Upd gitignore

.dockerignore

@@ -4,3 +4,4 @@
 .venv
 __pycache__
 *.pyc
+key

.gitignore

@@ -9,4 +9,5 @@
 **/.env
 **.DS_STORE
 
-review_vi.txt
+review_vi.txt
+key

src/emr/repositories/emr.py

@@ -24,8 +24,12 @@ def create():
         collection.create_index("patient_id")
         collection.create_index("doctor_id")
         collection.create_index("session_id")
+        collection.create_index("message_id")
         collection.create_index("created_at")
         collection.create_index([("patient_id", ASCENDING), ("created_at", DESCENDING)])
+        collection.create_index([("patient_id", ASCENDING), ("doctor_id", ASCENDING)])
+        collection.create_index([("session_id", ASCENDING), ("created_at", DESCENDING)])
+        collection.create_index("confidence_score")
         logger().info("EMR collection created successfully with indexes")
     except Exception as e:
         logger().error(f"Error creating EMR collection: {e}")
@@ -36,6 +40,13 @@ def create_emr_entry(emr_data: EMRCreateRequest, embeddings: List[float]) -> str
     """Create a new EMR entry in the database."""
     try:
         collection = get_collection(EMR_COLLECTION)
+        
+        # Check if EMR entry already exists for this message
+        existing = collection.find_one({"message_id": emr_data.message_id})
+        if existing:
+            logger().warning(f"EMR entry already exists for message {emr_data.message_id}")
+            return str(existing["_id"])
+        
         now = datetime.now(timezone.utc)
         
         doc = {
@@ -223,6 +234,17 @@ def delete_emr_entry(emr_id: str) -> bool:
         return False
 
 
+def check_emr_exists(message_id: str) -> bool:
+    """Check if an EMR entry already exists for a message."""
+    try:
+        collection = get_collection(EMR_COLLECTION)
+        existing = collection.find_one({"message_id": message_id})
+        return existing is not None
+    except Exception as e:
+        logger().error(f"Error checking EMR existence: {e}")
+        return False
+
+
 def get_emr_statistics(patient_id: str) -> Dict[str, Any]:
     """Get EMR statistics for a patient."""
     try:

src/emr/routes/emr.py

@@ -1,5 +1,6 @@
 # emr/routes/emr.py
 
+from datetime import datetime, timezone
 from typing import List, Optional
 
 from fastapi import APIRouter, HTTPException, Depends
@@ -12,6 +13,44 @@ from src.utils.logger import logger
 router = APIRouter(prefix="/emr", tags=["EMR"])
 
 
+@router.get("/check/{message_id}", response_model=dict)
+async def check_emr_exists(message_id: str):
+    """Check if EMR extraction has already been done for a message."""
+    try:
+        from src.emr.repositories.emr import check_emr_exists
+        exists = check_emr_exists(message_id)
+        return {
+            "message_id": message_id,
+            "emr_exists": exists
+        }
+    except Exception as e:
+        logger().error(f"Error checking EMR existence: {e}")
+        raise HTTPException(status_code=500, detail=str(e))
+
+
+@router.get("/health", response_model=dict)
+async def emr_health_check():
+    """Health check endpoint for EMR service."""
+    try:
+        from src.data.connection import get_collection
+        collection = get_collection("emr")
+        # Try to count documents to verify collection exists and is accessible
+        count = collection.count_documents({})
+        return {
+            "status": "healthy",
+            "collection": "emr",
+            "document_count": count,
+            "timestamp": datetime.now(timezone.utc).isoformat()
+        }
+    except Exception as e:
+        logger().error(f"EMR health check failed: {e}")
+        return {
+            "status": "unhealthy",
+            "error": str(e),
+            "timestamp": datetime.now(timezone.utc).isoformat()
+        }
+
+
 def get_emr_service(state: MedicalState = Depends(get_state)) -> EMRService:
     """Get EMR service instance."""
     return EMRService(state.gemini_rotator, state.embedding_client)
@@ -28,6 +67,18 @@ async def extract_emr_from_message(
 ):
     """Extract and store EMR data from a chat message."""
     try:
+        # Input validation
+        if not patient_id or not patient_id.strip():
+            raise HTTPException(status_code=400, detail="Patient ID is required")
+        if not doctor_id or not doctor_id.strip():
+            raise HTTPException(status_code=400, detail="Doctor ID is required")
+        if not message_id or not message_id.strip():
+            raise HTTPException(status_code=400, detail="Message ID is required")
+        if not session_id or not session_id.strip():
+            raise HTTPException(status_code=400, detail="Session ID is required")
+        if not message or not message.strip():
+            raise HTTPException(status_code=400, detail="Message content is required")
+        
         logger().info(f"EMR extraction requested for patient {patient_id}, message {message_id}")
         
