def set_ref_from_entry(key, bib_data, ref_doc):
stream = StringIO.StringIO()
writer = bib_out.Writer(encoding='ascii')
writer.write_entry(key, bib_data.entries[key], stream)
ref_doc['bibtex'] = stream.getvalue()
try:
for field in bib_data.entries[key].fields:
value = bib_data.entries[key].fields[field]
fieldname = field.strip().lower()
rawvalue = value
value = bibtex_purify(value)
if fieldname == 'year':
ref_doc['year'] = int(value)
elif fieldname == 'doi':
doiPrepender = 'http://dx.doi.org/'
if not rawvalue.startswith("http://"):
rawvalue = doiPrepender + rawvalue
ref_doc['url'] = rawvalue
elif fieldname == 'url':
ref_doc['url'] = rawvalue
else:
ref_doc[fieldname] = value
authorsAsText = ""
firstAuthorSortKey = ""
count = 0
if bib_data.entries[key].persons:
numberOfAuthors = len(bib_data.entries[key].persons['author'])
for person in bib_data.entries[key].persons['author']:
first = person.get_part_as_text('first')
last = person.get_part_as_text('last')
simpleAuthor = bibtex_purify(first + ' ' + last)
if 'emph' in simpleAuthor:
simpleAuthor = simpleAuthor.replace('emph', '')
authorsAsText += simpleAuthor
if numberOfAuthors > 1:
if count != (numberOfAuthors - 1):
authorsAsText += ', '
if count == (numberOfAuthors - 2):
authorsAsText += ' and '
count += 1
firstAuthor = bib_data.entries[key].persons['author'][0]
firstAuthorSortKey = firstAuthor.get_part_as_text(
'last') + firstAuthor.get_part_as_text('first')
ref_doc['authorsAsText'] = authorsAsText
ref_doc['firstAuthorSortKey'] = firstAuthorSortKey
except Exception, e:
print "**** BIBTEX PARSING SCREWED UP ****"
print e
def as_string(self):
"""Return entry as formatted bibtex string."""
writer = outparser.Writer()
with io.StringIO() as stream:
writer.write_stream(self._entry2db(), stream)
string = stream.getvalue()
string = string.strip()
return string
def bibtex_edit(filename, tax_id, ref_doc):
parser = bib_in.Parser()
bib_data = parser.parse_file(filename)
writer = bib_out.Writer(encoding='ascii')
assert len(bib_data.entries.keys()) == 1
firstEntry = bib_data.entries.keys()[0]
ref_doc = set_ref_from_entry(firstEntry, bib_data, ref_doc)
ReferenceFamily(tax_id).save_reference(ref_doc)
def bibtex_import(filename):
parser = bib_in.Parser()
bib_data = parser.parse_file(filename)
writer = bib_out.Writer(encoding='ascii')
for key in bib_data.entries.keys():
print 'Key ' + key
stream = StringIO.StringIO()
writer.write_entry(key, bib_data.entries[key], stream)
ref_obj = get_ref(key, stream.getvalue())
ref_obj.save()
for field in bib_data.entries[key].fields:
value = bib_data.entries[key].fields[field]
col = get_column(field)
if 'title' in field.lower():
ref_obj.title = value
elif 'journal' in field.lower():
ref_obj.journal = value
elif 'year' in field.lower():
ref_obj.year = int(value)
attr = ReferenceAttribute(column=col, value=value)
attr.save()
ref_obj.referenceAttributes.add(attr)
if bib_data.entries[key].persons:
for person in bib_data.entries[key].persons['author']:
first = person.get_part_as_text('first')
middle = person.get_part_as_text('middle')
prelast = person.get_part_as_text('prelast')
last = person.get_part_as_text('last')
lineage = person.get_part_as_text('lineage')
auth = ReferenceAuthor(first_name=first,
middle_name=middle,
prelast_name=prelast,
last_name=last,
lineage=lineage)
auth.save()
ref_obj.authors.add(auth)
ref_obj.save()
print "Imported %i BibTeX references." % len(bib_data.entries)
