def format_paper_citation_dict(citation, indent=' '):
"""
Format a citation dict for a paper or a list of papers into a BibTeX
record string.
:param citation: A ``Paper`` citation dict or list of such dicts.
:param indent: Indentation to be used in BibTeX output.
"""
if isinstance(citation, dict):
entries = [citation]
else:
entries = citation
# Handle conflicting ids for entries
entries_ids = collections.defaultdict(lambda: 0)
for entry in entries:
entry_id = entry['ID']
entries_ids[entry_id] += 1
if entries_ids[entry_id] > 1:
entry['ID'] = '%s_%s' % (entry_id, entries_ids[entry_id])
writer = BibTexWriter()
writer.indent = indent
with io.StringIO('') as bibfile:
db = BibDatabase()
db.entries = entries
bibfile.write(writer.write(db))
return bibfile.getvalue().strip()
def load_and_replace(bibtex_file):
with open(os.path.join('publications', bibtex_file),
'r',
encoding="utf-8") as f:
fdata = f.read()
pdict = BibTexParser(fdata).get_entry_dict()
plist = BibTexParser(fdata, bc.author).get_entry_list()
by_year = {}
for pub in plist:
pubd = pdict[pub['ID']]
db = BibDatabase()
db.entries = [pubd]
writer = BibTexWriter()
writer.indent = '\t'
bibentry = writer.write(db)
pub['BIB_ENTRY'] = bibentry
for field in pub:
if field == 'BIB_ENTRY':
continue
pub[field] = context.make_replacements(pub[field])
pub['author'] = _format_author_list(pub['author'])
y = int(pub['year']) if 'year' in pub else 1970
if y not in by_year:
by_year[y] = []
by_year[y].append(pub)
ret = []
for year, pubs in sorted(by_year.items(), reverse=True):
for pub in pubs:
ret.append(pub)
return ret
def work_to_bibtex(work, name=None, acronym=False, rules=None):
"""Convert work to bibtex text
Doctest:
.. doctest::
>>> reload()
>>> murta2014a = work_by_varname("murta2014a")
>>> print(work_to_bibtex(murta2014a))
@inproceedings{murta2014a,
address = {Cologne, Germany},
author = {Murta, Leonardo and Braganholo, Vanessa and Chirigati, Fernando and Koop, David and Freire, Juliana},
booktitle = {International Provenance and Annotation Workshop},
pages = {71--83},
publisher = {Springer},
title = {no{W}orkflow: capturing and analyzing provenance of scripts},
year = {2014}
}
<BLANKLINE>
<BLANKLINE>
Custom name:
>>> reload()
>>> murta2014a = work_by_varname("murta2014a")
>>> print(work_to_bibtex(murta2014a, name="other"))
@inproceedings{other,
address = {Cologne, Germany},
author = {Murta, Leonardo and Braganholo, Vanessa and Chirigati, Fernando and Koop, David and Freire, Juliana},
booktitle = {International Provenance and Annotation Workshop},
pages = {71--83},
publisher = {Springer},
title = {no{W}orkflow: capturing and analyzing provenance of scripts},
year = {2014}
}
<BLANKLINE>
<BLANKLINE>
Use acronym for place name:
>>> print(work_to_bibtex(murta2014a, acronym=True))
@inproceedings{murta2014a,
address = {Cologne, Germany},
author = {Murta, Leonardo and Braganholo, Vanessa and Chirigati, Fernando and Koop, David and Freire, Juliana},
booktitle = {IPAW},
pages = {71--83},
publisher = {Springer},
title = {no{W}orkflow: capturing and analyzing provenance of scripts},
year = {2014}
}
<BLANKLINE>
<BLANKLINE>
"""
result = work_to_bibtex_entry(work, name=name, acronym=acronym, rules=rules)
db = BibDatabase()
db.entries = [result]
writer = BibTexWriter()
writer.indent = " "
return writer.write(db)
def main_resps():
in_file = Path("data/resps-perturbed-tides.txt")
bibs = parse_citations(in_file)
db = BibDatabase()
db.entries = [
bib.to_bibtex() for bib in bibs
]
id_to_count = defaultdict(lambda : 0)
for entry in db.entries:
id_to_count[entry["ID"]] += 1
for the_id, count in id_to_count.items():
if count > 1:
for entry in [e for e in db.entries if e["ID"] == the_id]:
count -= 1
entry["ID"] += ascii_lowercase[count]
writer = BibTexWriter()
writer.indent = " "
with Path("data/resps-tides-perturbed-refs.bib").open("wb") as ref_file:
