def load_manual_references(self, *args, **kwargs):
"""
Load manual references
"""
from manubot.process.bibliography import load_manual_references
manual_refs = load_manual_references(*args, **kwargs)
self.manual_refs.update(manual_refs)
def generate_csl_items(args, citekeys_df):
"""
General CSL (citeproc) items for standard_citekeys in citekeys_df.
Writes references.json to disk and logs warnings for potential problems.
"""
# Read manual references (overrides) in JSON CSL
manual_refs = load_manual_references(args.manual_references_paths)
requests_cache.install_cache(args.requests_cache_path,
include_get_headers=True)
cache = requests_cache.get_cache()
if args.clear_requests_cache:
logging.info('Clearing requests-cache')
requests_cache.clear()
logging.info(
f'requests-cache starting with {len(cache.responses)} cached responses'
)
csl_items = list()
failures = list()
for standard_citekey in citekeys_df.standard_citekey.unique():
if standard_citekey in manual_refs:
csl_items.append(manual_refs[standard_citekey])
continue
elif standard_citekey.startswith('raw:'):
logging.error(
f'CSL JSON Data with a standard_citekey of {standard_citekey!r} not found in manual-references.json. '
'Metadata must be provided for raw citekeys.')
failures.append(standard_citekey)
try:
csl_item = citekey_to_csl_item(standard_citekey)
csl_items.append(csl_item)
except Exception:
logging.exception(
f'Citeproc retrieval failure for {standard_citekey!r}')
failures.append(standard_citekey)
logging.info(
f'requests-cache finished with {len(cache.responses)} cached responses'
)
requests_cache.uninstall_cache()
if failures:
message = 'CSL JSON Data retrieval failed for the following standardized citation keys:\n{}'.format(
'\n'.join(failures))
logging.error(message)
# Write JSON CSL bibliography for Pandoc.
with args.references_path.open('w', encoding='utf-8') as write_file:
json.dump(csl_items, write_file, indent=2, ensure_ascii=False)
write_file.write('\n')
return csl_items
def _generate_csl_items(args, citekeys_df):
"""
General CSL (citeproc) items for standard_citekeys in citekeys_df.
Writes references.json to disk and logs warnings for potential problems.
"""
# Read manual references (overrides) in JSON CSL
manual_refs = load_manual_references(args.manual_references_paths)
# Retrieve CSL Items
csl_items = generate_csl_items(
citekeys=citekeys_df.standard_citekey.unique(),
manual_refs=manual_refs,
requests_cache_path=args.requests_cache_path,
clear_requests_cache=args.clear_requests_cache,
)
# Write CSL JSON bibliography for Pandoc.
write_csl_json(csl_items, args.references_path)
return csl_items
def test_load_multiple_bibliography_paths():
citation_to_csl_item = load_manual_references(bibliography_paths)
print(list(citation_to_csl_item))
assert 'doi:10.7554/elife.32822' in citation_to_csl_item
csl_item_1 = citation_to_csl_item['doi:10.7554/elife.32822']
assert csl_item_1['title'].startswith('Sci-Hub')
assert 'CSL JSON Item was loaded by Manubot' in csl_item_1['note']
assert 'manual_reference_filename: bibliography.json' in csl_item_1['note']
assert 'standard_id: doi:10.7554/elife.32822' in csl_item_1['note']
# raw id corresponding to bibliography.bib
assert 'raw:noauthor_techblog:_nodate' in citation_to_csl_item
csl_item_2 = citation_to_csl_item['raw:noauthor_techblog:_nodate']
assert csl_item_2['title'].startswith('TechBlog')
assert 'manual_reference_filename: bibliography.bib' in csl_item_2['note']
assert 'original_id: noauthor_techblog:_nodate' in csl_item_2['note']
# id inferred by pandoc-citeproc during bib2json conversion of .nbib file
assert 'raw:Beaulieu-Jones2017' in citation_to_csl_item
csl_item_3 = citation_to_csl_item['raw:Beaulieu-Jones2017']
assert csl_item_3['author'][0]['family'] == 'Beaulieu-Jones'
assert 'manual_reference_filename: bibliography.nbib' in csl_item_3['note']
assert 'original_id: Beaulieu-Jones2017' in csl_item_3['note']
def setup_method(self):
bibliography_paths = sorted(
directory / x
for x in directory.glob("bibliographies/bibliography.*"))
self.citation_to_csl_item = load_manual_references(bibliography_paths)
print(list(self.citation_to_csl_item))
def setup_method(self):
self.citation_to_csl_item = load_manual_references(bibliography_paths)
print(list(self.citation_to_csl_item))