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 test_csl_item_set_standard_id_note():
"""
Test extracting standard_id from a note and setting additional
note fields.
"""
csl_item = {
'id': 'original-id',
'type': 'article-journal',
'note': 'standard_id: doi:10.1371/journal.PPAT.1006256',
}
csl_item_set_standard_id(csl_item)
assert csl_item['id'] == 'doi:10.1371/journal.ppat.1006256'
from manubot.cite.citeproc import parse_csl_item_note
note_dict = parse_csl_item_note(csl_item['note'])
assert note_dict['original_id'] == 'original-id'
assert note_dict['original_standard_id'] == 'doi:10.1371/journal.PPAT.1006256'
def test_parse_csl_item_note(note, dictionary):
assert parse_csl_item_note(note) == dictionary