ref_file.write(writer.write(db).encode())
def save(self, bibfile=-1):
"""
save the biblist with :
- the original filename without any arg
or
- the given file name if not empty
"""
if bibfile == -1:
bibfile = self.name
db = BibDatabase()
for item in self:
db.entries.append(item)
writer = BibTexWriter() # this class is needed to prepare format
writer.indent = ' ' # indent entries with 4 spaces instead of one
writer.comma_first = False # place the comma at the beginning of the line
writer.align_values = True # with a nice indentation
print('')
print(os.path.join(os.path.expandvars('$PYBLIO_BIB'), bibfile))
print('')
with open(os.path.join(os.path.expandvars('$PYBLIO_BIB'), bibfile), 'w') as bf:
bf.write('\n')
bf.write(writer.write(db))
bf.write('\n')
def metaDictToBib(jobid, metadict, omit_keys, path_prefix):
"""Export meta data to bibtex format
Args:
jobid (int): id of job.
metadict (DocMeta): meta dict of a doc.
alt_dict (dict): dict for key changes.
omit_keys (list): keys to omit in the converted dict.
path_prefix (str): folder path to prepend to attachment file paths.
Returns:
rec (int): 0 if successful, 1 otherwise.
jobid (int): the input jobid as it is.
dbtext (str): formated bibtex entry, '' if <rec>==1.
docid (int): id of the processed document.
"""
try:
alt_dict = INV_ALT_KEYS
ord_dict = toOrdinaryDict(metadict, alt_dict, omit_keys, path_prefix)
db = BibDatabase()
db.entries = [
ord_dict,
]
writer = BibTexWriter()
writer.indent = ' '
writer.comma_first = False
dbtext = writer.write(db)
return 0, jobid, dbtext, metadict['id']
except Exception:
LOGGER.exception('Failed to write to bibtex')
return 1, jobid, '', metadict['id']
def format_paper_citation_dict(citation, indent=' '):
"""
Format a citation dict for a paper or a list of papers into a BibTeX
record string.
:param citation: A ``Paper`` citation dict or list of such dicts.
:param indent: Indentation to be used in BibTeX output.
"""
if isinstance(citation, dict):
entries = [citation]
else:
entries = citation
# Handle conflicting ids for entries
entries_ids = collections.defaultdict(lambda: 0)
for entry in entries:
entry_id = entry['ID']
entries_ids[entry_id] += 1
if entries_ids[entry_id] > 1:
entry['ID'] = '%s_%s' % (entry_id, entries_ids[entry_id])
writer = BibTexWriter()
writer.indent = indent
with io.StringIO('') as bibfile:
db = BibDatabase()
db.entries = entries
bibfile.write(writer.write(db))
return bibfile.getvalue().strip()
def getcitation():
articlesparser = BibTexParser(common_strings=False)
articlesparser.ignore_nonstandard_types = False
with open('/home/limingtao/ircre-bibtex/ircreupdate/articles.bib', encoding='utf8') as articlesfile:
articles_database = bibtexparser.load(articlesfile, articlesparser)
articleentries = articles_database.entries
import random
samplelist = random.sample(range(len(articleentries)), 20)
print(samplelist)
for i in samplelist:
print("---------------------------")
print("Entry number: " + str(i))
title = articleentries[i]['title']
clusterid = articleentries[i]['clusterid']
print("Title: " + title)
print("Cluster ID: " + clusterid)
if not clusterid == "unknown":
print(str(i))
try:
citations = os.popen(
'''/usr/bin/python3 /home/limingtao/ircre-bibtex/ircreupdate/scholarpy/scholar.py -c 1 -C ''' + clusterid + ''' |grep -v list |grep Citations''').read().strip().split()[
-1]
except:
citations = "unknown"
else:
citations = "unknown"
print("new Citations: " + citations)
if 'cited' in articleentries[i]:
oldcitednumber = int(articleentries[i]['cited'])
else:
oldcitednumber = 0
print("Old Cited Number: " + str(oldcitednumber))
if not citations == "unknown":
citednumber = int(citations)
if citednumber > oldcitednumber and ((citednumber - oldcitednumber) < 8):
articleentries[i]['cited'] = str(citednumber)
writer = BibTexWriter()
writer.indent = ' '
writer.order_entries_by = ('order',)
