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.
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Phyks
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11
README.md
11
README.md
@ -31,6 +31,13 @@ Should be almost working and usable now, although still to be considered as **ex
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**Important note :** I use it for personal use, but I don't read articles from many journals. If you find any file which is not working, please fill an issue or send me an e-mail with the relevant information. There are alternative ways to get the metadata for example, and I didn't know really which one was the best one as writing this code.
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* Import
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* working : all (file / tags / bibtex modification / bibtex retrieval / remove watermark pages)
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* Download
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* working : all
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* Delete
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* working : all (by file and by id)
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## Installation
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* Clone this git repository where you want : `git clone https://github.com/Phyks/BMC`
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@ -123,8 +130,8 @@ Tree à la docear ?
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## Issues ?
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* Multiplication of {{}} => solved in bibtexparser
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* UTF-8 and bibtexparser => solved upstream
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* delete / edit => problem with filename encoding
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* UTF-8 and bibtexparser => solved upstream in bibtexparser
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===> TODO : update bibtexparser when available in pip
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## Thanks
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18
backend.py
18
backend.py
@ -54,16 +54,6 @@ def getNewName(src, bibtex, tag=''):
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return new_name
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def parsed2Bibtex(parsed):
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"""Convert a single bibtex entry dict to bibtex string"""
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bibtex = '@'+parsed['type']+'{'+parsed['id']+",\n"
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for field in [i for i in sorted(parsed) if i not in ['type', 'id']]:
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bibtex += "\t"+field+"={"+parsed[field]+"},\n"
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bibtex += "}\n\n"
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return bibtex
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def bibtexAppend(data):
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"""Append data to the main bibtex file
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@ -71,7 +61,7 @@ def bibtexAppend(data):
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"""
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try:
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with open(params.folder+'index.bib', 'a', encoding='utf-8') as fh:
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fh.write(parsed2Bibtex(data)+"\n")
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fh.write(tools.parsed2Bibtex(data)+"\n")
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except:
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tools.warning("Unable to open index file.")
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return False
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@ -100,7 +90,7 @@ def bibtexRewrite(data):
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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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bibtex += tools.parsed2Bibtex(data[entry])+"\n"
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try:
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with open(params.folder+'index.bib', 'w', encoding='utf-8') as fh:
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fh.write(bibtex)
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@ -113,7 +103,7 @@ def deleteId(ident):
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"""Delete a file based on its id in the bibtex file"""
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try:
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with open(params.folder+'index.bib', 'r', encoding='utf-8') as fh:
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bibtex = BibTexParser(fh.read())
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bibtex = BibTexParser(fh.read().decode('utf-8'))
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bibtex = bibtex.get_entry_dict()
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except:
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tools.warning("Unable to open index file.")
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@ -148,7 +138,7 @@ def deleteFile(filename):
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"""Delete a file based on its filename"""
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try:
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with open(params.folder+'index.bib', 'r', encoding='utf-8') as fh:
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bibtex = BibTexParser(fh.read())
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bibtex = BibTexParser(fh.read().decode('utf-8'))
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bibtex = bibtex.get_entry_dict()
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except:
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tools.warning("Unable to open index file.")
