Update api/routes/patients.py

api/routes/patients.py

@@ -1,439 +1,135 @@
 from fastapi import APIRouter, HTTPException, Depends, Query, status
 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
+from utils.helpers import calculate_age
+from models.entities import PatientCreate, Note
 from datetime import datetime
 from bson import ObjectId
 from bson.errors import InvalidId
-from typing import Optional, List, Dict
-from pymongo import UpdateOne
-from pymongo.errors import BulkWriteError
-import json
-from pathlib import Path
-import glob
+from typing import Optional, List
 import uuid
-import re
 import logging
-import time
-import os
 
-# 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)
-
-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),
+@router.post("/", status_code=status.HTTP_201_CREATED)
+async def create_patient(
+    patient_data: PatientCreate,
     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()
-    
+    """Create a new patient"""
     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"
+            detail="Only admins and doctors can create patients"
         )
-    
+
     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
+        patient = patient_data.dict()
+        now = datetime.utcnow().isoformat()
+        
+        patient.update({
+            "fhir_id": str(uuid.uuid4()),
+            "import_date": now,
+            "last_updated": now,
+            "source": "manual",
+            "created_by": current_user.get('email')
+        })
+
+        result = await patients_collection.insert_one(patient)
+        created = await patients_collection.find_one({"_id": result.inserted_id})
         
-        response = {
-            "status": "success",
-            "imported": imported,
-            "errors": errors,
-            "request_id": request_id,
-            "duration_seconds": time.time() - start_time
+        return {
+            "id": str(created["_id"]),
+            **{k: v for k, v in created.items() if k != "_id"}
         }
-        
-        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)
+        logger.error(f"Create patient error: {str(e)}")
         raise HTTPException(
             status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
-            detail=f"Import failed: {str(e)}"
+            detail="Failed to create patient"
         )
 
-@router.get("/patients", response_model=List[dict])
+@router.get("/", 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)
+    search: Optional[str] = None,
+    skip: int = 0,
+    limit: int = 100,
+    current_user: dict = Depends(get_current_user)
 ):
-    logger.info(f"Listing patients with search: {search}, limit: {limit}, skip: {skip}")
-    query = {"source": "synthea"}
-    
-    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}
-    
-    # Removed $slice to return full arrays for the frontend
-    projection = {
-        "fhir_id": 1,
-        "full_name": 1,
-        "gender": 1,
-        "date_of_birth": 1,
-        "city": 1,
-        "state": 1,
-        "conditions": 1,
-        "medications": 1,
-        "encounters": 1,
-        "notes": 1
-    }
-    
+    """List patients with pagination and search"""
     try:
-        cursor = patients_collection.find(query, projection).skip(skip).limit(limit)
+        query = {}
+        if search:
+            query["$or"] = [
+                {"full_name": {"$regex": search, "$options": "i"}},
+                {"fhir_id": search}
+            ]
+
+        cursor = patients_collection.find(query).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", []),
-                "age": calculate_age(patient.get("date_of_birth")),
-                "stats": {
-                    "notes": len(patient.get("notes", [])),
-                    "conditions": len(patient.get("conditions", [])),
-                    "medications": len(patient.get("medications", []))
-                }
-            })
+        async for doc in cursor:
+            doc["id"] = str(doc["_id"])
+            doc["age"] = calculate_age(doc.get("date_of_birth"))
+            patients.append(doc)
         
-        logger.info(f"Retrieved {len(patients)} patients")
         return patients
-        
+
     except Exception as e:
-        logger.error(f"Failed to list patients: {str(e)}")
+        logger.error(f"List patients error: {str(e)}")
         raise HTTPException(
             status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
-            detail=f"Failed to retrieve patients: {str(e)}"
+            detail="Failed to fetch patients"
         )
 
-@router.get("/patients/{patient_id}", response_model=dict)
-async def get_patient(patient_id: str):
-    logger.info(f"Retrieving patient: {patient_id}")
+@router.get("/{patient_id}", response_model=dict)
+async def get_patient(
+    patient_id: str,
+    current_user: dict = Depends(get_current_user)
+):
+    """Get patient by ID or FHIR ID"""
     try:
-        patient = await patients_collection.find_one({
-            "$or": [
-                {"_id": ObjectId(patient_id)},
-                {"fhir_id": patient_id}
-            ]
-        })
-        
+        # Try as ObjectId first
+        try:
+            patient = await patients_collection.find_one({"_id": ObjectId(patient_id)})
+        except (InvalidId, ValueError):
+            # Fall back to FHIR ID
+            patient = await patients_collection.find_one({"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"
-        )
+            raise HTTPException(status_code=404, detail="Patient not found")
+
+        patient["id"] = str(patient["_id"])
+        patient["age"] = calculate_age(patient.get("date_of_birth"))
+        return patient
+
     except Exception as e:
-        logger.error(f"Failed to retrieve patient {patient_id}: {str(e)}")
+        logger.error(f"Get patient error: {str(e)}")
         raise HTTPException(
             status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
-            detail=f"Failed to retrieve patient: {str(e)}"
+            detail="Failed to fetch patient"
         )
 
-@router.post("/patients/{patient_id}/notes", status_code=status.HTTP_201_CREATED)
-async def add_note(
+@router.post("/{patient_id}/notes", status_code=status.HTTP_201_CREATED)
+async def add_patient_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')}")
+    """Add a note to patient record"""
     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"
-        )
-    
+        raise HTTPException(status_code=403, detail="Only clinicians can add notes")
+
     try:
         note_data = note.dict()
         note_data.update({
-            "author": current_user.get('full_name', 'System'),
+            "author": current_user.get('email'),
             "timestamp": datetime.utcnow().isoformat()
         })
-        
+
         result = await patients_collection.update_one(
             {"$or": [
                 {"_id": ObjectId(patient_id)},
@@ -444,29 +140,17 @@ async def add_note(
                 "$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"
-        )
+            raise HTTPException(status_code=404, detail="Patient not found")
+
+        return {"status": "success"}
+
     except Exception as e:
-        logger.error(f"Failed to add note for patient {patient_id}: {str(e)}")
+        logger.error(f"Add note error: {str(e)}")
         raise HTTPException(
             status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
-            detail=f"Failed to add note: {str(e)}"
+            detail="Failed to add note"
         )
 
-# Export the router as 'patients' for api.__init__.py
 patients = router