with open('/home/limingtao/ircre-bibtex/ircreupdate/cited-add-articles.bib', 'w', encoding='utf8') as newarticlefile:
bibtexparser.dump(articles_database, newarticlefile, writer=writer)
os.popen("cp /home/limingtao/ircre-bibtex/ircreupdate/cited-add-articles.bib tempcited-add-articles.bib")
os.popen("cp /home/limingtao/ircre-bibtex/ircreupdate/articles.bib /home/limingtao/ircre-bibtex/ircreupdate/oldarticles.bib")
with open('/home/limingtao/ircre-bibtex/ircreupdate/articles.bib', 'w', encoding='utf8') as newarticlefile:
bibtexparser.dump(articles_database, newarticlefile, writer=writer)
return 0
def getBibtexStrFromAbstractDict(abstractDict):
abstractDict.pop('url')
abstractDict.pop('journal')
db = BibDatabase()
writer = BibTexWriter()
writer.indent = ' '
db.entries = [abstractDict]
return writer.write(db)
def write_bib(bib_database, filen="dl4m.bib"):
"""Description of write_bib
Write the items stored in bib_database into filen
"""
writer = BibTexWriter()
writer.indent = ' '
writer.order_entries_by = ('noneyear', "author")
with open(filen, "w", encoding="utf-8") as bibfile:
bibfile.write(writer.write(bib_database))
def write_bibtex(db, filename):
'''
Writes the database into the file named filename
'''
with open(filename, 'w', encoding='utf-8') as bibtex_file:
writer = BibTexWriter()
writer.add_trailing_comma = True
writer.indent = ''
bibtexparser.dump(db, bibtex_file, writer)
def _writer():
'''
Return a configured bibtex writer.
'''
writer = BibTexWriter()
writer.indent = ' '
writer.order_entries_by = ('ID',)
writer.display_order = ['title', 'author', 'editor']
return writer
def make_bibs(self, prefix, output):
all_bibs = self.get_all_bibs(prefix)
bib_db = BibDatabase()
bib_db.entries = all_bibs
writer = BibTexWriter()
writer.indent = '\t'
with open(output, 'w') as f:
bibtexparser.dump(bib_db, f, writer)
logging.info('processed %d bib entries', len(all_bibs))
def convert_to_bib(content, save_fpath):
papers = parse_api_response(content)
db = BibDatabase()
db.entries = papers
writer = BibTexWriter()
writer.indent = " "
writer.comma_first = True
with open(save_fpath, "w+") as bibfile:
bibfile.write(writer.write(db))
def dumps(bibman):
db = bibtexparser.bparser.BibDatabase()
db._entries_dict = bibman.cleaned
db.entries = list(bibman.cleaned.values())
writer = BibTexWriter()
# writer.order_entries_by = ('type', 'author', 'year')
writer.order_entries_by = None
writer.contents = ['comments', 'entries']
writer.indent = ' '
new_text = bibtexparser.dumps(db, writer)
return new_text
def bibtexclassify():
parser = BibTexParser(common_strings=False)
parser.ignore_nonstandard_types = False
with open('/home/limingtao/ircre-bibtex/ircreupdate/ircre.bib', encoding='utf8') as bibtexfile:
ircrebib_database = bibtexparser.load(bibtexfile, parser)
allentries = ircrebib_database.entries.copy()
# ----------------------------------------
# get all articles
# -----------------------------------------
article_entries = []
for i in range(len(allentries)):
if allentries[i]['ENTRYTYPE'] == 'article':
article_entries.append(allentries[i].copy())
article_database = BibDatabase()
article_database.entries = article_entries
writer = BibTexWriter()
writer.indent = ' '
writer.order_entries_by = ('order',)
with open('/home/limingtao/ircre-bibtex/ircreupdate/articles.bib', 'w', encoding='utf8') as article_file:
bibtexparser.dump(article_database, article_file, writer=writer)
otherentries= []
for i in range(len(allentries)):
if allentries[i]['ENTRYTYPE'] == 'inbook' or allentries[i]['ENTRYTYPE'] == 'inproceedings' or allentries[i]['ENTRYTYPE'] == 'incollection':
otherentries.append(allentries[i].copy())
other_database = BibDatabase()
other_database.entries = otherentries
writer2 = BibTexWriter()
writer2.indent = ' '
writer2.order_entries_by = ('order',)
