__all__ = ["ADICAPNormAttribute"]
import dataclasses
from typing import Any, Dict, Optional
from typing_extensions import Self
from medkit.core import dict_conv
from medkit.core.text import EntityNormAttribute
[docs]@dataclasses.dataclass
class ADICAPNormAttribute(EntityNormAttribute):
"""
Attribute describing tissue sample using the ADICAP (Association pour le
Développement de l'Informatique en Cytologie et Anatomo-Pathologie) coding.
Cf https://smt.esante.gouv.fr/wp-json/ans/terminologies/document?terminologyId=terminologie-adicap&fileName=cgts_sem_adicap_fiche-detaillee.pdf for a complete description of the coding.
This class is replicating EDS-NLP's `Adicap` class, making it a medkit
`Attribute`.
The `code` field fully describes the tissue sample. Additional information
is derived from `code` in human readable fields (`sampling_code`,
`technic`, `organ`, `pathology`, `pathology_type`, `behaviour_type`)
Attributes
----------
uid:
Identifier of the attribute
label:
The attribute label, always set to :attr:`EntityNormAttribute.LABEL
<.core.text.EntityNormAttribute.LABEL>`
value:
ADICAP code prefix with "adicap:" (ex: "adicap:BHGS0040")
code:
ADICAP code as a string (ex: "BHGS0040")
kb_id:
Same as `code`
sampling_mode:
Sampling mode (ex: "BIOPSIE CHIRURGICALE")
technic:
Sampling technic (ex: "HISTOLOGIE ET CYTOLOGIE PAR INCLUSION")
organ:
Organ and regions (ex: "SEIN (ÉGALEMENT UTILISÉ CHEZ L'HOMME)")
pathology:
General pathology (ex: "PATHOLOGIE GÉNÉRALE NON TUMORALE")
pathology_type:
Pathology type (ex: "ETAT SUBNORMAL - LESION MINEURE")
behaviour_type:
Behaviour type (ex: "CARACTERES GENERAUX")
metadata:
Metadata of the attribute
"""
sampling_mode: Optional[str]
technic: Optional[str]
organ: Optional[str]
pathology: Optional[str]
pathology_type: Optional[str]
behaviour_type: Optional[str]
def __init__(
self,
code: str,
sampling_mode: Optional[str] = None,
technic: Optional[str] = None,
organ: Optional[str] = None,
pathology: Optional[str] = None,
pathology_type: Optional[str] = None,
behaviour_type: Optional[str] = None,
metadata: Optional[Dict[str, Any]] = None,
uid: Optional[str] = None,
):
super().__init__(kb_name="adicap", kb_id=code, metadata=metadata, uid=uid)
self.sampling_mode = sampling_mode
self.technic = technic
self.organ = organ
self.pathology = pathology
self.pathology_type = pathology_type
self.behaviour_type = behaviour_type
@property
def code(self) -> str:
return self.kb_id
def to_dict(self) -> Dict[str, Any]:
adicap_dict = dict(
uid=self.uid,
code=self.code,
sampling_mode=self.sampling_mode,
technic=self.technic,
organ=self.organ,
pathology=self.pathology,
pathology_type=self.pathology_type,
behaviour_type=self.behaviour_type,
metadata=self.metadata,
)
dict_conv.add_class_name_to_data_dict(adicap_dict, self)
return adicap_dict
[docs] @classmethod
def from_dict(cls, adicap_dict: Dict[str, Any]) -> Self:
return cls(
uid=adicap_dict["uid"],
code=adicap_dict["code"],
sampling_mode=adicap_dict["sampling_mode"],
technic=adicap_dict["technic"],
organ=adicap_dict["organ"],
pathology=adicap_dict["pathology"],
pathology_type=adicap_dict["pathology_type"],
behaviour_type=adicap_dict["behaviour_type"],
metadata=adicap_dict["metadata"],
)
