def format_folder(folder, use_backup, context=None):
"""
Pretty print bibtex file in the given folder.
This function looks for a file named 'queried.bib' in the given folder,
and use it as an input to pretty print a file called 'biblio.bib'.
Args:
folder (str): absolute or relative path to the folder to process.
use_backup (bool): whether to backup previous files before writing.
context (set): set of existing bibtex keys in the current context.
Returns:
Nothing, but writes the results in a file called 'biblio.bib'.
"""
# Create database
db = utils.read_bib_file(os.path.join(folder, '.queried.bib'), homogenize=True)
utils.guess_manual_files(folder, db, update_queried_db=True)
if context is None:
context = set()
# Generate bibkeys
for entry in db.entries:
entry['ID'] = nomenclature.gen_bibkey(entry, context)
# Write output bibtex file
output_bib_path = os.path.join(folder, 'biblio.bib')
output_bib_str = utils.write_bib(db, order=True)
utils.write_with_backup(output_bib_path, output_bib_str, use_backup)
def format_folder(folder, use_backup, context=None):
"""
Pretty print bibtex file in the given folder.
This function looks for a file named 'queried.bib' in the given folder,
and use it as an input to pretty print a file called 'biblio.bib'.
Args:
folder (str): absolute or relative path to the folder to process.
use_backup (bool): whether to backup previous files before writing.
context (set): set of existing bibtex keys in the current context.
Returns:
Nothing, but writes the results in a file called 'biblio.bib'.
"""
# Create database
db = utils.read_bib_file(os.path.join(folder, '.queried.bib'),
homogenize=True)
utils.guess_manual_files(folder, db, update_queried_db=True)
if context is None:
context = set()
# Generate bibkeys
for entry in db.entries:
entry['ID'] = nomenclature.gen_bibkey(entry, context)
# Write output bibtex file
output_bib_path = os.path.join(folder, 'biblio.bib')
output_bib_str = utils.write_bib(db, order=True)
utils.write_with_backup(output_bib_path, output_bib_str, use_backup)
def query_crossref_folder(folder, use_backup):
"""
Query metadata information for unmatched pdf files in the given folder.
This function only queries Crossref.
Args:
folder (str): absolute or relative path to the folder to process.
use_backup (bool): whether to backup previous files before writing.
Returns:
Nothing, but writes the queried databases in bibtex format in the given
folder (and backup previous database if it differed).
"""
# Create database
db = utils.read_bib_file(os.path.join(folder, '.queried.bib'))
files = utils.guess_manual_files(folder, db, update_queried_db=False)
utils.add_skip_files(folder, files)
json_entries = []
rejected = []
# For each pdf in the folder
import pdb
pdb.set_trace()
for path in utils.get_pdf_list(folder):
file = os.path.basename(path)
parsed = nomenclature.parse_filename(file)
if parsed is None or file in files:
continue
print('Q: ' + os.path.basename(file))
authors, title = parsed
# Crossref
rbib, rjson, score = providers.crossref_query(authors, title)
if score >= config.crossref_accept_threshold:
# Append filename and store entry
rbib['file'] = utils.encode_filename_field(file)
json_entries.append(rjson)
db.entries.append(rbib)
else:
rejected.append(os.path.basename(file))
# Store results
bib_path = os.path.join(folder, '.queried.bib')
utils.write_with_backup(bib_path, utils.write_bib(db, order=False),
use_backup)
json_path = os.path.join(folder, '.queried.json')
json_str = json.dumps(json_entries,
sort_keys=True,
indent=4,
separators=(',', ': '))
utils.write_with_backup(json_path, json_str, use_backup)
rejected_path = os.path.join(folder, '.rejected.txt')
if len(rejected) > 0:
utils.write_with_backup(rejected_path, '\n'.join(rejected), use_backup)
def query_crossref_folder(folder, use_backup):
"""
Query metadata information for unmatched pdf files in the given folder.
This function only queries Crossref.
