summary markdown

ai_med_extract/api/routes.py

@@ -1202,7 +1202,8 @@ def register_routes(app, agents):
                         from ai_med_extract.utils.model_loader_gguf import create_fallback_pipeline
                         fallback_pipeline = create_fallback_pipeline()
                         fallback_summary = fallback_pipeline.generate_full_summary(prompt)
-                        markdown_summary = summary_to_markdown(fallback_summary)
+                        markdown_summary =fallback_summary
+                        # summary_to_markdown(fallback_summary)
                         return jsonify({
                             "summary": markdown_summary,
                             "baseline": baseline,
@@ -1236,7 +1237,8 @@ def register_routes(app, agents):
             text = pipeline.tokenizer.decode(outputs[0], skip_special_tokens=True)
             new_summary = text.split("Now generate the complete, updated clinical summary with all four sections in a markdown format:")[-1].strip()
             # For other models, after extracting new_summary:
-            markdown_summary = summary_to_markdown(new_summary)
+            markdown_summary = new_summary
+            # summary_to_markdown(new_summary)
             # Remove undefined timing variables and only log steps that are actually measured
             total_time = time.time() - start_total
             print(f"[TIMING] API call: {t_api_end-t_api_start:.2f}s, TOTAL: {total_time:.2f}s")

ai_med_extract/utils/openvino_summarizer_utils.py

@@ -143,7 +143,7 @@ def build_main_prompt(baseline, delta_text):
         "4) Direct Guidance for Physician - Specific recommendations for the treating physician\n\n"
         f"STRUCTURED BASELINE (current status):\n{baseline}\n\n"
         f"STRUCTURED DELTAS (changes from previous visits):\n{delta_text}\n\n"
-        "Now generate the complete clinical summary with all four sections in markdown format, paying special attention to detailed trend analysis in the Key Trends & Changes section:"
+        "Now generate the complete clinical summary with all four sections in markdown format:"
     )
 def validate_and_compare_summaries(old_summary, new_summary, update_name=""):
     report = f"### Validation Report for {update_name}\n"

test_summary_function.py

@@ -0,0 +1,118 @@
+#!/usr/bin/env python3
+"""
+Test script to verify the summary_to_markdown function works correctly
+with the 4-section structure validation.
+"""
+
+import sys
+import os
+
+# Add the current directory to Python path
+sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
+
+from ai_med_extract.api.routes import summary_to_markdown
+
+def test_summary_to_markdown():
+    """Test the summary_to_markdown function with various inputs"""
+    
+    # Test case 1: Summary with proper 4-section structure
+    test_summary_1 = """1. Clinical Assessment
+Patient presents with hypertension and diabetes. Blood pressure is elevated at 150/95 mmHg.
+
+2. Key Trends and Changes
+Blood pressure has increased from previous reading of 140/90 mmHg. Blood sugar levels remain stable.
+
+3. Plan and Suggested Actions
+Increase dosage of antihypertensive medication. Monitor blood pressure daily.
+
+4. Direct Guidance for Physician
+Consider adding ACE inhibitor if current regimen is insufficient."""
+
+    print("Test 1: Proper 4-section structure")
+    result_1 = summary_to_markdown(test_summary_1)
+    print("Input:")
+    print(test_summary_1)
+    print("\nOutput:")
+    print(result_1)
+    print("-" * 80)
+    
+    # Test case 2: Summary with numbered sections but different content
+    test_summary_2 = """1. Patient Information
+John Doe, 45 years old, male
+
+2. Vital Signs
+BP: 150/95, HR: 78, Temp: 98.6°F
+
+3. Laboratory Results
+HbA1c: 6.8%, Cholesterol: 210 mg/dL
+
+4. Medications
+Lisinopril 10mg daily, Metformin 500mg twice daily"""
+
+    print("Test 2: Different section content")
+    result_2 = summary_to_markdown(test_summary_2)
+    print("Input:")
+    print(test_summary_2)
+    print("\nOutput:")
+    print(result_2)
+    print("-" * 80)
+    
+    # Test case 3: Summary with markdown headers already
+    test_summary_3 = """# Clinical Assessment
+Patient presents with hypertension
+
+## Key Trends and Changes
+BP increased from previous visit
+
+## Plan and Suggested Actions
+Adjust medication dosage
+
+## Direct Guidance for Physician
+Monitor patient closely"""
+
+    print("Test 3: Already in markdown format")
+    result_3 = summary_to_markdown(test_summary_3)
+    print("Input:")
+    print(test_summary_3)
+    print("\nOutput:")
+    print(result_3)
+    print("-" * 80)
+    
+    # Test case 4: Summary with answer artifacts
+    test_summary_4 = """1. Clinical Assessment
+- answer: Patient presents with hypertension
+
+2. Key Trends and Changes
+- answer: BP increased from previous visit
+
+3. Plan and Suggested Actions
+- answer: Adjust medication dosage
+
+4. Direct Guidance for Physician
+- answer: Monitor patient closely"""
+
+    print("Test 4: Summary with answer artifacts")
+    result_4 = summary_to_markdown(test_summary_4)
+    print("Input:")
+    print(test_summary_4)
+    print("\nOutput:")
+    print(result_4)
+    print("-" * 80)
+    
+    # Test case 5: Incomplete summary (only 2 sections)
+    test_summary_5 = """1. Clinical Assessment
+Patient presents with hypertension
+
+2. Key Trends and Changes
+BP increased from previous visit"""
+
+    print("Test 5: Incomplete summary (2 sections)")
+    result_5 = summary_to_markdown(test_summary_5)
+    print("Input:")
+    print(test_summary_5)
+    print("\nOutput:")
+    print(result_5)
+    print("-" * 80)
+
+if __name__ == "__main__":
+    test_summary_to_markdown()