def preExecute(self):
set_strict_mode(
False) # allow incorrectly formatted author/editor names
# If this is invoked during a live serve, we need to recompile the list of '.bib' files and
# read them again, otherwise there's no way to distinguish existing entries from duplicates
self.__bib_files = []
for node in self.translator.findPages(
lambda p: p.source.endswith('.bib')):
self.__bib_files.append(node.source)
self.__database = BibliographyData()
for bfile in self.__bib_files:
try:
db = parse_file(bfile)
self.__bib_file_database[bfile] = db
except UndefinedMacro as e:
msg = "The BibTeX file %s has an undefined macro:\n%s"
LOG.warning(msg, bfile, e)
#TODO: https://bitbucket.org/pybtex-devs/pybtex/issues/93/
# databaseadd_entries-method-not-considering
for key in db.entries:
if key in self.__database.entries:
if self.get('duplicate_warning') and (
key not in self.get('duplicates')):
msg = "The BibTeX entry '%s' defined in %s already exists."
LOG.warning(msg, key, bfile)
else:
self.__database.add_entry(key, db.entries[key])
def preExecute(self):
duplicates = self.get('duplicates', list())
set_strict_mode(False)
self.__database = BibliographyData()
self.__bib_files = []
for node in self.translator.getPages():
if node.source.endswith('.bib'):
self.__bib_files.append(node.source)
for bfile in self.__bib_files:
try:
db = parse_file(bfile)
self.__bib_file_database[bfile] = db
except UndefinedMacro as e:
msg = "The BibTeX file %s has an undefined macro:\n%s"
LOG.warning(msg, bfile, e)
#TODO: https://bitbucket.org/pybtex-devs/pybtex/issues/93/
# databaseadd_entries-method-not-considering
warn = self.get('duplicate_warning')
for key in db.entries:
duplicate_key = key in self.__database.entries
duplicate_key_allowed = key in duplicates
if duplicate_key and (not duplicate_key_allowed):
if warn:
msg = "The BibTeX entry '%s' defined in %s already exists."
LOG.warning(msg, key, bfile)
elif not duplicate_key:
self.__database.add_entry(key, db.entries[key])
def handleNewBib(fileName):
"""
Handle a BibTeX file that has just appeared in the drop folder.
:param fileName: The name of the new BibTeX file.
"""
clipboard = ""
pybtexErrors.set_strict_mode(False) # do not exit on an exception
bib_data = readBib(fileName)
mode = Modes.REGULAR
index = -1
count = len(bib_data.entries)
# Doing it in two separate loops,
# so all entries would get the same time stamp.
newEntries = {}
for key in bib_data.entries:
index += 1
entry = bib_data.entries[key]
newKey = keygen(entry)
# '' -- no author, i.e. the venue itself
if newKey == '' or newKey == 'BadKey':
continue
(newKey, mode) = duplicateCheck(newKey, mode, index < count - 1)
if newKey == 'BadKey':
continue # the user decided to not create duplicate entry
# delete the crossref field; using a hack (access to _dict and order)
try:
entry.fields._dict.pop('crossref')
entry.fields.order.remove('crossref')
except:
pass
newEntries[newKey] = entry
for newKey in newEntries:
entry = newEntries[newKey]
paperDir = config.PAPERS_DIR + newKey
bibFileName = paperDir + "/paper.bib"
orgFileName = paperDir + "/paper.org"
try:
#pdb.set_trace()
os.system("mkdir -p " + paperDir) # create the paper directory
saveEntry(newKey, entry, bibFileName)
os.system("touch " + orgFileName) # create the org file
clipboard += newKey + ','
#pyperclip.copy(clipboard[:-1])
os.system("echo -n {s} | xsel -bi".format(s=clipboard[:-1]))
except:
tkMessageBox.showerror(
'LiteRef Error', 'Could not create the files for the key: ' +
newKey + '\nAbandoning the key.')
config.root.update()
os.system("mv {fileName} {archive}".format(fileName=fileName,
archive=config.DROP_DIR +
".last.bib"))
def main(self):
errors.set_strict_mode(False)
argv = self.recognize_legacy_optons(sys.argv[1:])
options, args = self.opt_parser.parse_args(argv)
if len(args) != self.num_args:
self.opt_parser.print_help()
sys.exit(1)
kwargs = self._extract_kwargs(options)
self.run(*args, **kwargs)
sys.exit(errors.error_code)
def main(self):
errors.set_strict_mode(False)
argv = self.recognize_legacy_optons(sys.argv[1:])
options, args = self.opt_parser.parse_args(argv)
if len(args) != self.num_args:
self.opt_parser.print_help()
sys.exit(1)
kwargs = self._extract_kwargs(options)
self.run(*args, **kwargs)
sys.exit(errors.error_code)
def main(path, strict=False):
set_strict_mode(strict)
loop = asyncio.get_event_loop()
newbib = loop.run_until_complete(fix_bibtex(path))
basename, ext = os.path.splitext(path)
newbib_path = '{}.new{}'.format(basename, ext)
newbib.to_file(newbib_path)
oldbib_path = '{}.old{}'.format(basename, ext)
parse_bibfile(path).to_file(oldbib_path)
print('\nPatched file:', newbib_path)
print('Original file:', oldbib_path)
print('Use a diff tool to see changes:')
print(' ', _difftool(), oldbib_path, newbib_path)
def is_valid_bibtex(reference):
"""
Use pybtex to validate that a reference is in proper BibTeX format
Args:
reference: A String reference in BibTeX format.
