api/routes/patients.py

from fastapi import APIRouter, HTTPException, Depends, Query, status, Body
from db.mongo import patients_collection
from core.security import get_current_user
from utils.db import create_indexes
from utils.helpers import calculate_age, standardize_language
from models.entities import Note, PatientCreate
from datetime import datetime
from bson import ObjectId
from bson.errors import InvalidId
from typing import Optional, List, Dict, Any
from pymongo import UpdateOne, DeleteOne
from pymongo.errors import BulkWriteError
import json
from pathlib import Path
import glob
import uuid
import re
import logging
import time
import os
from pydantic import BaseModel, Field

# Configure logging
logging.basicConfig(
    level=logging.INFO,
    format='%(asctime)s - %(levelname)s - %(name)s - %(message)s'
)
logger = logging.getLogger(__name__)

router = APIRouter()

# Configuration
BASE_DIR = Path(__file__).resolve().parent.parent.parent
SYNTHEA_DATA_DIR = BASE_DIR / "output" / "fhir"
os.makedirs(SYNTHEA_DATA_DIR, exist_ok=True)

# Pydantic models for update validation
class ConditionUpdate(BaseModel):
    id: Optional[str] = None
    code: Optional[str] = None
    status: Optional[str] = None
    onset_date: Optional[str] = None
    recorded_date: Optional[str] = None
    verification_status: Optional[str] = None
    notes: Optional[str] = None

class MedicationUpdate(BaseModel):
    id: Optional[str] = None
    name: Optional[str] = None
    status: Optional[str] = None
    prescribed_date: Optional[str] = None
    requester: Optional[str] = None
    dosage: Optional[str] = None

class EncounterUpdate(BaseModel):
    id: Optional[str] = None
    type: Optional[str] = None
    status: Optional[str] = None
    period: Optional[Dict[str, str]] = None
    service_provider: Optional[str] = None

class NoteUpdate(BaseModel):
    id: Optional[str] = None
    title: Optional[str] = None
    date: Optional[str] = None
    author: Optional[str] = None
    content: Optional[str] = None

class PatientUpdate(BaseModel):
    full_name: Optional[str] = None
    gender: Optional[str] = None
    date_of_birth: Optional[str] = None
    address: Optional[str] = None
    city: Optional[str] = None
    state: Optional[str] = None
    postal_code: Optional[str] = None
    country: Optional[str] = None
    marital_status: Optional[str] = None
    language: Optional[str] = None
    conditions: Optional[List[ConditionUpdate]] = None
    medications: Optional[List[MedicationUpdate]] = None
    encounters: Optional[List[EncounterUpdate]] = None
    notes: Optional[List[NoteUpdate]] = None

@router.get("/debug/count")
async def debug_patient_count():
    """Debug endpoint to verify patient counts"""
    try:
        total = await patients_collection.count_documents({})
        synthea = await patients_collection.count_documents({"source": "synthea"})
        manual = await patients_collection.count_documents({"source": "manual"})
        return {
            "total": total,
            "synthea": synthea,
            "manual": manual,
            "message": f"Found {total} total patients ({synthea} from synthea, {manual} manual)"
        }
    except Exception as e:
        logger.error(f"Error counting patients: {str(e)}")
        raise HTTPException(
            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
            detail=f"Error counting patients: {str(e)}"
        )

@router.post("/patients", status_code=status.HTTP_201_CREATED)
async def create_patient(
    patient_data: PatientCreate,
    current_user: dict = Depends(get_current_user)
):
    """Create a new patient in the database"""
    logger.info(f"Creating new patient by user {current_user.get('email')}")
    
    if current_user.get('role') not in ['admin', 'doctor']:
        logger.warning(f"Unauthorized create attempt by {current_user.get('email')}")
        raise HTTPException(
            status_code=status.HTTP_403_FORBIDDEN,
            detail="Only administrators and doctors can create patients"
        )
    
    try:
        # Prepare the patient document
        patient_doc = patient_data.dict()
        now = datetime.utcnow().isoformat()
        