         # Get patient context if available
@@ -192,3 +243,84 @@ async def get_emr_statistics(
     except Exception as e:
         logger().error(f"Error getting EMR statistics: {e}")
         raise HTTPException(status_code=500, detail=str(e))
+
+
+@router.post("/bulk-extract", response_model=dict)
+async def bulk_extract_emr(
+    extractions: List[dict],
+    emr_service: EMRService = Depends(get_emr_service)
+):
+    """Extract EMR data from multiple messages in bulk."""
+    try:
+        if not extractions or len(extractions) == 0:
+            raise HTTPException(status_code=400, detail="No extractions provided")
+        
+        if len(extractions) > 10:
+            raise HTTPException(status_code=400, detail="Maximum 10 extractions allowed per request")
+        
+        logger().info(f"Bulk EMR extraction requested for {len(extractions)} messages")
+        
+        results = []
+        errors = []
+        
+        for i, extraction in enumerate(extractions):
+            try:
+                # Validate required fields
+                required_fields = ['patient_id', 'doctor_id', 'message_id', 'session_id', 'message']
+                for field in required_fields:
+                    if field not in extraction or not extraction[field]:
+                        raise ValueError(f"Missing or empty {field}")
+                
+                # Get patient context
+                patient_context = None
+                try:
+                    from src.data.repositories.patient import get_patient_by_id
+                    patient = get_patient_by_id(extraction['patient_id'])
+                    if patient:
+                        patient_context = {
+                            "name": patient.get("name"),
+                            "age": patient.get("age"),
+                            "sex": patient.get("sex"),
+                            "medications": patient.get("medications", []),
+                            "past_assessment_summary": patient.get("past_assessment_summary")
+                        }
+                except Exception as e:
+                    logger().warning(f"Could not fetch patient context for extraction {i}: {e}")
+                
+                # Extract and store EMR data
+                emr_id = await emr_service.extract_and_store_emr(
+                    patient_id=extraction['patient_id'],
+                    doctor_id=extraction['doctor_id'],
+                    message_id=extraction['message_id'],
+                    session_id=extraction['session_id'],
+                    message=extraction['message'],
+                    patient_context=patient_context
+                )
+                
+                results.append({
+                    "index": i,
+                    "message_id": extraction['message_id'],
+                    "emr_id": emr_id,
+                    "status": "success"
+                })
+                
+            except Exception as e:
+                logger().error(f"Error in bulk extraction {i}: {e}")
+                errors.append({
+                    "index": i,
+                    "message_id": extraction.get('message_id', 'unknown'),
+                    "error": str(e),
+                    "status": "failed"
+                })
+        
+        return {
+            "message": f"Bulk extraction completed. {len(results)} successful, {len(errors)} failed.",
+            "results": results,
+            "errors": errors
+        }
+        
+    except HTTPException:
+        raise
+    except Exception as e:
+        logger().error(f"Error in bulk EMR extraction: {e}")
+        raise HTTPException(status_code=500, detail=str(e))

src/main.py

@@ -86,7 +86,7 @@ def startup_event(state: MedicalState):
 	#session_repo.create()
 	#message_repo.create()
 	#medical_repo.create()
-	#emr_repo.create()
+	emr_repo.create()
 
 def shutdown_event():
 	"""Cleanup on shutdown"""

