ea53e0720f
* Search the PDF file for DOI, manual fallback if not found * Move the PDF file * Add its Bibtex entry to the general bibtex file TODO : * Better renaming * Adding to bibtex file
147 lines
3.7 KiB
Python
Executable File
147 lines
3.7 KiB
Python
Executable File
#!/usr/bin/python2 -u
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# coding=utf8
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"""
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Main app
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"""
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import sys
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import shutil
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import requests
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import subprocess
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import re
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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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import params
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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 as the one from bibtexparser output
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"""
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bibtex = ''
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for field, value in data:
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bibtex += "\n" + field + ": " + value + ","
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# TODO : Write
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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 PDF2Doi(pdf):
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pdftotext = subprocess.Popen(["pdftotext", pdf, "-"],
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stdout=subprocess.PIPE,
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stderr=subprocess.PIPE)
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extractfull = pdftotext.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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r = requests.get(url, headers=headers)
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return r.text
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def addFile(src):
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"""
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Add a file to the library
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"""
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doi = PDF2Doi(src)
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if doi is False:
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print("Could not determine the DOI for "+src+", switching to manual " +
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"entry.")
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doi = raw_input('DOI ? ')
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else:
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print("DOI for "+src+" is "+doi+".")
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bibtex = doi2Bib(doi).strip().replace(',', ",\n")
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bibtex = StringIO(bibtex)
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bibtex = BibTexParser(bibtex).get_entry_dict()
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# TODO : Rename
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new_name = params.folder+"/"+doi
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bibtex[bibtex.keys()[0]]['file'] = new_name
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try:
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shutil.copy2(src, new_name)
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except IOError:
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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.")
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if __name__ == '__main__':
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if len(sys.argv) < 2:
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sys.exit("Usage : TODO")
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if sys.argv[1] == 'download':
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raise Exception('TODO')
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if sys.argv[1] == 'import':
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if len(sys.argv) < 3:
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sys.exit("Usage : " + sys.argv[0] + " import FILE")
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addFile(sys.argv[2])
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sys.exit()
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elif sys.argv[1] == 'list':
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raise Exception('TODO')
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elif sys.argv[1] == 'search':
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raise Exception('TODO')
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