        # Add system-generated fields
        patient_doc.update({
            "fhir_id": str(uuid.uuid4()),
            "import_date": now,
            "last_updated": now,
            "source": "manual",
            "created_by": current_user.get('email')
        })
        
        # Ensure arrays exist even if empty
        for field in ['conditions', 'medications', 'encounters', 'notes']:
            if field not in patient_doc:
                patient_doc[field] = []
        
        # Insert the patient document
        result = await patients_collection.insert_one(patient_doc)
        
        # Return the created patient with the generated ID
        created_patient = await patients_collection.find_one(
            {"_id": result.inserted_id}
        )
        
        if not created_patient:
            logger.error("Failed to retrieve created patient")
            raise HTTPException(
                status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
                detail="Failed to retrieve created patient"
            )
        
        created_patient["id"] = str(created_patient["_id"])
        del created_patient["_id"]
        
        logger.info(f"Successfully created patient {created_patient['fhir_id']}")
        return created_patient
        
    except Exception as e:
        logger.error(f"Failed to create patient: {str(e)}")
        raise HTTPException(
            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
            detail=f"Failed to create patient: {str(e)}"
        )

@router.delete("/patients/{patient_id}", status_code=status.HTTP_204_NO_CONTENT)
async def delete_patient(
    patient_id: str,
    current_user: dict = Depends(get_current_user)
):
    """Delete a patient from the database"""
    logger.info(f"Deleting patient {patient_id} by user {current_user.get('email')}")
    
    if current_user.get('role') not in ['admin', 'doctor']:
        logger.warning(f"Unauthorized delete attempt by {current_user.get('email')}")
        raise HTTPException(
            status_code=status.HTTP_403_FORBIDDEN,
            detail="Only administrators can delete patients"
        )
    
    try:
        # Build the query based on whether patient_id is a valid ObjectId
        query = {"fhir_id": patient_id}
        if ObjectId.is_valid(patient_id):
            query = {
                "$or": [
                    {"_id": ObjectId(patient_id)},
                    {"fhir_id": patient_id}
                ]
            }
        
        # Check if patient exists
        patient = await patients_collection.find_one(query)
        
        if not patient:
            logger.warning(f"Patient not found for deletion: {patient_id}")
            raise HTTPException(
                status_code=status.HTTP_404_NOT_FOUND,
                detail="Patient not found"
            )
        
        # Perform deletion
        result = await patients_collection.delete_one(query)
        
        if result.deleted_count == 0:
            logger.error(f"Failed to delete patient {patient_id}")
            raise HTTPException(
                status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
                detail="Failed to delete patient"
            )
        
        logger.info(f"Successfully deleted patient {patient_id}")
        return None
        
    except HTTPException:
        raise
    except Exception as e:
        logger.error(f"Failed to delete patient {patient_id}: {str(e)}")
        raise HTTPException(
            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
            detail=f"Failed to delete patient: {str(e)}"
        )

async def process_synthea_patient(bundle: dict, file_path: str) -> Optional[dict]:
    logger.debug(f"Processing patient from file: {file_path}")
    patient_data = {}
    notes = []
    conditions = []
    medications = []
    encounters = []
    
    # Validate bundle structure
    if not isinstance(bundle, dict) or 'entry' not in bundle:
        logger.error(f"Invalid FHIR bundle structure in {file_path}")
        return None
    
    for entry in bundle.get('entry', []):
        resource = entry.get('resource', {})
        resource_type = resource.get('resourceType')
        
        if not resource_type:
            logger.warning(f"Skipping entry with missing resourceType in {file_path}")
            continue
            
        try:
            if resource_type == 'Patient':
                name = resource.get('name', [{}])[0]
                address = resource.get('address', [{}])[0]
                