with open('/home/limingtao/ircre-bibtex/ircreupdate/others.bib', 'w', encoding='utf8') as others_file:
bibtexparser.dump(other_database, others_file, writer=writer2)
return 0
def test_comma_first(self):
with io.open(_data_path('book.bib'), 'r') as bibfile:
bib = BibTexParser(bibfile.read())
with io.open(_data_path('book_comma_first.bib'), 'r') as bibfile:
expected = bibfile.read()
writer = BibTexWriter()
writer.indent = ' '
writer.comma_first = True
result = writer.write(bib)
self.maxDiff = None
self.assertEqual(expected, result)
def printCandidates(candidates: List[Dict]):
writer = BibTexWriter()
writer.align_values = True
writer.indent = " "
db = BibDatabase()
db.entries = candidates
print(f"{len(candidates)} suggestions:\n")
output = writer.write(db)
print(output)
def bibtex_entries_to_string(entries: List[Dict]):
if len(entries) == 0:
return ""
writer = BibTexWriter()
writer.align_values = True
writer.indent = " "
db = BibDatabase()
db.entries = entries
return writer.write(db)
def test_comma_first(self):
with io.open(_data_path('book.bib'), 'r') as bibfile:
bib = BibTexParser(bibfile.read())
with io.open(_data_path('book_comma_first.bib'), 'r') as bibfile:
expected = bibfile.read()
writer = BibTexWriter()
writer.indent = ' '
writer.comma_first = True
result = writer.write(bib)
self.maxDiff = None
self.assertEqual(expected, result)
def write_bibliography(file, db):
"""Write bibliography entries to new file.
Parameters
----------
file : str or writable file object
db :
"""
writer = BibTexWriter()
writer.indent = ' '
with file_context(file, 'w', encoding='utf-8') as f:
f.write(writer.write(db))
def parsing_write(self, filename):
# print(self.booklist)
datalist = []
writer = BibTexWriter()
writer.indent = ' '
for ref in self.TreeView.full_list:
# print(type(ref))
datadict = dict((k, v) for k, v in
zip(self.entries, ref) if v is not None)
datalist.append(datadict)
self.db.entries = datalist
with open(filename, 'w') as bibfile:
bibfile.write(writer.write(self.db))
def ircrebibmerge():
articlesparser = BibTexParser(common_strings=False)
articlesparser.ignore_nonstandard_types = False
with open('/home/limingtao/ircre-bibtex/ircreupdate/sorted-articles.bib', encoding='utf8') as sortedarticle_file:
sortedarticle_database = bibtexparser.load(sortedarticle_file, articlesparser)
sortedarticles = sortedarticle_database.entries.copy()
top15parser = BibTexParser(common_strings=False)
top15parser.ignore_nonstandard_types = False
with open('/home/limingtao/ircre-bibtex/ircreupdate/top15.bib', encoding='utf8') as top15_file:
top15_database = bibtexparser.load(top15_file, top15parser)
top15articles = top15_database.entries.copy()
othersparser = BibTexParser(common_strings = False)
othersparser.ignore_nonstandard_types = False
with open('/home/limingtao/ircre-bibtex/ircreupdate/others.bib', encoding='utf8') as others_file:
others_database = bibtexparser.load(others_file, othersparser)
others = others_database.entries.copy()
alldb = BibDatabase()
entries = []
for i in range(len(top15articles)):
entries.append(top15articles[i].copy())
for i in range(len(sortedarticles)):
entries.append(sortedarticles[i].copy())
for i in range(len(others)):
entries.append(others[i].copy())
alldb.entries = entries
writer = BibTexWriter()
writer.indent = ' '
writer.order_entries_by = None
with open('/home/limingtao/ircre-bibtex/ircreupdate/newircre.bib', 'w', encoding='utf8') as newircrebibfile:
bibtexparser.dump(alldb, newircrebibfile, writer=writer)
return 0
def write_res(self, passed_entries, passed_name, failed_entries,
failed_name):
db = BibDatabase()
db.entries = passed_entries
writer = BibTexWriter()
writer.indent = ' '
writer.comma_first = False
with open("results/" + passed_name, 'w') as bibfile:
bibfile.write(writer.write(db))
with open("results/" + failed_name, 'w') as f:
json.dump(failed_entries, f, indent=4)
print("Writing data to filesystem!")
