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medcat.components.ner.trf.helpers

Functions:

make_or_update_cdb 

make_or_update_cdb(json_path: str, cdb: Optional[CDB] = None, min_count: int = 0) -> CDB

Creates a new CDB or updates an existing one with new concepts if the cdb argument is provided. All concepts that are less frequent than min_count will be ignored.

Parameters:

  • json_path

    (str) –

    The json path

  • cdb

    (Optional[CDB], default: None ) –

    The CDB if present. Defaults to None.

  • min_count

    (int, default: 0 ) –

    Minimum count to include. Defaults to 0.

Returns:

  • CDB ( CDB ) –

    The same or new CDB.

Source code in medcat-v2/medcat/components/ner/trf/helpers.py 
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def make_or_update_cdb(json_path: str, cdb: Optional[CDB] = None,
                       min_count: int = 0) -> CDB:
    """Creates a new CDB or updates an existing one with new
    concepts if the cdb argument is provided. All concepts that are less
    frequent than min_count will be ignored.

    Args:
        json_path (str): The json path
        cdb (Optional[CDB]): The CDB if present. Defaults to None.
        min_count (int): Minimum count to include. Defaults to 0.

    Returns:
        CDB: The same or new CDB.
    """
    with open(json_path) as f:
        json_data = json.load(f)
    cui2cnt = count_anns_per_concept(json_data)
    if cdb is None:
        cdb = CDB(config=Config())

    for cui in cui2cnt.keys():
        if cui2cnt[cui] > min_count:
            # We are adding only what is needed
            cinfo = cdb.cui2info.get(cui, None)
            if cinfo is None:
                cinfo = get_new_cui_info(
                    cui=cui, preferred_name=cui, names={cui})
                cdb.cui2info[cui] = cinfo
            else:
                cinfo['names'] = set([cui])
                cinfo['preferred_name'] = cui
    return cdb

replace_entities_in_text 

replace_entities_in_text(text: str, entities: Dict, get_cui_name: Callable[[str], str], redact: bool = False) -> str
Source code in medcat-v2/medcat/components/ner/trf/helpers.py 
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def replace_entities_in_text(text: str,
                             entities: Dict,
                             get_cui_name: Callable[[str], str],
                             redact: bool = False) -> str:
    new_text = str(text)
    for ent in sorted(entities.values(), key=lambda ent: ent['start'],
                      reverse=True):
        r = "*" * (ent['end'] - ent['start']
                 ) if redact else get_cui_name(ent['cui'])
        new_text = new_text[:ent['start']] + f'[{r}]' + new_text[ent['end']:]
    return new_text