                # Construct full name and remove numbers
                raw_full_name = f"{' '.join(name.get('given', ['']))} {name.get('family', '')}".strip()
                clean_full_name = re.sub(r'\d+', '', raw_full_name).strip()
                
                patient_data = {
                    'fhir_id': resource.get('id'),
                    'full_name': clean_full_name,
                    'gender': resource.get('gender', 'unknown'),
                    'date_of_birth': resource.get('birthDate', ''),
                    'address': ' '.join(address.get('line', [''])),
                    'city': address.get('city', ''),
                    'state': address.get('state', ''),
                    'postal_code': address.get('postalCode', ''),
                    'country': address.get('country', ''),
                    'marital_status': resource.get('maritalStatus', {}).get('text', ''),
                    'language': standardize_language(resource.get('communication', [{}])[0].get('language', {}).get('text', '')),
                    'source': 'synthea',
                    'last_updated': datetime.utcnow().isoformat()
                }
                
            elif resource_type == 'Encounter':
                encounter = {
                    'id': resource.get('id'),
                    'type': resource.get('type', [{}])[0].get('text', ''),
                    'status': resource.get('status'),
                    'period': resource.get('period', {}),
                    'service_provider': resource.get('serviceProvider', {}).get('display', '')
                }
                encounters.append(encounter)
                
                for note in resource.get('note', []):
                    if note.get('text'):
                        notes.append({
                            'date': resource.get('period', {}).get('start', datetime.utcnow().isoformat()),
                            'type': resource.get('type', [{}])[0].get('text', 'Encounter Note'),
                            'text': note.get('text'),
                            'context': f"Encounter: {encounter.get('type')}",
                            'author': 'System Generated'
                        })
                
            elif resource_type == 'Condition':
                conditions.append({
                    'id': resource.get('id'),
                    'code': resource.get('code', {}).get('text', ''),
                    'status': resource.get('clinicalStatus', {}).get('text', ''),
                    'onset_date': resource.get('onsetDateTime'),
                    'recorded_date': resource.get('recordedDate'),
                    'verification_status': resource.get('verificationStatus', {}).get('text', '')
                })
                
            elif resource_type == 'MedicationRequest':
                medications.append({
                    'id': resource.get('id'),
                    'name': resource.get('medicationCodeableConcept', {}).get('text', ''),
                    'status': resource.get('status'),
                    'prescribed_date': resource.get('authoredOn'),
                    'requester': resource.get('requester', {}).get('display', ''),
                    'dosage': resource.get('dosageInstruction', [{}])[0].get('text', '')
                })
                
        except Exception as e:
            logger.error(f"Error processing {resource_type} in {file_path}: {str(e)}")
            continue
    
    if patient_data:
        patient_data.update({
            'notes': notes,
            'conditions': conditions,
            'medications': medications,
            'encounters': encounters,
            'import_date': datetime.utcnow().isoformat()
        })
        logger.info(f"Successfully processed patient {patient_data.get('fhir_id')} from {file_path}")
        return patient_data
    logger.warning(f"No valid patient data found in {file_path}")
    return None

@router.post("/import", status_code=status.HTTP_201_CREATED)
async def import_patients(
    limit: int = Query(100, ge=1, le=1000),
    current_user: dict = Depends(get_current_user)
):
    request_id = str(uuid.uuid4())
    logger.info(f"Starting import request {request_id} by user {current_user.get('email')}")
    start_time = time.time()
    
    if current_user.get('role') not in ['admin', 'doctor']:
        logger.warning(f"Unauthorized import attempt by {current_user.get('email')}")
        raise HTTPException(
            status_code=status.HTTP_403_FORBIDDEN,
            detail="Only administrators and doctors can import data"
        )
    
    try:
        await create_indexes()
        
        if not SYNTHEA_DATA_DIR.exists():
            logger.error(f"Synthea data directory not found: {SYNTHEA_DATA_DIR}")
            raise HTTPException(
                status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
                detail="Data directory not found"
            )
            