print(" -successful results can be found in: results/" + passed_name)
print(" -failed results can be found in: results/" + failed_name)
def test_indent(self):
bib_database = BibDatabase()
bib_database.entries = [{'ID': 'abc123',
'ENTRYTYPE': 'book',
'author': 'test'}]
writer = BibTexWriter()
writer.indent = ' '
result = bibtexparser.dumps(bib_database, writer)
expected = \
"""@book{abc123,
author = {test}
}
"""
self.assertEqual(result, expected)
def reformatbib(infile,outfile):
with open(infile,'r') as bibfileIn:
try:
bib_database = bibtexparser.load(bibfileIn)
writer = BibTexWriter()
writer.align_values = True
writer.indent = ' ' # indent entries with spaces
# writer.comma_first = True # place the comma at the beginning of the line
with open(outfile, 'w') as bibfileOut:
bibfileOut.write(writer.write(bib_database))
print(f'Reformated {infile} written to {outfile}')
except:
print(f'{infile} not parsed')
def export_citations(citations, destination):
db = BibDatabase()
citation_dicts = (dict(row) for _, row in citations.iterrows())
citation_dicts = [{
attribute: value
for attribute, value in citation.items() if value is not np.nan
} for citation in citation_dicts]
db.entries = citation_dicts
with open(destination, "w") as bibtexfile:
writer = BibTexWriter()
writer.indent = " "
bibtexparser.dump(db, bibtexfile, writer)
def _cleanupBibTex(self, count):
""" Clean up bibtex and ensure uniform look. """
import bibtexparser
from bibtexparser.bparser import BibTexParser
parser = BibTexParser()
parser.customization = homogeneize_latex_encoding
bib = bibtexparser.loads(self.refs, parser=parser)
# save results
from bibtexparser.bwriter import BibTexWriter
writer = BibTexWriter()
writer.contents = ['entries']
writer.indent = ' '
writer.order_entries_by = ('id')
self.number = len(bib.entries)
self.refs = bibtexparser.dumps(bib, writer)
def getclusterid(title, author):
parser = BibTexParser(common_strings=False)
parser.ignore_nonstandard_types = False
with open('/home/limingtao/ircre-bibtex/ircreupdate/articles.bib', encoding='utf8') as article_file:
article_database = bibtexparser.load(article_file, parser)
article_entries = article_database.entries.copy()
entries = bib_database.entries
print("---------------------------")
print("---------------------------")
print("---------------------------")
print("Total articles number: " + str(len(entries)))
print("---------------------------")
print("---------------------------")
print("---------------------------")
writer = BibTexWriter()
writer.indent = ' '
writer.order_entries_by = ('order',)
for i in range(len(entries)):
if entries[i]['clusterid'] == 'unknown':
print("---------------------------")
print("Entry number: " + str(i))
title = entries[i]['title']
print("Title: " + title)
clusterid = ''
try:
clusterid = os.popen(
'''/home/limingtao/ircre-bibtex/ircreupdate/scholarpy/scholar.py -c 1 -t --phrase="''' + title + '''" |grep ID| grep Cluster''').read().strip().split()[
-1]
except:
clusterid = "unknown"
print("new Cluster ID: " + clusterid)
entries[i]['clusterid'] = clusterid
with open('/home/limingtao/ircre-bibtex/ircreupdate/clusterid-added-ircre.bib', 'w', encoding='utf8') as newbibfile:
bibtexparser.dump(bib_database, newbibfile, writer=writer)
os.popen("cp /home/limingtao/ircre-bibtex/ircreupdate/clusterid-added-ircre.bib /home/limingtao/ircre-bibtex/ircreupdate/tempclusterid-added-ircre.bib")