static/js/app.js

@@ -1816,7 +1816,7 @@ How can I assist you today?`;
         // Add EMR icon for assistant messages (system-generated)
         const emrIcon = message.role === 'assistant' ? 
             `<div class="message-actions">
-                <button class="emr-extract-btn" onclick="app.extractEMR('${message.id}')" title="Extract to EMR">
+                <button class="emr-extract-btn" onclick="app.extractEMR('${message.id}')" title="Extract to EMR" data-message-id="${message.id}">
                     <i class="fas fa-file-medical"></i>
                 </button>
             </div>` : '';
@@ -1831,6 +1831,11 @@ How can I assist you today?`;
         chatMessages.appendChild(messageElement);
         chatMessages.scrollTop = chatMessages.scrollHeight;
         if (this.currentSession) this.currentSession.lastActivity = new Date().toISOString();
+        
+        // Check EMR status for assistant messages
+        if (message.role === 'assistant' && this.currentPatientId) {
+            this.checkEMRStatus(message.id);
+        }
     }
 
     formatMessageContent(content) {
@@ -1925,7 +1930,9 @@ How can I assist you today?`;
                 // Show notification
                 this.showNotification('EMR data extracted successfully!', 'success');
             } else {
-                throw new Error(`HTTP ${response.status}: ${response.statusText}`);
+                const errorData = await response.json().catch(() => ({ detail: 'Unknown error' }));
+                const errorMessage = errorData.detail || `HTTP ${response.status}: ${response.statusText}`;
+                throw new Error(errorMessage);
             }
 
         } catch (error) {
@@ -1943,6 +1950,24 @@ How can I assist you today?`;
         }
     }
 
+    async checkEMRStatus(messageId) {
+        try {
+            const response = await fetch(`/emr/check/${messageId}`);
+            if (response.ok) {
+                const result = await response.json();
+                const button = document.querySelector(`[data-message-id="${messageId}"]`);
+                if (button && result.emr_exists) {
+                    button.innerHTML = '<i class="fas fa-check"></i>';
+                    button.style.color = 'var(--success-color)';
+                    button.title = 'EMR data already extracted';
+                    button.disabled = true;
+                }
+            }
+        } catch (error) {
+            console.warn('Could not check EMR status:', error);
+        }
+    }
+
     showNotification(message, type = 'info') {
         // Create notification element
         const notification = document.createElement('div');

static/js/emr.js

@@ -9,7 +9,7 @@ class EMRPage {
         this.filteredEntries = [];
         this.currentPage = 1;
         this.entriesPerPage = 20;
-        
+
         this.init();
     }
 
@@ -182,7 +182,7 @@ class EMRPage {
         if (!this.currentPatientId) return;
 
         this.showLoading(true);
-        
+
         try {
             const response = await fetch(`/emr/patient/${this.currentPatientId}?limit=100`);
             if (response.ok) {
@@ -195,7 +195,7 @@ class EMRPage {
             }
         } catch (error) {
             console.error('Error loading EMR data:', error);
-            this.showEmptyState();
+            this.showErrorState('Failed to load EMR data. Please try again.');
         } finally {
             this.showLoading(false);
         }
@@ -232,7 +232,7 @@ class EMRPage {
                             </button>
                             <button class="action-btn danger" onclick="emrPage.deleteEMREntry('${entry.emr_id}')" title="Delete">
                                 <i class="fas fa-trash"></i>
-                            </button>
+                </button>
                         </div>
                     </td>
                 </tr>
@@ -480,7 +480,7 @@ class EMRPage {
         }
 
         this.showLoading(true);
-        
+
         try {
             let searchResults = [];
             
@@ -507,7 +507,7 @@ class EMRPage {
                 if (semanticQuery) {
                     const exactIds = new Set(exactResults.map(r => r.emr_id));
                     searchResults = searchResults.concat(exactResults.filter(r => !exactIds.has(r.emr_id)));
-                } else {
+            } else {
                     searchResults = exactResults;
                 }
             }
@@ -543,6 +543,19 @@ class EMRPage {
         emptyState.style.display = 'block';
         tableContainer.style.display = 'none';
     }
+
+    showErrorState(message) {
+        const emptyState = document.getElementById('emptyState');
+        const tableContainer = document.querySelector('.emr-table-container');
+        
+        // Update the empty state to show error message
+        emptyState.querySelector('h3').textContent = 'Error Loading EMR Data';
+        emptyState.querySelector('p').textContent = message;
+        emptyState.querySelector('.btn').style.display = 'none';
+        
+        emptyState.style.display = 'block';
+        tableContainer.style.display = 'none';
+    }
 }
 
 // Initialize the EMR page when DOM is loaded