        # Filter out non-patient files
        files = [
            f for f in glob.glob(str(SYNTHEA_DATA_DIR / "*.json"))
            if not re.search(r'(hospitalInformation|practitionerInformation)\d+\.json$', f)
        ]
        if not files:
            logger.warning("No valid patient JSON files found in synthea data directory")
            return {
                "status": "success",
                "message": "No patient data files found",
                "imported": 0,
                "request_id": request_id
            }
            
        operations = []
        imported = 0
        errors = []
        
        for file_path in files[:limit]:
            try:
                logger.debug(f"Processing file: {file_path}")
                
                # Check file accessibility
                if not os.path.exists(file_path):
                    logger.error(f"File not found: {file_path}")
                    errors.append(f"File not found: {file_path}")
                    continue
                    
                # Check file size
                file_size = os.path.getsize(file_path)
                if file_size == 0:
                    logger.warning(f"Empty file: {file_path}")
                    errors.append(f"Empty file: {file_path}")
                    continue
                    
                with open(file_path, 'r', encoding='utf-8') as f:
                    try:
                        bundle = json.load(f)
                    except json.JSONDecodeError as je:
                        logger.error(f"Invalid JSON in {file_path}: {str(je)}")
                        errors.append(f"Invalid JSON in {file_path}: {str(je)}")
                        continue
                        
                patient = await process_synthea_patient(bundle, file_path)
                if patient:
                    if not patient.get('fhir_id'):
                        logger.warning(f"Missing FHIR ID in patient data from {file_path}")
                        errors.append(f"Missing FHIR ID in {file_path}")
                        continue
                        
                    operations.append(UpdateOne(
                        {"fhir_id": patient['fhir_id']},
                        {"$setOnInsert": patient},
                        upsert=True
                    ))
                    imported += 1
                else:
                    logger.warning(f"No valid patient data in {file_path}")
                    errors.append(f"No valid patient data in {file_path}")
                    
            except Exception as e:
                logger.error(f"Error processing {file_path}: {str(e)}")
                errors.append(f"Error in {file_path}: {str(e)}")
                continue
        
        response = {
            "status": "success",
            "imported": imported,
            "errors": errors,
            "request_id": request_id,
            "duration_seconds": time.time() - start_time
        }
        
        if operations:
            try:
                result = await patients_collection.bulk_write(operations, ordered=False)
                response.update({
                    "upserted": result.upserted_count,
                    "existing": len(operations) - result.upserted_count
                })
                logger.info(f"Import request {request_id} completed: {imported} patients processed, "
                           f"{result.upserted_count} upserted, {len(errors)} errors")
            except BulkWriteError as bwe:
                logger.error(f"Partial bulk write failure for request {request_id}: {str(bwe.details)}")
                response.update({
                    "upserted": bwe.details.get('nUpserted', 0),
                    "existing": len(operations) - bwe.details.get('nUpserted', 0),
                    "write_errors": [
                        f"Index {err['index']}: {err['errmsg']}" for err in bwe.details.get('writeErrors', [])
                    ]
                })
                logger.info(f"Import request {request_id} partially completed: {imported} patients processed, "
                           f"{response['upserted']} upserted, {len(errors)} errors")
            except Exception as e:
                logger.error(f"Bulk write failed for request {request_id}: {str(e)}")
                raise HTTPException(
                    status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
                    detail=f"Database operation failed: {str(e)}"
                )
        else:
            logger.info(f"Import request {request_id} completed: No new patients to import, {len(errors)} errors")
            response["message"] = "No new patients found to import"
            
        return response
        
    except HTTPException:
        raise
    except Exception as e:
        logger.error(f"Import request {request_id} failed: {str(e)}", exc_info=True)
        raise HTTPException(
            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
            detail=f"Import failed: {str(e)}"
        )