with open('/home/limingtao/ircre-bibtex/ircreupdate/clusterid-added-ircre.bib', 'w', encoding='utf8') as newbibfile:
bibtexparser.dump(bib_database, newbibfile, writer=writer)
return 0
def proc_bib(input_io: TextIOWrapper,
output_io: TextIOWrapper,
jdb: JournalDB,
silent: bool = False,
output_format: str = "bib",
abbrev_type="iso4"):
if not hasattr(Journal, abbrev_type):
raise ValueError(f"Invalid abbreviation type `{abbrev_type}`")
bib_db = bibtexparser.load(input_io)
for entry in bib_db.entries:
journaltitle = entry.get("journaltitle")
if journaltitle is None:
continue
journaltitle = braces_regex.sub("", journaltitle)
name_pattern = re.compile(fr"^{re.escape(journaltitle)}(:?.*)$",
RegexFlag.IGNORECASE)
# TODO: query using lambdas?
# TODO: normalize names (just in index?).
res = jdb.journals.query_one(Journal.names_key, name_pattern)
if res:
_, journal = res
abbrev = getattr(journal, abbrev_type)
if output_format == "bib":
entry["journaltitle"] = f"{{{abbrev or journaltitle}}}"
elif output_format == "sourcemap":
gen_sourcemap_map(journal, journaltitle, abbrev, output_io)
abbrev_msg = f"abbreviating to '{abbrev}'" if res else f"no abbreviation found"
if not silent:
info(f"found journal name '{journaltitle}'; {abbrev_msg}.")
if output_format == "bib":
bib_writer = BibTexWriter()
bib_writer.add_trailing_comma = True
bib_writer.display_order = None
bib_writer.indent = "\t"
bib_writer.order_entries_by = None
bibtex_code = bib_writer.write(bib_db)
output_io.write(bibtex_code)
elif output_format == "sourcemap":
pass
def main():
import bibtexparser
from bibtexparser.bwriter import BibTexWriter
with open('ircre.bib', encoding='utf8') as bibtex_file:
bib_database = bibtexparser.load(bibtex_file)
entries = bib_database.entries
print("---------------------------")
print("---------------------------")
print("---------------------------")
print("Total articles number: " + str(len(entries)))
print("---------------------------")
print("---------------------------")
print("---------------------------")
writer = BibTexWriter()
writer.indent = ' '
writer.order_entries_by = ('order', )
for i in range(len(entries)):
if entries[i]['clusterid'] == 'unknown':
print("---------------------------")
print("Entry number: " + str(i))
title = entries[i]['title']
print("Title: " + title)
clusterid = ''
try:
clusterid = os.popen(
'''./scholarpy/scholar.py -c 1 -t --phrase="''' + title +
'''" |grep ID| grep Cluster''').read().strip().split()[-1]
except:
clusterid = "unknown"
print("new Cluster ID: " + clusterid)
entries[i]['clusterid'] = clusterid
with open('clusterid-added-ircre.bib', 'w',
encoding='utf8') as newbibfile:
bibtexparser.dump(bib_database, newbibfile, writer=writer)
os.popen("cp clusterid-added-ircre.bib tempclusterid-added-ircre.bib")
with open('clusterid-added-ircre.bib', 'w', encoding='utf8') as newbibfile:
bibtexparser.dump(bib_database, newbibfile, writer=writer)
return 0
def main():
output = sys.argv[1]
mds = sys.argv[2:]
es = []
for fn in mds:
# print(f"loading {fn}")
with open(fn, "r", encoding='UTF-8') as f:
ls = f.readlines()[1:]
ls = itertools.takewhile(lambda x: x != "---\n", ls)
e = yaml.load("".join(ls), Loader=yaml.FullLoader)
e['ID'] = fn.split("/")[1][0:-3]
for i in ['title', 'booktitle']:
if i in e:
s = e[i]
s = s.replace("#", "\#")
s = s.replace("&", "\&")
e[i] = s
e['title'] = "{" + e['title'] + "}"
