cehrgpt 0.0.1__py3-none-any.whl

cehrgpt/generation/omop_entity.py

@@ -0,0 +1,515 @@
+from abc import ABC, abstractmethod
+from datetime import date, datetime
+from typing import Union
+
+
+def fill_datetime(year: int) -> str:
+    """Helper function to create an ISO 8601 datetime string for 01/01 of a given year."""
+    return datetime.strptime(f"{year}-01-01", "%Y-%m-%d").isoformat()
+
+
+def fill_start_datetime(d: Union[date, datetime]) -> str:
+    """Helper function to create an ISO 8601 string at 00:00:00 (start of day)."""
+    if isinstance(d, datetime):
+        return d.isoformat()
+    elif isinstance(d, date):
+        return datetime.combine(d, datetime.min.time()).isoformat()
+    raise RuntimeError(f"{type(d)} is not supported by this function.")
+
+
+def fill_end_datetime(d: Union[date, datetime]) -> str:
+    """Helper function to create an ISO 8601 string at 23:59:59.999999 (end of day)."""
+    if isinstance(d, datetime):
+        return d.isoformat()
+    elif isinstance(d, date):
+        return datetime.combine(d, datetime.max.time()).isoformat()
+    raise RuntimeError(f"{type(d)} is not supported by this function.")
+
+
+class OmopEntity(ABC):
+    """
+    Abstract base class that all OMOP CDM entities inherit from.
+
+    Ensures that each entity can export its data as JSON,
+    retrieve its schema, and provide a table name.
+    """
+
+    @abstractmethod
+    def export_as_json(self):
+        pass
+
+    @classmethod
+    @abstractmethod
+    def get_schema(cls):
+        pass
+
+    @abstractmethod
+    def get_table_name(self):
+        pass
+
+
+# -----------------------------------------------------------------------------
+# PERSON
+# https://ohdsi.github.io/CommonDataModel/cdm54.html#person
+# -----------------------------------------------------------------------------
+class Person(OmopEntity):
+    def __init__(self, person_id, gender_concept_id, year_of_birth, race_concept_id):
+        self._person_id = person_id
+        self._gender_concept_id = gender_concept_id
+        self._year_of_birth = year_of_birth
+        self._race_concept_id = race_concept_id
+
+    def export_as_json(self):
+        return {
+            "person_id": self._person_id,
+            "gender_concept_id": self._gender_concept_id,
+            "year_of_birth": self._year_of_birth,
+            "month_of_birth": 1,
+            "day_of_birth": 1,
+            "birth_datetime": fill_datetime(self._year_of_birth),
+            "race_concept_id": self._race_concept_id,
+            "ethnicity_concept_id": 0,
+            "location_id": 0,
+            "provider_id": 0,
+            "care_site_id": 0,
+            "person_source_value": "",
+            "gender_source_value": "",
+            "gender_source_concept_id": 0,
+            "race_source_value": "",
+            "race_source_concept_id": 0,
+            "ethnicity_source_value": "",
+            "ethnicity_source_concept_id": 0,
+        }
+
+    @classmethod
+    def get_schema(cls):
+        return {
+            "person_id": int,
+            "gender_concept_id": int,
+            "year_of_birth": int,
+            "month_of_birth": int,
+            "day_of_birth": int,
+            "birth_datetime": datetime,
+            "race_concept_id": int,
+            "ethnicity_concept_id": int,
+            "location_id": int,
+            "provider_id": int,
+            "care_site_id": int,
+            "person_source_value": str,
+            "gender_source_value": str,
+            "gender_source_concept_id": int,
+            "race_source_value": str,
+            "race_source_concept_id": int,
+            "ethnicity_source_value": str,
+            "ethnicity_source_concept_id": int,
+        }
+
+    def get_table_name(self):
+        return "person"
+
+
+# -----------------------------------------------------------------------------
+# VISIT_OCCURRENCE
+# https://ohdsi.github.io/CommonDataModel/cdm54.html#visit_occurrence
+# -----------------------------------------------------------------------------
+class VisitOccurrence(OmopEntity):
+    def __init__(
+        self,
+        visit_occurrence_id: int,
+        visit_concept_id: int,
+        visit_start_datetime: datetime,
+        person: Person,
+        discharged_to_concept_id: int = 0,
+    ):
+        self._visit_occurrence_id = visit_occurrence_id
+        self._visit_concept_id = visit_concept_id
+        self._visit_start_date = visit_start_datetime.date()
+        self._visit_start_datetime = fill_start_datetime(visit_start_datetime)
+        self._visit_end_date = visit_start_datetime.date()
+        self._visit_end_datetime = fill_end_datetime(visit_start_datetime)
+        self._person = person
+        self._discharged_to_concept_id = discharged_to_concept_id
+
+    def export_as_json(self):
+        return {
+            "visit_occurrence_id": self._visit_occurrence_id,
+            "visit_concept_id": self._visit_concept_id,
+            "person_id": self._person._person_id,