@router.get("/patients", response_model=List[dict])
async def list_patients(
    search: Optional[str] = Query(None),
    min_notes: int = Query(0, ge=0),
    min_conditions: int = Query(0, ge=0),
    limit: int = Query(100, ge=1, le=500),
    skip: int = Query(0, ge=0)
):
    logger.info(f"Listing patients with search: {search}, limit: {limit}, skip: {skip}")
    query = {}
    
    if search:
        query["$or"] = [
            {"full_name": {"$regex": search, "$options": "i"}},
            {"fhir_id": search}
        ]
    
    if min_notes > 0:
        query[f"notes.{min_notes-1}"] = {"$exists": True}
    
    if min_conditions > 0:
        query[f"conditions.{min_conditions-1}"] = {"$exists": True}
    
    projection = {
        "fhir_id": 1,
        "full_name": 1,
        "gender": 1,
        "date_of_birth": 1,
        "city": 1,
        "state": 1,
        "conditions": 1,
        "medications": 1,
        "encounters": 1,
        "notes": 1,
        "source": 1
    }
    
    try:
        cursor = patients_collection.find(query, projection).skip(skip).limit(limit)
        patients = []
        
        async for patient in cursor:
            patients.append({
                "id": str(patient["_id"]),
                "fhir_id": patient.get("fhir_id"),
                "full_name": patient.get("full_name"),
                "gender": patient.get("gender"),
                "date_of_birth": patient.get("date_of_birth"),
                "city": patient.get("city"),
                "state": patient.get("state"),
                "conditions": patient.get("conditions", []),
                "medications": patient.get("medications", []),
                "encounters": patient.get("encounters", []),
                "notes": patient.get("notes", []),
                "source": patient.get("source", "unknown"),
                "age": calculate_age(patient.get("date_of_birth")),
                "stats": {
                    "notes": len(patient.get("notes", [])),
                    "conditions": len(patient.get("conditions", [])),
                    "medications": len(patient.get("medications", []))
                }
            })
        
        logger.info(f"Retrieved {len(patients)} patients")
        return patients
        
    except Exception as e:
        logger.error(f"Failed to list patients: {str(e)}")
        raise HTTPException(
            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
            detail=f"Failed to retrieve patients: {str(e)}"
        )

@router.get("/patients/{patient_id}", response_model=dict)
async def get_patient(patient_id: str):
    logger.info(f"Retrieving patient: {patient_id}")
    try:
        patient = await patients_collection.find_one({
            "$or": [
                {"_id": ObjectId(patient_id)},
                {"fhir_id": patient_id}
            ]
        })
        
        if not patient:
            logger.warning(f"Patient not found: {patient_id}")
            raise HTTPException(
                status_code=status.HTTP_404_NOT_FOUND,
                detail="Patient not found"
            )
        
        response = {
            "demographics": {
                "id": str(patient["_id"]),
                "fhir_id": patient.get("fhir_id"),
                "full_name": patient.get("full_name"),
                "gender": patient.get("gender"),
                "date_of_birth": patient.get("date_of_birth"),
                "age": calculate_age(patient.get("date_of_birth")),
                "address": {
                    "line": patient.get("address"),
                    "city": patient.get("city"),
                    "state": patient.get("state"),
                    "postal_code": patient.get("postal_code"),
                    "country": patient.get("country")
                },
                "marital_status": patient.get("marital_status"),
                "language": patient.get("language")
            },
            "clinical_data": {
                "notes": patient.get("notes", []),
                "conditions": patient.get("conditions", []),
                "medications": patient.get("medications", []),
                "encounters": patient.get("encounters", [])
            },
            "metadata": {
                "source": patient.get("source"),
                "import_date": patient.get("import_date"),
                "last_updated": patient.get("last_updated")
            }
        }
        
        logger.info(f"Successfully retrieved patient: {patient_id}")
        return response
        
    except ValueError as ve:
        logger.error(f"Invalid patient ID format: {patient_id}, error: {str(ve)}")
        raise HTTPException(
            status_code=status.HTTP_400_BAD_REQUEST,
            detail="Invalid patient ID format"
        )
    except Exception as e:
        logger.error(f"Failed to retrieve patient {patient_id}: {str(e)}")
        raise HTTPException(
            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
            detail=f"Failed to retrieve patient: {str(e)}"
        )

