Fixed patient generation with separate script approach

module_generator/anthropic_patch.py

@@ -0,0 +1,23 @@
+"""
+Patch for Anthropic client to fix 'proxies' parameter issue
+Place this file in the same directory as module_generator.py
+"""
+import anthropic
+import inspect
+
+# Store the original __init__ method
+original_init = anthropic.Client.__init__
+
+# Define a new __init__ method that filters out problematic parameters
+def patched_init(self, *args, **kwargs):
+    # Remove 'proxies' from kwargs if present
+    if 'proxies' in kwargs:
+        del kwargs['proxies']
+    
+    # Call the original __init__ with filtered kwargs
+    original_init(self, *args, **kwargs)
+
+# Replace the original __init__ with our patched version
+anthropic.Client.__init__ = patched_init
+
+print("Applied patch to fix Anthropic client proxies parameter issue")

module_generator/simple_module_generator.py

@@ -0,0 +1,122 @@
+#!/usr/bin/env python3
+"""
+Simple Module Generator for Synthea Nextflow Pipeline
+Using Direct HTTP Requests to avoid client library issues
+"""
+
+import os
+import json
+import argparse
+import requests
+from dotenv import load_dotenv
+
+def generate_module(disease_name, output_file):
+    """Generate a Synthea module for the specified disease"""
+    # Load API key from environment
+    load_dotenv()
+    api_key = os.getenv("ANTHROPIC_API_KEY")
+    
+    if not api_key:
+        raise ValueError("ANTHROPIC_API_KEY environment variable not set")
+    
+    print(f"Generating module for {disease_name}...")
+    
+    # Current Anthropic API endpoint and format (as of 2024)
+    url = "https://api.anthropic.com/v1/messages"
+    
+    headers = {
+        "Content-Type": "application/json",
+        "x-api-key": api_key,
+        "anthropic-version": "2023-06-01"
+    }
+    
+    system_prompt = """
+    You are an expert in medical informatics and Synthea module creation. 
+    Generate a complete, valid JSON module for the specified disease.
+    The module must follow Synthea's format conventions.
+    """
+    
+    user_prompt = f"""
+    Create a complete Synthea module for {disease_name}.
+    
+    The module should include:
+    - Initial states for disease onset and progression
+    - Diagnostic procedures and criteria
+    - Treatment options and medication regimens
+    - Complications and their management
+    - Follow-up care protocols
+    
+    Return ONLY valid JSON that can be directly used in Synthea without any explanation or markdown.
+    """
+    
+    data = {
+        "model": "claude-3-opus-20240229",
+        "system": system_prompt,
+        "messages": [
+            {
+                "role": "user",
+                "content": user_prompt
+            }
+        ],
+        "max_tokens": 4000,
+        "temperature": 0.2
+    }
+    
+    try:
+        # Make direct API request
+        response = requests.post(url, headers=headers, json=data)
+        
+        # Check for errors
+        if response.status_code != 200:
+            print(f"API request failed with status code {response.status_code}: {response.text}")
+            raise Exception(f"API request failed with status code {response.status_code}")
+        
+        # Parse response
+        result = response.json()
+        module_content = result["content"][0]["text"]
+        
+        # Extract the JSON part if wrapped in markdown
+        if "```json" in module_content:
+            module_content = module_content.split("```json")[1].split("```")[0].strip()
+        elif "```" in module_content:
+            module_content = module_content.split("```")[1].split("```")[0].strip()
+            
+        # Validate JSON
+        try:
+            module_json = json.loads(module_content)
+            with open(output_file, 'w') as f:
+                json.dump(module_json, f, indent=2)
+            print(f"Successfully generated module and saved to {output_file}")
+            return True
+        except json.JSONDecodeError as e:
+            print(f"Generated content is not valid JSON: {e}")
+            with open(f"{output_file}.raw", 'w') as f:
+                f.write(module_content)
+            print(f"Raw content saved to {output_file}.raw")
+            return False
+            
+    except Exception as e:
+        print(f"Error generating module: {e}")
+        if isinstance(e, requests.exceptions.RequestException):
+            print(f"Request error details: {e.response.text if hasattr(e, 'response') else 'No response details'}")
+        return False
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description='Generate Synthea disease module')
+    parser.add_argument('--disease', required=True, help='Disease name to generate module for')
+    parser.add_argument('--output', required=True, help='Output filename for the module')
+    
+    args = parser.parse_args()
+    
+    # Install required packages if needed
+    try:
+        import requests
+    except ImportError:
+        import subprocess
+        print("Installing required packages...")
+        subprocess.check_call(["pip", "install", "requests"])
+        
+    success = generate_module(args.disease, args.output)
+    
+    if not success:
+        exit(1)