from __future__ import print_function, unicode_literals, with_statement
import re
import sys
from os import path
from shutil import rmtree
from subprocess import PIPE, Popen
from tempfile import mkdtemp
from pybtex.database import BibliographyData, Entry, Person
from pybtex.database.output import bibtex
from pybtex.errors import report_error
from pybtex.exceptions import PybtexError
writer = bibtex.Writer(encoding='ascii')
def write_aux(filename, citations):
with open(filename, 'w') as aux_file:
for citation in citations:
aux_file.write('\\citation{%s}\n' % citation)
aux_file.write('\\bibdata{test}\n')
aux_file.write('\\bibstyle{test}\n')
def write_bib(filename, database):
writer.write_file(database, filename)
def write_bst(filename, style):
def bibtex_import(filename, taxonomyItem):
parser = bib_in.Parser()
bib_data = parser.parse_file(filename)
writer = bib_out.Writer(encoding='ascii')
for key in bib_data.entries.keys():
stream = StringIO.StringIO()
writer.write_entry(key, bib_data.entries[key], stream)
title = getTitle(bib_data.entries[key].fields)
ref_obj = get_ref(key, title, stream.getvalue())
try:
ref_obj.save()
for field in bib_data.entries[key].fields:
value = bib_data.entries[key].fields[field]
col = get_column(field)
if 'title' in field.lower():
ref_obj.title = title
elif 'journal' in field.lower():
ref_obj.journal = bibtex_purify(value)
elif 'year' in field.lower():
ref_obj.year = int(value)
elif 'url' in field.lower():
ref_obj.url = value
elif 'abstract' in field.lower():
ref_obj.abstract = value
elif 'doi' in field.lower():
doiPrepender = 'http://dx.doi.org/'
if not value.startswith(doiPrepender):
value = doiPrepender + value
ref_obj.url = value
attr = ReferenceAttribute(column=col, value=value)
attr.save()
ref_obj.referenceAttributes.add(attr)
authorsAsText = ""
count = 0
if bib_data.entries[key].persons:
numberOfAuthors = len(bib_data.entries[key].persons['author'])
for person in bib_data.entries[key].persons['author']:
first = person.get_part_as_text('first')
middle = person.get_part_as_text('middle')
prelast = person.get_part_as_text('prelast')
last = person.get_part_as_text('last')
lineage = person.get_part_as_text('lineage')
simpleAuthor = bibtex_purify(first + ' ' + last)
if 'emph' in simpleAuthor:
simpleAuthor = simpleAuthor.replace('emph', '')
authorsAsText += simpleAuthor
if numberOfAuthors > 1:
if count != (numberOfAuthors -1):
authorsAsText += ', '
if count == (numberOfAuthors - 2):
authorsAsText += ' and '
count += 1
try:
author, created = ReferenceAuthor.objects.get_or_create(first_name=first, last_name=last)
except Exception, e:
logger.debug(
'Author ' + first + ' ' + last + ' exists in multiple places. Error is ' + e.message)
author = ReferenceAuthor.objects.filter(first_name=first).filter(last_name=last).__getitem__(0)
created = False
if created:
author.middle_name = middle
author.prelast_name = prelast
author.lineage = lineage
author.save()
if not author in ref_obj.authors.all():
ref_obj.authors.add(author)
ref_obj.authorsAsText = authorsAsText
ref_obj.save()
if not ref_obj in taxonomyItem.references.all():
taxonomyItem.references.add(ref_obj)
except Exception, e:
logger.log(e.message)
connection._rollback()
def to_file(self, path):
"""Write entry bibtex to file."""
writer = outparser.Writer(encoding='utf-8')
writer.write_file(self._entry2db(), path)
def write_output(args, bibs):
writer = bibtex_output.Writer()
writer.write_file(bibs, args.output_bibtex)