@router.post("/{patient_id}/notes", status_code=status.HTTP_201_CREATED)
async def add_note(
    patient_id: str,
    note: Note,
    current_user: dict = Depends(get_current_user)
):
    logger.info(f"Adding note for patient {patient_id} by user {current_user.get('email')}")
    if current_user.get('role') not in ['doctor', 'admin']:
        logger.warning(f"Unauthorized note addition attempt by {current_user.get('email')}")
        raise HTTPException(
            status_code=status.HTTP_403_FORBIDDEN,
            detail="Only clinicians can add notes"
        )
    
    try:
        note_data = note.dict()
        note_data.update({
            "author": current_user.get('full_name', 'System'),
            "timestamp": datetime.utcnow().isoformat()
        })
        
        result = await patients_collection.update_one(
            {"$or": [
                {"_id": ObjectId(patient_id)},
                {"fhir_id": patient_id}
            ]},
            {
                "$push": {"notes": note_data},
                "$set": {"last_updated": datetime.utcnow().isoformat()}
            }
        )
        
        if result.modified_count == 0:
            logger.warning(f"Patient not found for note addition: {patient_id}")
            raise HTTPException(
                status_code=status.HTTP_404_NOT_FOUND,
                detail="Patient not found"
            )
        
        logger.info(f"Note added successfully for patient {patient_id}")
        return {"status": "success", "message": "Note added"}
        
    except ValueError as ve:
        logger.error(f"Invalid patient ID format: {patient_id}, error: {str(ve)}")
        raise HTTPException(
            status_code=status.HTTP_400_BAD_REQUEST,
            detail="Invalid patient ID format"
        )
    except Exception as e:
        logger.error(f"Failed to add note for patient {patient_id}: {str(e)}")
        raise HTTPException(
            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
            detail=f"Failed to add note: {str(e)}"
        )

@router.put("/patients/{patient_id}", status_code=status.HTTP_200_OK)
async def update_patient(
    patient_id: str,
    update_data: PatientUpdate,
    current_user: dict = Depends(get_current_user)
):
    """Update a patient's record in the database"""
    logger.info(f"Updating patient {patient_id} by user {current_user.get('email')}")
    
    if current_user.get('role') not in ['admin', 'doctor']:
        logger.warning(f"Unauthorized update attempt by {current_user.get('email')}")
        raise HTTPException(
            status_code=status.HTTP_403_FORBIDDEN,
            detail="Only administrators and doctors can update patients"
        )
    
    try:
        # Build the query based on whether patient_id is a valid ObjectId
        query = {"fhir_id": patient_id}
        if ObjectId.is_valid(patient_id):
            query = {
                "$or": [
                    {"_id": ObjectId(patient_id)},
                    {"fhir_id": patient_id}
                ]
            }
        
        # Check if patient exists
        patient = await patients_collection.find_one(query)
        if not patient:
            logger.warning(f"Patient not found for update: {patient_id}")
            raise HTTPException(
                status_code=status.HTTP_404_NOT_FOUND,
                detail="Patient not found"
            )
        
        # Prepare update operations
        update_ops = {"$set": {"last_updated": datetime.utcnow().isoformat()}}
        
        # Handle demographic updates
        demographics = {
            "full_name": update_data.full_name,
            "gender": update_data.gender,
            "date_of_birth": update_data.date_of_birth,
            "address": update_data.address,
            "city": update_data.city,
            "state": update_data.state,
            "postal_code": update_data.postal_code,
            "country": update_data.country,
            "marital_status": update_data.marital_status,
            "language": update_data.language
        }
        for key, value in demographics.items():
            if value is not None:
                update_ops["$set"][key] = value
        