+            "visit_start_date": self._visit_start_date,
+            "visit_start_datetime": self._visit_start_datetime,
+            "visit_end_date": self._visit_end_date,
+            "visit_end_datetime": self._visit_end_datetime,
+            "visit_type_concept_id": 44818702,  # default concept (e.g. Inpatient Visit)
+            "provider_id": 0,
+            "care_site_id": 0,
+            "visit_source_value": "",
+            "visit_source_concept_id": self._visit_concept_id,
+            "admitted_from_concept_id": 0,  # replaced "admitting_source_concept_id"
+            "admitted_from_source_value": "",  # replaced "admitting_source_value"
+            "discharged_to_concept_id": self._discharged_to_concept_id,
+            "discharged_to_source_value": "",
+            "preceding_visit_occurrence_id": 0,
+        }
+
+    @classmethod
+    def get_schema(cls):
+        return {
+            "visit_occurrence_id": int,
+            "visit_concept_id": int,
+            "person_id": int,
+            "visit_start_date": date,
+            "visit_start_datetime": datetime,
+            "visit_end_date": date,
+            "visit_end_datetime": datetime,
+            "visit_type_concept_id": int,
+            "provider_id": int,
+            "care_site_id": int,
+            "visit_source_value": str,
+            "visit_source_concept_id": int,
+            "admitted_from_concept_id": int,
+            "admitted_from_source_value": str,
+            "discharged_to_concept_id": int,
+            "discharged_to_source_value": str,
+            "preceding_visit_occurrence_id": int,
+        }
+
+    def get_table_name(self):
+        return "visit_occurrence"
+
+    @property
+    def person(self):
+        return self._person
+
+    @property
+    def discharged_to_concept_id(self):
+        return self._discharged_to_concept_id
+
+    def set_discharged_to_concept_id(self, discharged_to_concept_id: int):
+        self._discharged_to_concept_id = discharged_to_concept_id
+
+    def set_visit_end_date(self, visit_end_datetime: datetime):
+        self._visit_end_date = visit_end_datetime.date()
+        self._visit_end_datetime = fill_end_datetime(visit_end_datetime)
+
+
+# -----------------------------------------------------------------------------
+# CONDITION_OCCURRENCE
+# https://ohdsi.github.io/CommonDataModel/cdm54.html#condition_occurrence
+# -----------------------------------------------------------------------------
+class ConditionOccurrence(OmopEntity):
+    def __init__(
+        self,
+        condition_occurrence_id: int,
+        condition_concept_id: int,
+        visit_occurrence: VisitOccurrence,
+        condition_datetime: datetime,
+    ):
+        self._condition_occurrence_id = condition_occurrence_id
+        self._condition_concept_id = condition_concept_id
+        self._visit_occurrence = visit_occurrence
+        self._condition_start_date = condition_datetime.date()
+        self._condition_start_datetime = fill_start_datetime(condition_datetime)
+        self._condition_end_date = condition_datetime.date()
+        self._condition_end_datetime = fill_start_datetime(condition_datetime)
+
+    def export_as_json(self):
+        return {
+            "condition_occurrence_id": self._condition_occurrence_id,
+            "person_id": self._visit_occurrence._person._person_id,
+            "condition_concept_id": self._condition_concept_id,
+            "condition_start_date": self._condition_start_date,
+            "condition_start_datetime": self._condition_start_datetime,
+            "condition_end_date": self._condition_end_date,
+            "condition_end_datetime": self._condition_end_datetime,
+            "condition_type_concept_id": 32817,  # default concept
+            "stop_reason": "",
+            "provider_id": 0,
+            "visit_occurrence_id": self._visit_occurrence._visit_occurrence_id,
+            "visit_detail_id": 0,
+            "condition_source_value": "",
+            "condition_source_concept_id": self._condition_concept_id,
+            "condition_status_source_value": "",
+            "condition_status_concept_id": 0,
+        }
+
+    @classmethod
+    def get_schema(cls):
+        return {
+            "condition_occurrence_id": int,
+            "person_id": int,
+            "condition_concept_id": int,
+            "condition_start_date": date,
+            "condition_start_datetime": datetime,
+            "condition_end_date": date,
+            "condition_end_datetime": datetime,
+            "condition_type_concept_id": int,
+            "stop_reason": str,
+            "provider_id": int,
+            "visit_occurrence_id": int,
+            "visit_detail_id": int,
+            "condition_source_value": str,
+            "condition_source_concept_id": int,
+            "condition_status_source_value": str,
+            "condition_status_concept_id": int,
+        }
+
+    def get_table_name(self):
