added sanctuary intake model and schema to api

app/api/models/__init__.py

@@ -1,2 +1,6 @@
 from api.models.user import User
 from api.models.patient_encounter import PatientEncounter
+
+# TODO: uncomment this for sanctuary dev db
+# Ticket: https://mediform.atlassian.net/browse/MEDI-30
+# from api.models.intake import Intake

app/api/models/intake.py

@@ -0,0 +1,160 @@
+import uuid
+from typing import Optional, List, Dict, Any
+
+import argon2 as standalone_argon2
+import logging
+from passlib.hash import argon2
+from sqlalchemy import Column, DateTime, Integer, String, Boolean
+from sqlalchemy.dialects.postgresql import UUID
+from sqlalchemy.orm import Session
+
+from api.main.database import Base
+from api.models.mixins import BasicMetrics
+
+logger = logging.getLogger(__name__)
+
+class Intake(Base, BasicMetrics):
+    __tablename__ = "intakes"
+
+    intake_uuid = Column(UUID(as_uuid=True), primary_key=True, default=uuid.uuid4, unique=True)
+    user_uuid = Column(UUID(as_uuid=True), default=uuid.uuid4)
+    guest_rfid = Column(String, nullable=True)
+    arrival_date = Column(DateTime, nullable=True)
+    arrival_time = Column(DateTime, nullable=True)
+    arrival_method = Column(String, nullable=True)
+    identified_gender = Column(String, nullable=True)
+    first_visit = Column(Boolean, nullable=True)
+    presenting_complaint = Column(String, nullable=True)
+    guest_consciousness_level = Column(String, nullable=True)
+    guest_emotional_state = Column(String, nullable=True)
+    substance_categories = Column(String, nullable=True)
+    time_since_last_dose = Column(Integer, nullable=True)
+    discharge_date = Column(DateTime, nullable=True)
+    discharge_time = Column(DateTime, nullable=True)
+    discharge_method = Column(String, nullable=True)
+
+
+def get_intake_by_id(db: Session, id: int) -> Optional[Intake]:
+    return (
+        db.query(Intake)
+        .filter(Intake.id == id, Intake.deleted == False)
+        .first()
+    )
+
+
+def get_intake_by_uuid(
+    db: Session, uuid: uuid.UUID
+) -> Optional[Intake]:
+    return (
+        db.query(Intake)
+        .filter(
+            Intake.intake_uuid == uuid,
+            Intake.deleted == False,
+        )
+        .first()
+    )
+
+
+def get_latest_intake_by_guest_rfid(
+    db: Session, guest_rfid: str
+) -> Optional[Intake]:
+    """
+    Returns the latest patient encounter for a given patient RFID.
+
+    If the patient RFID is found returns the latest patient encounter; otherwise, returns None.
+
+
+    Returns:
+        A Intake.
+    """
+    intakes = (
+        db.query(Intake)
+        .filter(Intake.deleted == False)
+        .order_by(Intake.last_updated_timestamp.desc())
+        .all()
+    )
+
+    for encounter in intakes:
+        if encounter.guest_rfid.startswith("$argon2"):
+            try:
+                if argon2.verify(guest_rfid, encounter.guest_rfid):
+                    return encounter
+
+            except standalone_argon2.exceptions.VerifyMismatchError:
+                continue
+            except (
+                standalone_argon2.exceptions.VerificationError,
+                standalone_argon2.exceptions.InvalidHash,
+            ) as e:
+                logger.error(e, exc_info=True)
+        elif encounter.guest_rfid == guest_rfid:
+            return encounter
+
+    return None
+
+
+def get_all_intakes(db: Session) -> Optional[List[Intake]]:
+    return db.query(Intake).filter(Intake.deleted == False)
+
+
+def create_intake(db: Session, data: Intake) -> Intake:
+    """Create a patient encounter with a unique ID.
+
+    If provided, the patient RFID is hashed before being stored in the database; otherwise, it is stored as null.
+
+    Returns:
+        A Intake.
+    """
+
+    created_intake = data
+
+    if (
+        created_intake.guest_rfid
+        and created_intake.guest_rfid != ""
+    ):
+        hashed_rfid = argon2.hash(created_intake.guest_rfid)
+        created_intake.guest_rfid = hashed_rfid
+
+    db.add(created_intake)
+    db.commit()
+    db.refresh(created_intake)
+
+    return created_intake
+
+
+def update_intake(
+    db: Session, encounter: Intake, updated_values: Dict[str, Any]
+) -> Intake:
+    """
+    Update an existing patient encounter document using its existing UUID. Returns the updated patient encounter.
+
+    If provided, the patient RFID is hashed before being stored in the database; otherwise, it is stored as null.
+
+    """
+    updated_encounter = encounter
+
+    # Check if the patient RFID has been updated
+    if "guest_rfid" in updated_values:
+        updated_rfid = updated_values["guest_rfid"]
+
+        hashed_rfid = argon2.hash(updated_rfid)
+        updated_values["guest_rfid"] = hashed_rfid
+
+    db.query(Intake).filter(
+        Intake.deleted == False,
+        Intake.intake_uuid == encounter.intake_uuid,
+    ).update(values=updated_values)
+    db.commit()
+    db.refresh(updated_encounter)
+
+    return updated_encounter
+
+
+def soft_delete_intake(db: Session, uuid: uuid.UUID) -> None:
+    """
+    Update patient encounter property to set deleted to True.
+    """
+    db.query(Intake).filter(
+        Intake.intake_uuid == uuid
+    ).update(values={"deleted": True})
+    db.commit()

app/api/schemas/intake.py

@@ -0,0 +1,37 @@
+from datetime import datetime
+from uuid import UUID
+from typing import List, Optional
+from pydantic import BaseModel
+
+
+class IntakeSchema(BaseModel):
+    """
+    An intake for a given patient.
+    """
+    guest_rfid: Optional[str]
+    arrival_date = Optional[DateTime]
+    arrival_time = Optional[DateTime]
+    arrival_method = Optional[String]
+    identified_gender = Optional[String]
+    first_visit = Optional[Boolean]
+    presenting_complaint = Optional[String]
+    guest_consciousness_level = Optional[String]
+    guest_emotional_state = Optional[String]
+    substance_categories = Optional[String]
+    time_since_last_dose = Optional[Integer]
+    discharge_date = Optional[DateTime]
+    discharge_time = Optional[DateTime]
+    discharge_method = Optional[String]
+
+
+    class Config:
+        orm_mode = True
+
+class IntakeResponseSchema(IntakeSchema):
+    """
+    The intake response schema.
+    """
+    intake_uuid: Optional[UUID]
+
+    class Config:
+        orm_mode = True