def test_align(self):
bib_database = BibDatabase()
bib_database.entries = [{
'ID': 'abc123',
'ENTRYTYPE': 'book',
'author': 'test',
'thisisaverylongkey': 'longvalue'
}]
writer = BibTexWriter()
writer.align_values = True
result = bibtexparser.dumps(bib_database, writer)
expected = \
"""@book{abc123,
author = {test},
thisisaverylongkey = {longvalue}
}
"""
self.assertEqual(result, expected)
with open('bibtexparser/tests/data/multiple_entries_and_comments.bib'
) as bibtex_file:
bib_database = bibtexparser.load(bibtex_file)
writer = BibTexWriter()
writer.contents = ['entries']
writer.align_values = True
result = bibtexparser.dumps(bib_database, writer)
expected = \
"""@book{Toto3000,
author = {Toto, A and Titi, B},
title = {A title}
}
@article{Wigner1938,
author = {Wigner, E.},
doi = {10.1039/TF9383400029},
issn = {0014-7672},
journal = {Trans. Faraday Soc.},
owner = {fr},
pages = {29--41},
publisher = {The Royal Society of Chemistry},
title = {The transition state method},
volume = {34},
year = {1938}
}
@book{Yablon2005,
author = {Yablon, A.D.},
publisher = {Springer},
title = {Optical fiber fusion slicing},
year = {2005}
}
"""
self.assertEqual(result, expected)
def test_align(self):
bib_database = BibDatabase()
bib_database.entries = [{'ID': 'abc123',
'ENTRYTYPE': 'book',
'author': 'test',
'thisisaverylongkey': 'longvalue'}]
writer = BibTexWriter()
writer.align_values = True
result = bibtexparser.dumps(bib_database, writer)
expected = \
"""@book{abc123,
author = {test},
thisisaverylongkey = {longvalue}
}
"""
self.assertEqual(result, expected)
with open('bibtexparser/tests/data/multiple_entries_and_comments.bib') as bibtex_file:
bib_database = bibtexparser.load(bibtex_file)
writer = BibTexWriter()
writer.contents = ['entries']
writer.align_values = True
result = bibtexparser.dumps(bib_database, writer)
expected = \
"""@book{Toto3000,
author = {Toto, A and Titi, B},
title = {A title}
}
@article{Wigner1938,
author = {Wigner, E.},
doi = {10.1039/TF9383400029},
issn = {0014-7672},
journal = {Trans. Faraday Soc.},
owner = {fr},
pages = {29--41},
publisher = {The Royal Society of Chemistry},
title = {The transition state method},
volume = {34},
year = {1938}
}
@book{Yablon2005,
author = {Yablon, A.D.},
publisher = {Springer},
title = {Optical fiber fusion slicing},
year = {2005}
}
"""
self.assertEqual(result, expected)
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 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 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 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 main():
"""Main function of the script.
Loads the bib file, does the chcecking on it and prints out
sorted and formated database.
"""
parser = argparse.ArgumentParser()
parser.add_argument("--input",
type=argparse.FileType('r'),
default=sys.stdin,
help="Input file, default is stdin.")
parser.add_argument("--output",
type=argparse.FileType('w'),
default=sys.stdout,
help="Optional output file.")
parser.add_argument("--try-fix",
default=False,
action="store_true",
help="Flag to search information to fix the dtabase.")
parser.add_argument("--anthologies",
type=str,
nargs='+',
help="List of BibTeX files with know papers.")
