Initial commit

skills/phenoml-workflow/scripts/setup_fhir_provider.py

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+#!/usr/bin/env python3
+"""
+FHIR Provider Setup Script
+
+Creates a FHIR provider using credentials from .env or CLI arguments.
+
+Usage:
+  python3 setup_fhir_provider.py
+  python3 setup_fhir_provider.py --name "My FHIR Server" --provider medplum
+  python3 setup_fhir_provider.py --help
+
+Required .env variables:
+  PHENOML_USERNAME, PHENOML_PASSWORD, PHENOML_BASE_URL
+  FHIR_PROVIDER_BASE_URL, FHIR_PROVIDER_CLIENT_ID, FHIR_PROVIDER_CLIENT_SECRET
+
+Example FHIR_PROVIDER_BASE_URL values:
+  - Medplum: https://api.medplum.com/fhir/R4
+  - Athena: https://api.preview.platform.athenahealth.com/fhir/r4
+  - Epic: https://fhir.epic.com/interconnect-fhir-oauth/api/FHIR/R4
+  - Cerner: https://fhir-myrecord.cerner.com/r4/[tenant-id]
+
+Optional .env variables:
+  FHIR_PROVIDER_NAME (default: "FHIR Server")
+  FHIR_PROVIDER_TYPE (default: "medplum")
+  FHIR_AUTH_METHOD (default: "client_secret")
+"""
+
+import os
+import sys
+import argparse
+from phenoml import Client
+from dotenv import load_dotenv
+
+def save_to_env(key, value):
+    """Save or update a key-value pair in .env file"""
+    env_file = ".env"
+
+    if not os.path.exists(env_file):
+        with open(env_file, 'w') as f:
+            f.write(f"{key}={value}\n")
+        return
+
+    with open(env_file, 'r') as f:
+        lines = f.readlines()
+
+    found = False
+    for i, line in enumerate(lines):
+        if line.startswith(f"{key}="):
+            lines[i] = f"{key}={value}\n"
+            found = True
+            break
+
+    if not found:
+        if lines and not lines[-1].endswith('\n'):
+            lines.append('\n')
+        lines.append(f"{key}={value}\n")
+
+    with open(env_file, 'w') as f:
+        f.writelines(lines)
+
+def main():
+    parser = argparse.ArgumentParser(description='Create a FHIR provider for PhenoML workflows')
+    parser.add_argument('--name', help='FHIR provider name')
+    parser.add_argument('--provider', help='Provider type (medplum, epic, cerner, etc.)')
+    parser.add_argument('--auth-method', help='Auth method (default: client_secret)')
+    parser.add_argument('--base-url', help='FHIR base URL')
+    parser.add_argument('--client-id', help='Client ID')
+    parser.add_argument('--client-secret', help='Client secret')
+
+    args = parser.parse_args()
+
+    # Load environment
+    load_dotenv()
+
+    # Get configuration (CLI args override .env)
+    name = args.name or os.getenv("FHIR_PROVIDER_NAME", "FHIR Server")
+    provider_type = args.provider or os.getenv("FHIR_PROVIDER_TYPE", "medplum")
+    auth_method = args.auth_method or os.getenv("FHIR_AUTH_METHOD", "client_secret")
+
+    # Get FHIR provider credentials (CLI args override .env)
+    base_url = args.base_url or os.getenv("FHIR_PROVIDER_BASE_URL")
+    client_id = args.client_id or os.getenv("FHIR_PROVIDER_CLIENT_ID")
+    client_secret = args.client_secret or os.getenv("FHIR_PROVIDER_CLIENT_SECRET")
+
+    # Validate required fields
+    if not base_url:
+        print("❌ Error: FHIR base URL is required")
+        print("   Set FHIR_PROVIDER_BASE_URL in .env, or use --base-url")
+        print("\n   Example values:")
+        print("   - Medplum: https://api.medplum.com/fhir/R4")
+        print("   - Athena: https://api.preview.platform.athenahealth.com/fhir/r4")
+        print("   - Epic: https://fhir.epic.com/interconnect-fhir-oauth/api/FHIR/R4")
+        print("   - Cerner: https://fhir-myrecord.cerner.com/r4/[tenant-id]")
+        sys.exit(1)
+
+    if not client_id:
+        print("❌ Error: Client ID is required")
+        print("   Set FHIR_PROVIDER_CLIENT_ID in .env, or use --client-id")
+        sys.exit(1)
+
+    if not client_secret:
+        print("❌ Error: Client secret is required")
+        print("   Set FHIR_PROVIDER_CLIENT_SECRET in .env, or use --client-secret")
+        sys.exit(1)
+
+    # Initialize PhenoML client
+    print("Initializing PhenoML client...")
+    try:
+        client = Client(
+            username=os.getenv("PHENOML_USERNAME"),
+            password=os.getenv("PHENOML_PASSWORD"),
+            base_url=os.getenv("PHENOML_BASE_URL")
+        )
+        print("✅ PhenoML client initialized\n")
+    except Exception as e:
+        print(f"❌ Failed to initialize PhenoML client: {e}")
+        print("   Make sure PHENOML_USERNAME, PHENOML_PASSWORD, and PHENOML_BASE_URL are set in .env")
+        sys.exit(1)
+
+    # Create FHIR provider
+    print(f"Creating FHIR provider:")
+    print(f"  Name: {name}")
+    print(f"  Provider: {provider_type}")
+    print(f"  Base URL: {base_url}")
+    print(f"  Auth method: {auth_method}\n")
+
+    try:
+        fhir_provider = client.fhir_provider.create(
+            name=name,
+            provider=provider_type,
+            auth_method=auth_method,
+            base_url=base_url,
+            client_id=client_id,
+            client_secret=client_secret
+        )
+
+        provider_id = fhir_provider.data.id
+        print(f"✅ FHIR provider created successfully!")
+        print(f"   Provider ID: {provider_id}\n")
+
+        # Save to .env
+        save_to_env("FHIR_PROVIDER_ID", provider_id)
+        print(f"💾 Provider ID saved to .env")
+        print(f"\n🎉 Setup complete! You can now create workflows using this provider.")
+
+    except Exception as e:
+        print(f"❌ Failed to create FHIR provider: {e}")
+        import traceback
+        traceback.print_exc()
+        sys.exit(1)
+
+if __name__ == "__main__":
+    main()