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 test_trailing_comma(self):
with io.open(_data_path('article.bib'), 'r') as bibfile:
bib = BibTexParser(bibfile.read())
with io.open(_data_path('article_trailing_comma_output.bib'), 'r') as bibfile:
expected = bibfile.read()
writer = BibTexWriter()
writer.add_trailing_comma = True
result = writer.write(bib)
self.maxDiff = None
self.assertEqual(expected, result)
def test_trailing_comma(self):
with io.open(_data_path('article.bib'), 'r') as bibfile:
bib = BibTexParser(bibfile.read())
with io.open(_data_path('article_trailing_comma_output.bib'),
'r') as bibfile:
expected = bibfile.read()
writer = BibTexWriter()
writer.add_trailing_comma = True
result = writer.write(bib)
self.maxDiff = None
self.assertEqual(expected, result)
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 generate_bib_from_arxiv(arxiv_item, value, field="id"):
if field == "ti":
article_id = arxiv_item["id"].split("http://arxiv.org/abs/")[1]
else:
article_id = value
key = "arxiv:" + article_id
title = arxiv_item.title
authors = arxiv_item.authors
if len(authors) > 0:
authors = " and ".join([author["name"] for author in authors])
published = arxiv_item.published.split("-")
year = ''
if len(published) > 1:
year = published[0]
bib = BibDatabase()
bib.entries = [{
"title": title,
"author": authors,
"year": year,
"eprinttype": "arxiv",
"eprint": article_id,
"keywords": "",
"abstract": arxiv_item.summary,
"ID": key,
"ENTRYTYPE": "article"
}]
writer = BibTexWriter()
writer.add_trailing_comma = True
writer.display_order = [
'title', 'author', 'year', 'eprinttype', 'eprint', 'keywords',
'abstract'
]
writer.indent = " "
bib = writer.write(bib)
return bib
else:
print(f'I detected a duplicate based on the key {id}. '
f'I will augment it with a letter and try again. '
f'Please double-check, if this is correct.. '
f'my duplicate detection algorithm is pretty bad.\n\n')
id = id_orig + letters[i]
i += 1
if not duplicate:
bib = re.sub(r'(@[a-z]*{)(.*),', r'\1' + id + ',', bib)
bib_db = bibtexparser.loads(bib)
db.entries.extend(bib_db.get_entry_list())
else:
bib_db = None
if id_list:
writer = BibTexWriter()
writer.indent = '\t'
writer.order_entries_by = ('year', 'ID')
writer.add_trailing_comma = True
with open('../_bibliography/pint.bib', 'w') as bibfile:
bibfile.write(writer.write(db))
for line in fileinput.input('../_bibliography/pint.bib', inplace=True):
if '@comment{' in line:
line = line.replace('@comment{', '')
if re.match(r'%}+', line) is not None:
line = re.sub(r'%}+', '%', line)
line = line.rstrip('\r\n')
print(line)
