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CU-8699np02n: Update CDB legacy conversion #28

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Jul 4, 2025
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CU-8699np02n: Update CDB legacy conversion #28

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5 changes: 4 additions & 1 deletion medcat-v2/medcat/utils/legacy/convert_cdb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,7 @@ def load_old_raw_data(old_path: str) -> dict:
]
NAME2KEYS = {'name2cuis', 'name2cuis2status', 'name2count_train',
'name_isupper'}
OPTIONAL_NAME2_KEYS = {"name_isupper", }
CUI2KEYS = {'cui2names', 'cui2snames', 'cui2context_vectors',
'cui2count_train', 'cui2info', 'cui2tags', 'cui2type_ids',
'cui2preferred_name', 'cui2average_confidence', }
Expand Down Expand Up @@ -167,6 +168,8 @@ def _add_cui_info(cdb: CDB, data: dict) -> CDB:
def _add_name_info(cdb: CDB, data: dict) -> CDB:
all_names = set()
for key in NAME2KEYS:
if key in OPTIONAL_NAME2_KEYS and key not in data:
continue
cnames = data[key].keys()
logger.debug("Adding %d names based on '%s", len(cnames), key)
all_names.update(cnames)
Expand All @@ -181,7 +184,7 @@ def _add_name_info(cdb: CDB, data: dict) -> CDB:
# so v2 only uses the latter since it provides extra information
name2cuis2status = data['name2cuis2status']
name2cnt_train = data['name2count_train']
name2is_upper = data['name_isupper']
name2is_upper = data.get('name_isupper', {})
for name in all_names:
cuis2status: dict[str, str] = {}
_cuis2status = name2cuis2status.get(name, {})
Expand Down