading…
Reference in New Issue