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32
fetcher.py
32
fetcher.py
@ -8,6 +8,8 @@ import subprocess
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import arxiv2bib as arxiv_metadata
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import tools
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import params
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from bibtexparser.bparser import BibTexParser
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from isbntools.dev.fmt import fmtbib
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def download(url):
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@ -41,7 +43,8 @@ def download(url):
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return False
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isbn_re = re.compile(r"isbn (([0-9]{3}[ -])?[0-9][ -][0-9]{2}[ -][0-9]{6}[-][0-9])")
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isbn_re = re.compile(r"isbn (([0-9]{3}[ -])?[0-9][ -][0-9]{2}[ -][0-9]{6}[ -][0-9])",
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re.IGNORECASE)
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def findISBN(src):
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@ -84,17 +87,13 @@ def findISBN(src):
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def isbn2Bib(isbn):
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"""Tries 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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return fmtbib('bibtex', isbntools.meta(isbn, 'default'))
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doi_re = re.compile('(?<=doi)/?:?\s?[0-9\.]{7}/\S*[0-9]')
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doi_pnas_re = re.compile('(?<=doi).?10.1073/pnas\.\d+')
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doi_jsb_re = re.compile('10\.1083/jcb\.\d{9}')
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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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@ -183,7 +182,7 @@ def doi2Bib(doi):
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return ''
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arXiv_re = re.compile(r'arXiv:\s*([\w\.\/\-]+)')
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arXiv_re = re.compile(r'arXiv:\s*([\w\.\/\-]+)', re.IGNORECASE)
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def findArXivId(src):
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@ -215,8 +214,10 @@ def findArXivId(src):
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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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elif extractID is not None:
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return extractID.group(1)
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else:
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return False
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def arXiv2Bib(arxiv):
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@ -229,7 +230,14 @@ def arXiv2Bib(arxiv):
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if isinstance(bib, arxiv_metadata.ReferenceErrorInfo):
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continue
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else:
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return bib.bibtex()
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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[fetched_bibtex.keys()[0]]
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try:
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del(fetched_bibtex['file'])
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except:
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pass
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return tools.parsed2Bibtex(fetched_bibtex)
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return False
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12
main.py
12
main.py
@ -27,7 +27,7 @@ def checkBibtex(filename, bibtex):
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if len(bibtex) > 0:
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bibtex_name = bibtex.keys()[0]
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bibtex = bibtex[bibtex_name]
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bibtex_string = backend.parsed2Bibtex(bibtex)
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bibtex_string = tools.parsed2Bibtex(bibtex)
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else:
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bibtex_string = ''
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print(bibtex_string)
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@ -54,7 +54,7 @@ def checkBibtex(filename, bibtex):
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if len(bibtex) > 0:
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bibtex_name = bibtex.keys()[0]
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bibtex = bibtex[bibtex_name]
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bibtex_string = backend.parsed2Bibtex(bibtex)
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bibtex_string = tools.parsed2Bibtex(bibtex)
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else:
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bibtex_string = ''
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print("\nThe bibtex entry for "+filename+" is:")
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@ -80,17 +80,17 @@ def addFile(src, filetype, manual):
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if not manual:
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if filetype == 'article' or filetype is None:
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doi = fetcher.findDOI(src)
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if (filetype == 'article' or filetype is None) and doi is False:
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if doi is False and (filetype == 'article' or filetype is None):
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arxiv = fetcher.findArXivId(src)
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if filetype == 'book' or (filetype is None and doi is False and
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arxiv is False):
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if filetype == 'book' or (doi is False and arxiv is False and
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filetype is None):
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isbn = fetcher.findISBN(src)
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if doi is False and isbn is False and arxiv is False:
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if filetype is None:
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tools.warning("Could not determine the DOI nor the arXiv id nor " +
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"the ISBN for "+src+"."+"Switching to manual entry.")
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"the ISBN for "+src+". Switching to manual entry.")
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doi_arxiv_isbn = ''
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while doi_arxiv_isbn not in ['doi', 'arxiv', 'isbn', 'manual']:
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doi_arxiv_isbn = tools.rawInput("DOI / arXiv " +
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10
tools.py
10
tools.py
@ -24,6 +24,16 @@ def slugify(value):
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return _slugify_hyphenate_re.sub('_', value)
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def parsed2Bibtex(parsed):
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"""Convert a single bibtex entry dict to bibtex string"""
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bibtex = '@'+parsed['type']+'{'+parsed['id']+",\n"
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for field in [i for i in sorted(parsed) if i not in ['type', 'id']]:
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bibtex += "\t"+field+"={"+parsed[field]+"},\n"
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bibtex += "}\n\n"
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return bibtex
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def getExtension(filename):
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"""Get the extension of filename"""
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return filename[filename.rfind('.'):]
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