Initial commit

skills/phenoml-workflow/scripts/check_env.py

@@ -0,0 +1,139 @@
+#!/usr/bin/env python3
+"""
+Environment Variables Checker
+
+Safely checks which environment variables are set without exposing their values.
+This prevents accidental credential leakage in LLM conversations.
+
+Usage:
+  python3 check_env.py
+  python3 check_env.py --help
+
+Security: This script only reports presence (true/false), never actual values.
+"""
+
+import os
+import sys
+import json
+import argparse
+from dotenv import load_dotenv
+
+def check_env_vars():
+    """Check presence of required environment variables without exposing values"""
+    load_dotenv()
+
+    # Core credentials (always required)
+    core_vars = {
+        "PHENOML_USERNAME": bool(os.getenv("PHENOML_USERNAME")),
+        "PHENOML_PASSWORD": bool(os.getenv("PHENOML_PASSWORD")),
+        "PHENOML_BASE_URL": bool(os.getenv("PHENOML_BASE_URL"))
+    }
+
+    # FHIR provider credentials (required for setup)
+    fhir_credentials = {
+        "FHIR_PROVIDER_BASE_URL": bool(os.getenv("FHIR_PROVIDER_BASE_URL")),
+        "FHIR_PROVIDER_CLIENT_ID": bool(os.getenv("FHIR_PROVIDER_CLIENT_ID")),
+        "FHIR_PROVIDER_CLIENT_SECRET": bool(os.getenv("FHIR_PROVIDER_CLIENT_SECRET"))
+    }
+
+    # Generated IDs (created by scripts)
+    generated_ids = {
+        "FHIR_PROVIDER_ID": bool(os.getenv("FHIR_PROVIDER_ID")),
+        "WORKFLOW_ID": bool(os.getenv("WORKFLOW_ID"))
+    }
+
+    return {
+        "core_credentials": core_vars,
+        "fhir_credentials": fhir_credentials,
+        "generated_ids": generated_ids
+    }
+
+def print_status(status, verbose=False):
+    """Print status in a user-friendly format"""
+
+    def check_mark(present):
+        return "✅" if present else "❌"
+
+    print("\n" + "=" * 60)
+    print("ENVIRONMENT VARIABLES STATUS")
+    print("=" * 60 + "\n")
+
+    # Core credentials
+    print("Core PhenoML Credentials:")
+    for key, present in status["core_credentials"].items():
+        print(f"  {check_mark(present)} {key}")
+
+    core_ready = all(status["core_credentials"].values())
+    if not core_ready:
+        print("\n⚠️  Missing core credentials. Add them to .env file:")
+        print("   PHENOML_USERNAME=your_username")
+        print("   PHENOML_PASSWORD=your_password")
+        print("   PHENOML_BASE_URL=your_base_url")
+
+    # FHIR credentials
+    print("\nFHIR Provider Credentials:")
+    for key, present in status["fhir_credentials"].items():
+        print(f"  {check_mark(present)} {key}")
+
+    fhir_ready = all(status["fhir_credentials"].values())
+    if not fhir_ready:
+        print("\n⚠️  Missing FHIR credentials. Add them to .env file:")
+        print("   FHIR_PROVIDER_BASE_URL=https://api.medplum.com/fhir/R4")
+        print("   FHIR_PROVIDER_CLIENT_ID=your_client_id")
+        print("   FHIR_PROVIDER_CLIENT_SECRET=your_client_secret")
+
+    # Generated IDs
+    print("\nGenerated IDs:")
+    for key, present in status["generated_ids"].items():
+        print(f"  {check_mark(present)} {key}")
+
+    if not status["generated_ids"]["FHIR_PROVIDER_ID"]:
+        print("\n💡 Run setup_fhir_provider.py to create FHIR provider")
+    if not status["generated_ids"]["WORKFLOW_ID"]:
+        print("💡 Run create_workflow.py to create a workflow")
+
+    # Overall status
+    print("\n" + "=" * 60)
+    if core_ready and fhir_ready:
+        print("✅ Ready to create FHIR provider and workflows!")
+    elif core_ready:
+        print("✅ Core credentials ready")
+        print("⚠️  Add FHIR credentials to proceed with provider setup")
+    else:
+        print("⚠️  Add missing credentials to .env to proceed")
+    print("=" * 60 + "\n")
+
+    if verbose:
+        print("\nJSON Output:")
+        print(json.dumps(status, indent=2))
+
+def main():
+    parser = argparse.ArgumentParser(
+        description='Check environment variable status without exposing values'
+    )
+    parser.add_argument(
+        '--json',
+        action='store_true',
+        help='Output in JSON format only'
+    )
+    parser.add_argument(
+        '--verbose',
+        action='store_true',
+        help='Include JSON output with formatted output'
+    )
+
+    args = parser.parse_args()
+
+    status = check_env_vars()
+
+    if args.json:
+        print(json.dumps(status, indent=2))
+    else:
+        print_status(status, verbose=args.verbose)
+
+    # Exit with error code if core credentials are missing
+    if not all(status["core_credentials"].values()):
+        sys.exit(1)
+
+if __name__ == "__main__":
+    main()