        # Handle array updates (conditions, medications, encounters, notes)
        array_fields = {
            "conditions": update_data.conditions,
            "medications": update_data.medications,
            "encounters": update_data.encounters,
            "notes": update_data.notes
        }
        
        for field, items in array_fields.items():
            if items is not None:
                # Fetch existing items
                existing_items = patient.get(field, [])
                updated_items = []
                
                for item in items:
                    item_dict = item.dict(exclude_unset=True)
                    if not item_dict:
                        continue
                    
                    # Generate ID for new items
                    if not item_dict.get("id"):
                        item_dict["id"] = str(uuid.uuid4())
                    
                    # Validate required fields
                    if field == "conditions" and not item_dict.get("code"):
                        raise HTTPException(
                            status_code=status.HTTP_400_BAD_REQUEST,
                            detail=f"Condition code is required for {field}"
                        )
                    if field == "medications" and not item_dict.get("name"):
                        raise HTTPException(
                            status_code=status.HTTP_400_BAD_REQUEST,
                            detail=f"Medication name is required for {field}"
                        )
                    if field == "encounters" and not item_dict.get("type"):
                        raise HTTPException(
                            status_code=status.HTTP_400_BAD_REQUEST,
                            detail=f"Encounter type is required for {field}"
                        )
                    if field == "notes" and not item_dict.get("content"):
                        raise HTTPException(
                            status_code=status.HTTP_400_BAD_REQUEST,
                            detail=f"Note content is required for {field}"
                        )
                    
                    updated_items.append(item_dict)
                
                # Replace the entire array
                update_ops["$set"][field] = updated_items
        
        # Perform the update
        result = await patients_collection.update_one(query, update_ops)
        
        if result.modified_count == 0 and result.matched_count == 0:
            logger.warning(f"Patient not found for update: {patient_id}")
            raise HTTPException(
                status_code=status.HTTP_404_NOT_FOUND,
                detail="Patient not found"
            )
        
        # Retrieve and return the updated patient
        updated_patient = await patients_collection.find_one(query)
        if not updated_patient:
            logger.error(f"Failed to retrieve updated patient: {patient_id}")
            raise HTTPException(
                status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
                detail="Failed to retrieve updated patient"
            )
        
        response = {
            "id": str(updated_patient["_id"]),
            "fhir_id": updated_patient.get("fhir_id"),
            "full_name": updated_patient.get("full_name"),
            "gender": updated_patient.get("gender"),
            "date_of_birth": updated_patient.get("date_of_birth"),
            "address": updated_patient.get("address"),
            "city": updated_patient.get("city"),
            "state": updated_patient.get("state"),
            "postal_code": updated_patient.get("postal_code"),
            "country": updated_patient.get("country"),
            "marital_status": updated_patient.get("marital_status"),
            "language": updated_patient.get("language"),
            "conditions": updated_patient.get("conditions", []),
            "medications": updated_patient.get("medications", []),
            "encounters": updated_patient.get("encounters", []),
            "notes": updated_patient.get("notes", []),
            "source": updated_patient.get("source"),
            "import_date": updated_patient.get("import_date"),
            "last_updated": updated_patient.get("last_updated")
        }
        
        logger.info(f"Successfully updated patient {patient_id}")
        return response
        
    except ValueError as ve:
        logger.error(f"Invalid patient ID format: {patient_id}, error: {str(ve)}")
        raise HTTPException(
            status_code=status.HTTP_400_BAD_REQUEST,
            detail="Invalid patient ID format"
        )
    except HTTPException:
        raise
    except Exception as e:
        logger.error(f"Failed to update patient {patient_id}: {str(e)}")
        raise HTTPException(
            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
            detail=f"Failed to update patient: {str(e)}"
        )

# Export the router as 'patients' for api.__init__.py
patients = router