if 'authors' in e:
e['author'] = " and ".join(e['authors'])
del e['authors']
for i in ['isbn', 'pages', 'volume', 'year']:
if i in e: e[i] = str(e[i])
for i in [
'added', 'layout', 'notes', 'papers', 'read', 'readings',
'topics'
]:
if i in e: del e[i]
es.append(e)
db = BibDatabase()
db.entries = es
writer = BibTexWriter()
writer.contents = ['entries']
writer.indent = ' '
# writer.order_entries_by = ('ENTRYTYPE', 'author', 'year')
bibtex_str = bibtexparser.dumps(db, writer)
with open(output, "w") as f:
print(("#############################################\n"
"# This file is machine generated, do not edit\n"
"#############################################\n"),
file=f)
print(bibtex_str, file=f)
def write_bibtex_dict(stream, entries):
"""bibtexparser.write converts the entire database to one big string and
writes it out in one go. I'm sure it will always all fit in RAM but some
things just will not stand.
"""
from bibtexparser.bwriter import BibTexWriter
writer = BibTexWriter()
writer.indent = ' '
writer.entry_separator = ''
first = True
for rec in entries:
if first:
first = False
else:
stream.write(b'\n')
stream.write(writer._entry_to_bibtex(rec).encode('utf8'))
def print_candidates(candidates: List[Dict]):
count = len(candidates)
if count == 0:
print("No suggestions.")
else:
if count == 1:
print("One suggestion:\n")
else:
print(f"{count} suggestions:\n")
writer = BibTexWriter()
writer.align_values = True
writer.indent = " "
db = BibDatabase()
db.entries = candidates
output = writer.write(db)
print(output)
def write_bibtex_dict (stream, entries):
"""bibtexparser.write converts the entire database to one big string and
writes it out in one go. I'm sure it will always all fit in RAM but some
things just will not stand.
"""
from bibtexparser.bwriter import BibTexWriter
writer = BibTexWriter ()
writer.indent = ' '
writer.entry_separator = ''
first = True
for rec in entries:
if first:
first = False
else:
stream.write ('\n')
stream.write (writer._entry_to_bibtex (rec))
def write_bib(db, order=False):
"""
Write bibtex string.
Args:
db (BibDatabase): database object to dump..
order (bool): whether to reorder entries upon writing.
Returns:
The dumped string.
"""
# Custom writer
writer = BibTexWriter()
writer.indent = '\t'
writer.order_entries_by = None
# Replace month by numeric value
for entry in db.entries:
if 'month' in entry and entry['month'] in MONTHS:
entry['month'] = '{:02d}'.format(MONTHS.index(entry['month']) + 1)
if order:
# Manual sort
order_entries_by = ('year', 'author', 'ID')
sort_entries(db, order_entries_by)
if not config.use_utf8_characters:
db.entries = [nomenclature.encode_ascii_latex(entry) for entry in db.entries]
if config.protect_uppercase:
for entry in db.entries:
entry["title"] = latex.protect_uppercase(entry["title"])
# Write bib string
return writer.write(db)
def formatText(self):
if self.BibtexfilePath != '':
self.openfile()
else:
self.readcontent()
m = self.getMap()
m['IEEE Global Communications Conference'] = m['IEEE Global Communications Conference, incorporating the Global Internet Symposium']
del m['IEEE Global Communications Conference, incorporating the Global Internet Symposium']
print m
length = 0
nb = {}
for bibtex in self.allbibtex:
for key in bibtex.keys():
if len(key) > length and key != 'ENTRYTYPE':
length = len(key)
for k, v in bibtex.items():
if k == 'ENTRYTYPE' or k == 'ID':
nb[k] = v
continue