+        return "condition_occurrence"
+
+
+# -----------------------------------------------------------------------------
+# DRUG_EXPOSURE
+# https://ohdsi.github.io/CommonDataModel/cdm54.html#drug_exposure
+# -----------------------------------------------------------------------------
+class DrugExposure(OmopEntity):
+    def __init__(
+        self,
+        drug_exposure_id: int,
+        drug_concept_id: int,
+        visit_occurrence: VisitOccurrence,
+        drug_datetime: datetime,
+    ):
+        self._drug_exposure_id = drug_exposure_id
+        self._drug_concept_id = drug_concept_id
+        self._visit_occurrence = visit_occurrence
+        self._drug_exposure_start_date = drug_datetime.date()
+        self._drug_exposure_start_datetime = fill_start_datetime(drug_datetime)
+        self._drug_exposure_end_date = drug_datetime.date()
+        self._drug_exposure_end_datetime = fill_start_datetime(drug_datetime)
+
+    def export_as_json(self):
+        return {
+            "drug_exposure_id": self._drug_exposure_id,
+            "person_id": self._visit_occurrence._person._person_id,
+            "drug_concept_id": self._drug_concept_id,
+            "drug_exposure_start_date": self._drug_exposure_start_date,
+            "drug_exposure_start_datetime": self._drug_exposure_start_datetime,
+            "drug_exposure_end_date": self._drug_exposure_end_date,
+            "drug_exposure_end_datetime": self._drug_exposure_end_datetime,
+            "verbatim_end_date": self._drug_exposure_end_date,
+            "drug_type_concept_id": 38000177,  # default concept
+            "stop_reason": "",
+            "refills": None,
+            "quantity": None,
+            "days_supply": None,
+            "sig": "",
+            "route_concept_id": 0,
+            "lot_number": "",
+            "provider_id": 0,
+            "visit_occurrence_id": self._visit_occurrence._visit_occurrence_id,
+            "visit_detail_id": 0,
+            "drug_source_value": "",
+            "drug_source_concept_id": self._drug_concept_id,
+            "route_source_value": "",
+            "dose_unit_source_value": "",
+        }
+
+    @classmethod
+    def get_schema(cls):
+        return {
+            "drug_exposure_id": int,
+            "person_id": int,
+            "drug_concept_id": int,
+            "drug_exposure_start_date": date,
+            "drug_exposure_start_datetime": datetime,
+            "drug_exposure_end_date": date,
+            "drug_exposure_end_datetime": datetime,
+            "verbatim_end_date": date,
+            "drug_type_concept_id": int,
+            "stop_reason": str,
+            "refills": int,
+            "quantity": int,
+            "days_supply": int,
+            "sig": str,
+            "route_concept_id": int,
+            "lot_number": str,
+            "provider_id": int,
+            "visit_occurrence_id": int,
+            "visit_detail_id": int,
+            "drug_source_value": str,
+            "drug_source_concept_id": int,
+            "route_source_value": str,
+            "dose_unit_source_value": str,
+        }
+
+    def get_table_name(self):
+        return "drug_exposure"
+
+
+# -----------------------------------------------------------------------------
+# PROCEDURE_OCCURRENCE
+# https://ohdsi.github.io/CommonDataModel/cdm54.html#procedure_occurrence
+# -----------------------------------------------------------------------------
+class ProcedureOccurrence(OmopEntity):
+    def __init__(
+        self,
+        procedure_occurrence_id: int,
+        procedure_concept_id: int,
+        visit_occurrence: VisitOccurrence,
+        procedure_datetime: datetime,
+    ):
+        self._procedure_occurrence_id = procedure_occurrence_id
+        self._procedure_concept_id = procedure_concept_id
+        self._visit_occurrence = visit_occurrence
+        self._procedure_date = procedure_datetime.date()
+        self._procedure_datetime = fill_start_datetime(procedure_datetime)
+
+    def export_as_json(self):
+        return {
+            "procedure_occurrence_id": self._procedure_occurrence_id,
+            "person_id": self._visit_occurrence._person._person_id,
+            "procedure_concept_id": self._procedure_concept_id,
+            "procedure_date": self._procedure_date,
+            "procedure_datetime": self._procedure_datetime,
+            "procedure_type_concept_id": 38000178,  # default
+            "modifier_concept_id": 0,
+            "quantity": 1,
+            "provider_id": 0,
+            "visit_occurrence_id": self._visit_occurrence._visit_occurrence_id,
+            "visit_detail_id": 0,
+            "procedure_source_value": "",
+            "procedure_source_concept_id": self._procedure_concept_id,
+            "qualifier_source_value": "",
+        }
+
+    @classmethod
+    def get_schema(cls):
+        return {
+            "procedure_occurrence_id": int,
+            "person_id": int,
+            "procedure_concept_id": int,