args = parser.parse_args()
if args.anthologies is not None:
load_anthologies(args.anthologies)
bib_database = bibtexparser.load(args.input, get_bibparser())
cache_journal_issn(bib_database)
authors, journals, booktitles = check_database(bib_database, args.try_fix)
look_for_misspellings(authors, 'Authors')
look_for_misspellings(journals, 'Journals')
look_for_misspellings(booktitles,
'Booktitles (proceedings)',
threshold=0.9)
writer = BibTexWriter()
writer.indent = ' '
writer.order_by = ['author', 'year', 'title']
writer.display_order = ['author', 'title', 'booktitle', 'journal']
writer.align_values = True
args.output.write(writer.write(bib_database))
def main():
print("Reading from stdin ...", end="", file=sys.stderr)
input_records = sys.stdin.read().split("\n\n")
print("done.", file=sys.stderr)
bib_parser = BibTexParser(ignore_nonstandard_types=True,
homogenize_fields=True,
common_strings=True)
writer = BibTexWriter()
writer.indent = ' '
writer.order_by = ['author', 'year', 'title']
writer.display_order = ['author', 'title', 'booktitle', 'journal']
writer.align_values = True
records = 0
skipped = 0
for record in input_records:
if not record:
continue
try:
parsed = bibtexparser.loads(record, bib_parser)
records += 1
if records % 1000 == 0:
print("Processed {} records.".format(records), file=sys.stderr)
except (pyparsing.ParseException,
bibtexparser.bibdatabase.UndefinedString):
skipped += 1
for item in parsed.get_entry_list():
if "abstract" in item:
del item["abstract"]
parsed.comments = []
parsed.entries = [e for e in parsed.entries if e["ENTRYTYPE"] != "book"]
parsed.entries = list(parsed.get_entry_dict().values())
print(writer.write(parsed))
print("Finished. {} records kept, {} skipped.".format(records, skipped),
file=sys.stderr)
def main():
args = parser.parse_args()
args.output = abspath(expanduser(args.output))
logging.info("Targeting: {}".format(args.target))
logging.info("Output to: {}".format(args.output))
#load each of the specified files
target_files = retrieval.get_data_files(args.target, ".bib")
dbs = [BU.parse_bib_files(x, bib_proc.nop) for x in target_files]
main_db = b.bibdatabase.BibDatabase()
# Load the main database
if exists(args.output):
BU.parse_bib_files(args.output, bib_proc.nop, database=main_db)
main_set = set(main_db.get_entry_dict().keys())
total_entries = main_db.entries[:]
missing_keys_main = set()
# Get entries missing from the main database
for db in dbs:
db_dict = db.get_entry_dict()
db_set = set(db_dict.keys())
missing_keys = db_set.difference(main_set)
missing_keys_main.update(missing_keys)
total_entries += [db_dict[x] for x in missing_keys]
logging.info("{} missing entries".format(len(total_entries)))
main_db.entries = total_entries
# Write out the combined database
logging.info("Bibtex loaded")
writer = BibTexWriter()
writer.align_values = True
with open(join(args.output), 'a') as f:
f.write(writer.write(main_db))
tags = [
i.strip()
for i in re.split(',|;', entry["tags"].replace("\n", ""))
]
for tag in tags:
if tag not in db_dict:
db_dict[tag] = BibDatabase()
db_dict[tag].entries.append(entry)
if args.YEARS:
if 'year' not in entry:
raise Exception(
"Years specified, entry has no year: {}".format(
entry['ID']))
if entry['year'] not in db_dict:
db_dict[entry['year']] = BibDatabase()
db_dict[entry['year']].entries.append(entry)
if args.AUTHORS:
raise Exception("not implemented AUTHORS yet")
# Write out split bibtex files
logging.info("Writing Bibtex")
writer = BibTexWriter()
writer.align_values = True
for k, v in db_dict.items():
clean_name = k.replace("/", "_")
with open(join(args.output, "{}.bib".format(clean_name)), 'w') as f:
f.write(writer.write(v))
value = re.sub('<i>|</i>', '', value)
md.write('%-10s "%s"\n' % (field + ':', value))
md.write('%-10s "%s-01-01"\n' % ('date:', bibentry.fields['year']))
md.write(FM_DELIM + '\n\n')
md.write('## Abstract\n')
if 'abstract' in bibentry.fields:
md.write(bibentry.fields['abstract'] + '\n')
else:
md.write('Unavailable :(' + '\n')
md.write('\n')
with open(args.input, encoding="utf8") as bibtex_file:
bibtex_str = bibtex_file.read()
bib_database = bibtexparser.loads(bibtex_str)
for entry in bib_database.entries:
markdown = os.path.join(args.dir, '{}.md'.format(entry['ID']))
with open(markdown, 'a', encoding="utf8") as md:
bibdb = BibDatabase()
bibdb.entries = [entry]
bibtw = BibTexWriter()
bibtw.align_values = True # TOP CARALHO
bibtw.indent = ' '
md.write('## BibTeX Citation\n')
md.write('{{< highlight bibtex >}}' +
'\n') # FIXME bibtex supported?
md.write(bibtw.write(bibdb).rstrip() + '\n')
md.write('{{< /highlight >}}' + '\n')