Args:
folder (str): absolute or relative path to the folder to process.
use_backup (bool): whether to backup previous files before writing.
Returns:
Nothing, but writes the queried databases in bibtex format in the given
folder (and backup previous database if it differed).
"""
# Create database
db = utils.read_bib_file(os.path.join(folder, '.queried.bib'))
files = utils.guess_manual_files(folder, db, update_queried_db=False)
utils.add_skip_files(folder, files)
json_entries = []
rejected = []
# For each pdf in the folder
for path in utils.get_pdf_list(folder):
file = os.path.basename(path)
parsed = nomenclature.parse_filename(file)
if parsed is None or file in files:
continue
print('Q: ' + os.path.basename(file))
authors, title = parsed
# Crossref
rbib, rjson, score = providers.crossref_query(authors, title)
if score >= config.crossref_accept_threshold:
# Append filename and store entry
rbib['file'] = utils.encode_filename_field(file)
json_entries.append(rjson)
db.entries.append(rbib)
else:
rejected.append(os.path.basename(file))
# Store results
bib_path = os.path.join(folder, '.queried.bib')
utils.write_with_backup(bib_path, utils.write_bib(db, order=False), use_backup)
json_path = os.path.join(folder, '.queried.json')
json_str = json.dumps(json_entries, sort_keys=True, indent=4, separators=(',', ': '))
utils.write_with_backup(json_path, json_str, use_backup)
rejected_path = os.path.join(folder, '.rejected.txt')
if len(rejected) > 0:
utils.write_with_backup(rejected_path, '\n'.join(rejected), use_backup)
def query_google_folder(folder, use_backup):
"""
Query metadata information for unmatched pdf files in the given folder.
This function only queries Google Scholar.
Args:
folder (str): absolute or relative path to the folder to process.
use_backup (bool): whether to backup previous files before writing.
Returns:
Nothing, but writes the queried databases in bibtex format in the given
folder (and backup previous database if it differed).
"""
# Create database
db = utils.read_bib_file(os.path.join(folder, '.queried.bib'))
files = utils.guess_manual_files(folder, db, update_queried_db=False)
utils.add_skip_files(folder, files)
for path in utils.get_pdf_list(folder):
file = os.path.basename(path)
parsed = nomenclature.parse_filename(file)
if parsed is None or file in files:
continue
print('Q: ' + os.path.basename(file))
authors, title = parsed
# Google Scholar
rbib = providers.scholarly_query(authors, title)
if rbib is None:
continue
# Append filename and store entry
rbib['file'] = utils.encode_filename_field(file)
db.entries.append(rbib)
# Store results
bib_path = os.path.join(folder, '.queried.bib')
utils.write_with_backup(bib_path, utils.write_bib(db, order=False),
use_backup)
def query_google_folder(folder, use_backup):
"""
Query metadata information for unmatched pdf files in the given folder.
This function only queries Google Scholar.
Args:
folder (str): absolute or relative path to the folder to process.
use_backup (bool): whether to backup previous files before writing.
Returns:
Nothing, but writes the queried databases in bibtex format in the given
folder (and backup previous database if it differed).
"""
# Create database
db = utils.read_bib_file(os.path.join(folder, '.queried.bib'))
files = utils.guess_manual_files(folder, db, update_queried_db=False)
utils.add_skip_files(folder, files)
for path in utils.get_pdf_list(folder):
file = os.path.basename(path)
parsed = nomenclature.parse_filename(file)
if parsed is None or file in files:
continue
print('Q: ' + os.path.basename(file))
authors, title = parsed
# Google Scholar
rbib = providers.scholarly_query(authors, title)
if rbib is None:
continue
# Append filename and store entry
rbib['file'] = utils.encode_filename_field(file)
db.entries.append(rbib)
# Store results
bib_path = os.path.join(folder, '.queried.bib')
utils.write_with_backup(bib_path, utils.write_bib(db, order=False), use_backup)