Initial commit

skills/phenoml-workflow/scripts/create_workflow.py

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+#!/usr/bin/env python3
+"""
+Workflow Creation Script
+
+Creates a PhenoML workflow using configuration from .env or CLI arguments.
+
+Usage:
+  python3 create_workflow.py
+  python3 create_workflow.py --name "My Workflow" --instructions "..." --sample-data '{"key": "value"}'
+  python3 create_workflow.py --help
+
+Required .env variables:
+  PHENOML_USERNAME, PHENOML_PASSWORD, PHENOML_BASE_URL
+  FHIR_PROVIDER_ID (from setup_fhir_provider.py)
+
+Workflow configuration (.env or CLI args):
+  WORKFLOW_NAME or --name
+  WORKFLOW_INSTRUCTIONS or --instructions
+  WORKFLOW_SAMPLE_DATA (JSON string) or --sample-data
+
+Optional:
+  WORKFLOW_DYNAMIC_GENERATION (true/false) or --dynamic-generation
+  WORKFLOW_VERBOSE (true/false) or --verbose
+"""
+
+import os
+import sys
+import json
+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 str_to_bool(s):
+    """Convert string to boolean"""
+    return s.lower() in ('true', '1', 'yes', 'y')
+
+def main():
+    parser = argparse.ArgumentParser(description='Create a PhenoML workflow')
+    parser.add_argument('--name', help='Workflow name')
+    parser.add_argument('--instructions', help='Workflow instructions')
+    parser.add_argument('--sample-data', help='Sample data as JSON string')
+    parser.add_argument('--dynamic-generation', type=str_to_bool, help='Enable dynamic generation (true/false)')
+    parser.add_argument('--verbose', type=str_to_bool, help='Verbose mode (true/false)')
+    parser.add_argument('--provider-id', help='FHIR provider ID (overrides .env)')
+
+    args = parser.parse_args()
+
+    # Load environment
+    load_dotenv()
+
+    # Get configuration (CLI args override .env)
+    name = args.name or os.getenv("WORKFLOW_NAME")
+    instructions = args.instructions or os.getenv("WORKFLOW_INSTRUCTIONS")
+    sample_data_str = args.sample_data or os.getenv("WORKFLOW_SAMPLE_DATA")
+    dynamic_generation = args.dynamic_generation if args.dynamic_generation is not None else str_to_bool(os.getenv("WORKFLOW_DYNAMIC_GENERATION", "true"))
+    verbose = args.verbose if args.verbose is not None else str_to_bool(os.getenv("WORKFLOW_VERBOSE", "false"))
+    provider_id = args.provider_id or os.getenv("FHIR_PROVIDER_ID")
+
+    # Validate required fields
+    if not name:
+        print("❌ Error: Workflow name is required")
+        print("   Set WORKFLOW_NAME in .env, or use --name")
+        sys.exit(1)
+
+    if not instructions:
+        print("❌ Error: Workflow instructions are required")
+        print("   Set WORKFLOW_INSTRUCTIONS in .env, or use --instructions")
+        sys.exit(1)
+
+    if not sample_data_str:
+        print("❌ Error: Sample data is required")
+        print("   Set WORKFLOW_SAMPLE_DATA in .env, or use --sample-data")
+        sys.exit(1)
+
+    if not provider_id:
+        print("❌ Error: FHIR provider ID is required")
+        print("   Run setup_fhir_provider.py first, or use --provider-id")
+        sys.exit(1)
+
+    # Parse sample data
+    try:
+        sample_data = json.loads(sample_data_str)
+    except json.JSONDecodeError as e:
+        print(f"❌ Error: Invalid JSON in sample data: {e}")
+        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 workflow
+    print(f"Creating workflow:")
+    print(f"  Name: {name}")
+    print(f"  Provider ID: {provider_id}")
+    print(f"  Dynamic generation: {dynamic_generation}")
+    print(f"  Verbose: {verbose}")
+    print(f"  Sample data: {json.dumps(sample_data, indent=2)}\n")
+
+    try:
+        workflow = client.workflows.create(
+            name=name,
+            workflow_instructions=instructions,
+            sample_data=sample_data,
+            fhir_provider_id=provider_id,
+            verbose=verbose,
+            dynamic_generation=dynamic_generation
+        )
+
+        workflow_id = workflow.workflow_id
+        print(f"✅ Workflow created successfully!")
+        print(f"   Workflow ID: {workflow_id}\n")
+
+        # Save to .env
+        save_to_env("WORKFLOW_ID", workflow_id)
+        print(f"💾 Workflow ID saved to .env")
+        print(f"\n🎉 Workflow creation complete! You can now test it with test_workflow.py")
+
+    except Exception as e:
+        print(f"❌ Failed to create workflow: {e}")
+        import traceback
+        traceback.print_exc()
+        sys.exit(1)
+
+if __name__ == "__main__":
+    main()