bmc/main.py

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Python
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#!/usr/bin/python2 -u
# coding=utf8
"""
Main app
"""
import sys
import shutil
import requests
import subprocess
import re
try:
from cStringIO import StringIO
except:
from StringIO import StringIO
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from bibtexparser.bparser import BibTexParser
import params
def bibtexAppend(data):
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"""
Append data to the main bibtex file
data is a dict as the one from bibtexparser output
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"""
bibtex = ''
for field, value in data:
bibtex += "\n" + field + ": " + value + ","
# TODO : Write
def replaceAll(text, dic):
for i, j in dic.iteritems():
text = text.replace(i, j)
return text
def PDF2Doi(pdf):
pdftotext = subprocess.Popen(["pdftotext", pdf, "-"],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
extractfull = pdftotext.communicate()
if extractfull[1] is not "":
return False
extractfull = extractfull[0]
extractDOI = re.search('(?<=doi)/?:?\s?[0-9\.]{7}/\S*[0-9]',
extractfull.lower().replace('&#338;', '-'))
if not extractDOI:
# PNAS fix
extractDOI = re.search('(?<=doi).?10.1073/pnas\.\d+',
extractfull.lower().replace('pnas', '/pnas'))
if not extractDOI:
# JSB fix
extractDOI = re.search('10\.1083/jcb\.\d{9}', extractfull.lower())
cleanDOI = False
if extractDOI:
cleanDOI = extractDOI.group(0).replace(':', '').replace(' ', '')
if re.search('^/', cleanDOI):
cleanDOI = cleanDOI[1:]
# FABSE J fix
if re.search('^10.1096', cleanDOI):
cleanDOI = cleanDOI[:20]
# Second JCB fix
if re.search('^10.1083', cleanDOI):
cleanDOI = cleanDOI[:21]
if len(cleanDOI) > 40:
cleanDOItemp = re.sub(r'\d\.\d', '000', cleanDOI)
reps = {'.': 'A', '-': '0'}
cleanDOItemp = 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):
"""
Return 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"}
r = requests.get(url, headers=headers)
return r.text
def addFile(src):
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"""
Add a file to the library
"""
doi = PDF2Doi(src)
if doi is False:
print("Could not determine the DOI for "+src+", switching to manual " +
"entry.")
doi = raw_input('DOI ? ')
else:
print("DOI for "+src+" is "+doi+".")
bibtex = doi2Bib(doi).strip().replace(',', ",\n")
bibtex = StringIO(bibtex)
bibtex = BibTexParser(bibtex).get_entry_dict()
# TODO : Rename
new_name = params.folder+"/"+doi
bibtex[bibtex.keys()[0]]['file'] = new_name
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try:
shutil.copy2(src, new_name)
except IOError:
sys.exit("Unable to move file to library dir " + params.folder+".")
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bibtexAppend(bibtex)
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print("File " + src + " successfully imported.")
if __name__ == '__main__':
if len(sys.argv) < 2:
sys.exit("Usage : TODO")
if sys.argv[1] == 'download':
raise Exception('TODO')
if sys.argv[1] == 'import':
if len(sys.argv) < 3:
sys.exit("Usage : " + sys.argv[0] + " import FILE")
addFile(sys.argv[2])
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sys.exit()
elif sys.argv[1] == 'list':
raise Exception('TODO')
elif sys.argv[1] == 'search':
raise Exception('TODO')