run_engine.py

"""
Main Nexus Bio Engine orchestration script.
Execute complete drug repurposing pipeline for rare diseases.
"""

import asyncio
import sys
from nexus.core.types import DiseaseRequest
from nexus.core.agents import CodySperber, MarcusFabritius
from nexus.core.agents.agent8_semien import Semien


async def main():
    """Execute full pipeline."""
    print("=" * 60)
    print("NEXUS BIO ENGINE: Drug Repurposing Pipeline")
    print("=" * 60)
    print()
    
    # Initialize managers
    cody = CodySperber(max_concurrent=2)
    marcus = MarcusFabritius()
    semien = Semien()
    
    # Example: neuro-inflammatory disease targets
    requests = [
        DiseaseRequest(
            disease_id="neuro_inflam_001",
            disease_name="neuro-inflammatory",
            target_count=5,
            confidence_threshold=0.65,
        ),
    ]
    
    print(f"Processing {len(requests)} disease request(s)...")
    print()
    
    # Stage 1: Route through pipeline (Seth -> Chyna -> Kingsley -> ...)
    print("Stage 1: Signal ingestion & pathway mapping...")
    dossiers = await cody.run(requests)
    print(f"  Generated {len(dossiers)} dossier candidates")
    print()
    
    if not dossiers:
        print("No candidates survived pipeline. Exiting.")
        return
    
    # Stage 2: Regulatory compliance audit (Marcus)
    print("Stage 2: Regulatory compliance audit (Marcus)...")
    dossiers = await marcus.run(dossiers)
    
    regulatory_ready = sum(1 for d in dossiers if d.regulatory_ready)
    print(f"  {regulatory_ready}/{len(dossiers)} candidates regulatory_ready")
    print()
    
    # Stage 3: Export
    print("Stage 3: Export results...")
    
    # JSON export
    json_output = await semien.run(dossiers, format="json", min_confidence=0.65)
    print("  JSON export:")
    print(json_output)
    print()
    
    # Markdown export
    md_output = await semien.run(dossiers, format="markdown", min_confidence=0.65)
    print("  Markdown export:")
    print(md_output)
    print()
    
    # CSV export
    csv_output = await semien.run(dossiers, format="csv", min_confidence=0.65)
    print("  CSV export:")
    print(csv_output)
    print()
    
    print("=" * 60)
    print("Pipeline complete.")
    print("=" * 60)


if __name__ == "__main__":
    asyncio.run(main())