elif k == 'ID':
nb[k] = v
continue
elif k == 'doi' or k == 'ISSN' or k == 'keywords':
continue
elif v == '':
continue
elif 'url' in k:
continue
nk = k + (length - len(k)) * ' '
if 'booktitle' in nk:
if '(' in v:
v1 = v.split('(')[1].split(')')[0]
nb[nk] = 'Proc. of ' + v1
continue
flag = 0 # 未更改booktitle
to_remove = "~`!@#$%^&*(){}[];':<>|-=_+"
table = {ord(char): None for char in to_remove}
clean_v = v.translate(table)
#clean_v = v.translate(string.punctuation)
#print clean_v
for kk, vv in m.items():
if kk in clean_v:
nb[nk] = 'Proc. of ' + vv[0]
publish = 'publish' + (length - 7) * ' '
nb[publish] = vv[1]
flag = 1
break
if flag == 0:
nb[nk] = v
print v
continue
elif nk.strip() == 'title' and 'booktitle' not in nk:
self.tilte = v
nv = v.split(' ')
for i in range(len(nv)):
# 标题除介词和冠词外，首字母大写
if nv[i] in self.prep or nv[i] in self.artie:
continue
# 首字母大写
else:
if 97 <= ord(nv[i][0]) <= 122:
nv[i] = chr(ord(nv[i][0])-32)+nv[i][1:]
v = ' '.join(nv)
nb[nk] = '{' + v + '}'
continue
elif 'pages' in nk:
if '--' in v:
nb[nk] = v
continue
nb[nk] = v.replace('-', '--')
continue
elif 'author' in nk:
if '\n' in v:
nb[nk] = v.replace('\n', ' ')
continue
# 其他不做改变
nb[nk] = v
db = BibDatabase()
db.entries = [nb]
writer = BibTexWriter()
writer.indent = '\t' # indent entries with 4 spaces instead of one
writer.comma_first = False # place the comma at the beginning of the line
with open(self.tilte+'.bib', 'wb') as bibfile:
bibfile.write(writer.write(db))
print("Looking for Dois...")
before = 0
new = 0
total = len(bibliography.entries)
for i,entry in enumerate(bibliography.entries):
print("\r{i}/{total} entries processed, please wait...".format(i=i,total=total),flush=True,end="")
try:
if "doi" not in entry or entry["doi"].isspace():
title = entry["title"]
authors = get_authors(entry)
for author in authors:
doi_match = searchdoi(title,author)
if doi_match:
doi = doi_match.groups()[0]
entry["doi"] = doi
new += 1
else:
before += 1
except:
pass
print("")
template="We added {new} DOIs !\nBefore: {before}/{total} entries had DOI\nNow: {after}/{total} entries have DOI"
print(template.format(new=new,before=before,after=before+new,total=total))
outfile = sys.argv[1]+"_doi.bib"
print("Writing result to ",outfile)
writer = BibTexWriter()
writer.indent = ' ' # indent entries with 4 spaces instead of one
with open(outfile, 'w') as bibfile:
bibfile.write(writer.write(bibliography))
'class':'logging.StreamHandler',
},
},
'loggers': {
'': {
'handlers': ['default'],
'level': 'ERROR',
'formatter': 'standard',
'propagate': True
}
}
})
writer = BibTexWriter()
writer.contents = ['comments', 'entries']
writer.indent = ' '
writer.order_entries_by = ('ENTRYTYPE', 'author', 'year')
def create_id(t, year, title):
return str(t) + "_" + str(year) + "_" + str(space_to_underscore(title))
def pdf(pdf_files, shared_pdf, bibtex_folder, bibtex_files, gscholar):
for pdf in pdf_files:
txt = re.sub("\W", " ", gs.convert_pdf_to_txt(pdf)).lower()
#Research determined that the cutting of 35 words gives the
#highest accuracy
words = txt.strip().split()[:35]
words = " ".join(words)
print words
if gscholar == True:
bib = load(gs.pdflookup(pdf, all, gs.FORMAT_BIBTEX)[0])
def toString(e):
writer = BibTexWriter()
writer.indent = ' ' # indent entries with 4 spaces instead of one
writer.comma_first = True # place the comma at the beginning of the line
return writer._entry_to_bibtex(e)