Returns:
Boolean indicating if reference is valid bibtex.
"""
# str is necessary since pybtex seems to have an issue with unicode. The
# filter expression removes all non-ASCII characters.
sio = StringIO(remove_non_ascii(reference))
parser = bibtex.Parser()
errors.set_strict_mode(False)
bib_data = parser.parse_stream(sio)
return len(bib_data.entries) > 0
def is_valid_bibtex(reference):
"""
Use pybtex to validate that a reference is in proper BibTeX format
Args:
reference: A String reference in BibTeX format.
Returns:
Boolean indicating if reference is valid bibtex.
"""
# str is necessary since pybtex seems to have an issue with unicode. The
# filter expression removes all non-ASCII characters.
sio = StringIO(remove_non_ascii(reference))
parser = bibtex.Parser()
errors.set_strict_mode(False)
bib_data = parser.parse_stream(sio)
return len(bib_data.entries) > 0
def backwards_search(file):
set_strict_mode(False)
bibfile = parse_file(file)
entries = bibfile.entries.values()
#entries = entries[0:7]
pool = Pool(processes=8)
rows = []
for result in pool.imap(get_references_for_entry, entries):
if result:
entry, refs = result
entry_name = get_entry_name(entry)
for ref in refs:
ref_name = clean_raw_ref(ref["raw_ref"][0])
rows.append((entry.key, entry_name, ref_name))
df = DataFrame(rows, columns=['paper_key', 'paper_name', 'ref_name'])
return df
def make_standard_option(*args, **kwargs):
option = make_option(*args, **kwargs)
PybtexOption.STANDARD_OPTIONS[option.dest] = option
return option
def standard_option(name):
return PybtexOption.STANDARD_OPTIONS[name]
make_standard_option(
'--strict',
dest='strict',
help='turn warnings into errors',
action='callback',
callback=lambda option, opt, value, parser: errors.set_strict_mode(True))
make_standard_option(
'-f',
'--bibliography-format',
dest='bib_format',
help='bibliograpy format (%plugin_choices)',
type='load_plugin',
plugin_group='pybtex.database.input',
metavar='FORMAT',
)
make_standard_option(
'-b',
'--output-backend',
dest='output_backend',
#Synthesize LaTeX author compilation from .bib and processed .aux
#Brygg Ullmer, Clemson University
#Begun 2021-02-27
#https://stackoverflow.com/questions/30768745/is-there-a-reliable-python-library-for-taking-a-bibtex-entry-and-outputting-it-i
from pybtex.database.input import bibtex
from pybtex import errors
import pandas as pd
import sys
errors.set_strict_mode(False)
parser = bibtex.Parser()
bib_data = parser.parse_file('tangibles-common6.bib')
citationsFn = 'citations4.txt'
citationsF = open(citationsFn, 'r+t')
lines = citationsF.readlines()
citations = {}
for line in lines:
cleanline = line.rstrip()
citations[cleanline] = True
authors = {}
for el in bib_data.entries:
bibref = str(el)
#if bibref in citations:
# print('Y', bibref)
#else:
# print('N', bibref)
def make_standard_option(*args, **kwargs):
option = make_option(*args, **kwargs)
PybtexOption.STANDARD_OPTIONS[option.dest] = option
return option
def standard_option(name):
return PybtexOption.STANDARD_OPTIONS[name]
make_standard_option(
'--strict', dest='strict',
help='turn warnings into errors',
action='callback',
callback=lambda option, opt, value, parser: errors.set_strict_mode(True)
)
make_standard_option(
'-f', '--bibliography-format', dest='bib_format',
help='bibliograpy format (%plugin_choices)',
type='load_plugin',
plugin_group='pybtex.database.input',
metavar='FORMAT',
)
make_standard_option(
'-b', '--output-backend', dest='output_backend',
help='output backend (%plugin_choices)',
type='load_plugin',
plugin_group='pybtex.backends',