+            "procedure_date": date,
+            "procedure_datetime": datetime,
+            "procedure_type_concept_id": int,
+            "modifier_concept_id": int,
+            "quantity": int,
+            "provider_id": int,
+            "visit_occurrence_id": int,
+            "visit_detail_id": int,
+            "procedure_source_value": str,
+            "procedure_source_concept_id": int,
+            "qualifier_source_value": str,
+        }
+
+    def get_table_name(self):
+        return "procedure_occurrence"
+
+
+# -----------------------------------------------------------------------------
+# DEATH
+# https://ohdsi.github.io/CommonDataModel/cdm54.html#death
+# -----------------------------------------------------------------------------
+class Death(OmopEntity):
+    def __init__(
+        self,
+        person: Person,
+        death_date: date,
+        death_type_concept_id: int = 0,
+    ):
+        self._person = person
+        self._death_date = death_date
+        self._death_datetime = fill_end_datetime(death_date)
+        self._death_type_concept_id = death_type_concept_id
+
+    def export_as_json(self):
+        return {
+            "person_id": self._person._person_id,
+            "death_date": self._death_date,
+            "death_datetime": self._death_datetime,
+            "death_type_concept_id": self._death_type_concept_id,
+            "cause_concept_id": 0,
+            "cause_source_value": "",
+            "cause_source_concept_id": 0,
+        }
+
+    @classmethod
+    def get_schema(cls):
+        return {
+            "person_id": int,
+            "death_date": date,
+            "death_datetime": datetime,
+            "death_type_concept_id": int,
+            "cause_concept_id": int,
+            "cause_source_value": str,
+            "cause_source_concept_id": int,
+        }
+
+    def get_table_name(self):
+        return "death"
+
+
+# -----------------------------------------------------------------------------
+# MEASUREMENT
+# https://ohdsi.github.io/CommonDataModel/cdm54.html#measurement
+# -----------------------------------------------------------------------------
+class Measurement(OmopEntity):
+    def __init__(
+        self,
+        measurement_id: int,
+        measurement_concept_id: int,
+        value_as_number: float,
+        is_numeric_type,
+        value_as_concept_id,
+        visit_occurrence: VisitOccurrence,
+        measurement_datetime: datetime,
+        unit_source_value,
+    ):
+        self._measurement_id = measurement_id
+        self._measurement_concept_id = measurement_concept_id
+        self._value_as_number = value_as_number
+        self._value_as_concept_id = value_as_concept_id
+        self._visit_occurrence = visit_occurrence
+        self._measurement_date = measurement_datetime.date()
+        self._measurement_datetime = fill_start_datetime(measurement_datetime)
+        self._operator_concept_id = 4172703 if is_numeric_type == 1 else 0
+        self._unit_source_value = unit_source_value
+
+    def export_as_json(self):
+        return {
+            "measurement_id": self._measurement_id,
+            "person_id": self._visit_occurrence._person._person_id,
+            "measurement_concept_id": self._measurement_concept_id,
+            "measurement_date": self._measurement_date,
+            "measurement_datetime": self._measurement_datetime,
+            "measurement_type_concept_id": 0,
+            "operator_concept_id": self._operator_concept_id,
+            "value_as_number": self._value_as_number,
+            "value_as_concept_id": self._value_as_concept_id,
+            "unit_concept_id": 0,
+            "range_low": None,
+            "range_high": None,
+            "provider_id": 0,
+            "visit_occurrence_id": self._visit_occurrence._visit_occurrence_id,
+            "visit_detail_id": 0,
+            "measurement_source_value": "",
+            "measurement_source_concept_id": self._measurement_concept_id,
+            "unit_source_value": self._unit_source_value,
+            "value_source_value": "",
+        }
+
+    @classmethod
+    def get_schema(cls):
+        return {
+            "measurement_id": int,
+            "person_id": int,
+            "measurement_concept_id": int,
+            "measurement_date": date,
+            "measurement_datetime": datetime,
+            "measurement_type_concept_id": int,
+            "operator_concept_id": int,
+            "value_as_number": float,
+            "value_as_concept_id": int,
+            "unit_concept_id": int,
+            "range_low": float,
+            "range_high": float,
+            "provider_id": int,
+            "visit_occurrence_id": int,
+            "visit_detail_id": int,
+            "measurement_source_value": str,
+            "measurement_source_concept_id": int,
+            "unit_source_value": str,
+            "value_source_value": str,
+        }
+
+    def get_table_name(self):
+        return "measurement"