def standardize_id(self):
"""
Extract the standard_id (standard citation key) for a csl_item and modify the csl_item in-place to set its "id" field.
The standard_id is extracted from a "standard_citation" field, the "note" field, or the "id" field.
If extracting the citation from the "id" field, uses the infer_citekey_prefix function to set the prefix.
For example, if the extracted standard_id does not begin with a supported prefix (e.g. "doi:", "pmid:" or "raw:"),
the citation is assumed to be raw and given a "raw:" prefix.
The extracted citation is checked for validity and standardized, after which it is the final "standard_id".
Regarding csl_item modification, the csl_item "id" field is set to the standard_citation and the note field
is created or updated with key-value pairs for standard_id and original_id.
Note that the Manubot software generally refers to the "id" of a CSL Item as a citekey.
However, in this context, we use "id" rather than "citekey" for consistency with CSL's "id" field.
"""
original_id = self.get("id")
self.infer_id()
original_standard_id = self["id"]
assert is_valid_citekey(original_standard_id, allow_raw=True)
standard_id = standardize_citekey(original_standard_id,
warn_if_changed=False)
add_to_note = {}
note_dict = self.note_dict
if original_id and original_id != standard_id:
if original_id != note_dict.get("original_id"):
add_to_note["original_id"] = original_id
if original_standard_id and original_standard_id != standard_id:
if original_standard_id != note_dict.get("original_standard_id"):
add_to_note["original_standard_id"] = original_standard_id
if standard_id != note_dict.get("standard_id"):
add_to_note["standard_id"] = standard_id
self.note_append_dict(dictionary=add_to_note)
self.set_id(standard_id)
return self
def standardize_citation(*args, **kwargs):
import warnings
warnings.warn(
"'standardize_citation' has been renamed to 'standardize_citekey'"
" and will be removed in a future release.",
category=FutureWarning)
return standardize_citekey(*args, **kwargs)
def csl_item_set_standard_id(csl_item):
"""
Extract the standard_id (standard citation key) for a csl_item and modify the csl_item in-place to set its "id" field.
The standard_id is extracted from a "standard_citation" field, the "note" field, or the "id" field.
If extracting the citation from the "id" field, uses the infer_citekey_prefix function to set the prefix.
For example, if the extracted standard_id does not begin with a supported prefix (e.g. "doi:", "pmid:"
or "raw:"), the citation is assumed to be raw and given a "raw:" prefix. The extracted citation
(referred to as "original_standard_id") is checked for validity and standardized, after which it is
the final "standard_id".
Regarding csl_item modification, the csl_item "id" field is set to the standard_citation and the note field
is created or updated with key-value pairs for standard_id, original_standard_id, and original_id.
Note that the Manubot software generally refers to the "id" of a CSL Item as a citekey.
However, in this context, we use "id" rather than "citekey" for consistency with CSL's "id" field.
"""
if not isinstance(csl_item, dict):
raise ValueError(
"csl_item must be a CSL Data Item represented as a Python dictionary")
from manubot.cite.citeproc import (
append_to_csl_item_note,
parse_csl_item_note,
)
note_dict = parse_csl_item_note(csl_item.get('note', ''))
original_id = None
original_standard_id = None
if 'id' in csl_item:
original_id = csl_item['id']
original_standard_id = infer_citekey_prefix(original_id)
if 'standard_id' in note_dict:
original_standard_id = note_dict['standard_id']
if 'standard_citation' in csl_item:
original_standard_id = csl_item.pop('standard_citation')
if original_standard_id is None:
raise ValueError(
'csl_item_set_standard_id could not detect a field with a citation / standard_citation. '
'Consider setting the CSL Item "id" field.')
assert is_valid_citekey(original_standard_id, allow_raw=True)
standard_id = standardize_citekey(
original_standard_id, warn_if_changed=False)
add_to_note = {}
if original_id and original_id != standard_id:
if original_id != note_dict.get('original_id'):
add_to_note['original_id'] = original_id
if original_standard_id and original_standard_id != standard_id:
if original_standard_id != note_dict.get('original_standard_id'):
add_to_note['original_standard_id'] = original_standard_id
if standard_id != note_dict.get('standard_id'):
add_to_note['standard_id'] = standard_id
append_to_csl_item_note(csl_item, dictionary=add_to_note)
csl_item['id'] = standard_id
return csl_item
def cli_cite(args):
"""
Main function for the manubot cite command-line interface.
Does not allow user to directly specify Pandoc's --to argument, due to
inconsistent citaiton rendering by output format. See
https://github.com/jgm/pandoc/issues/4834
"""
# generate CSL JSON data
csl_list = list()
for citekey in args.citekeys:
try:
if not is_valid_citekey(citekey):
continue
citekey = standardize_citekey(citekey)
csl_item = citekey_to_csl_item(citekey, prune=args.prune_csl)
csl_list.append(csl_item)
except Exception as error:
logging.error(f'citekey_to_csl_item for {citekey!r} failed '
f'due to a {error.__class__.__name__}:\n{error}')
logging.info(error, exc_info=True)
# output CSL JSON data, if --render is False
if not args.render:
write_file = args.output.open(
'w', encoding='utf-8') if args.output else sys.stdout
with write_file:
json.dump(csl_list, write_file, ensure_ascii=False, indent=2)
write_file.write('\n')
return
# use Pandoc to render references
if not args.format and args.output:
vars(args)['format'] = extension_to_format.get(args.output.suffix)
if not args.format:
vars(args)['format'] = 'plain'
pandoc_metadata = {
'nocite': '@*',
'csl': args.csl,
'references': csl_list,
}
call_pandoc(
metadata=pandoc_metadata,
path=args.output,
format=args.format,
)
def process_record(record):
"""
Expand a catalog record with retrieved metadata
"""
output = {}
html_url = record.pop('html_url')
output['manubot'] = {
'repo_url': record.pop('repo_url'),
'url': html_url,
'citation': f"url:{html_url}",
}
if 'thumbnail_url' in record:
thumbnail_url = record.pop('thumbnail_url')
else:
thumbnail_url = get_thumbnail_url_from_html(html_url)
if thumbnail_url:
output['manubot']['thumbnail_url'] = thumbnail_url
for publication_type in 'preprint', 'journal':
citation = record.pop(f'{publication_type}_citation', None)
if not citation:
continue
if not is_valid_citekey(citation):
continue
output[publication_type] = {
'citation': citation,
}
for item in output.values():
citation = standardize_citekey(item['citation'])
csl_item = citekey_to_csl_item(citation)
if 'url' not in item and 'URL' in csl_item:
item['url'] = csl_item['URL']
item['title'] = get_title(csl_item)
item['authors'] = get_authors_text(csl_item)
item['journal'] = get_journal(csl_item)
item['date_iso'] = get_date(csl_item)
item['date_human'] = get_date_summary(csl_item)
item['csl_item'] = csl_item
output['extras'] = record
return output