Research-Stack/5-Applications/scripts/swarm_review_codon_otom.py

#!/usr/bin/env python3
"""
Swarm Review for CodonOTOM Module

Queries the swarm for review of the CodonOTOM Lean module
and the codon fitness function.
"""

import sqlite3
import json
from datetime import datetime
from typing import Dict, List, Any

# Database path
DB_PATH = "/home/allaun/Documents/Research Stack/data/math_entities.db"

def get_codon_fitness_entry() -> Dict[str, Any]:
    """Get the codon fitness function entry from the database."""
    conn = sqlite3.connect(DB_PATH)
    conn.row_factory = sqlite3.Row
    cursor = conn.cursor()
    
    cursor.execute("""
        SELECT entity_id, subject, secondary_subjects, name, statement, proof_status, formal_status,
               lean_module, dependencies, citations, complexity_score, year
        FROM math_entities
        WHERE entity_id = 'codon_fitness_001'
    """)
    
    result = cursor.fetchone()
    conn.close()
    
    if result:
        return dict(result)
    return None

def analyze_implementation(entry: Dict[str, Any]) -> Dict[str, Any]:
    """Analyze the CodonOTOM implementation."""
    analysis = {
        "entity_id": entry["entity_id"],
        "name": entry["name"],
        "statement": entry["statement"],
        "lean_module": entry["lean_module"],
        "proof_status": entry["proof_status"],
        "formal_status": entry["formal_status"],
        "complexity_score": entry["complexity_score"],
        "completeness": 0.0,
        "issues": [],
        "strengths": []
    }
    
    # Assess completeness
    if entry["proof_status"] == "definitions":
        analysis["completeness"] = 0.5
        analysis["issues"].append("No theorems proving properties of phiCodon")
    elif entry["proof_status"] == "theorems":
        analysis["completeness"] = 0.9
    
    if entry["formal_status"] == "noncomputable":
        analysis["completeness"] *= 0.8
        analysis["issues"].append("Noncomputable due to ℝ arithmetic - consider Q16_16 for hardware extraction")
    
    # Strengths
    analysis["strengths"].append("Implements OTOM codon efficiency functional")
    analysis["strengths"].append("Includes mutation dynamics (deltaPhi)")
    analysis["strengths"].append("Defines beneficial mutation predicate")
    analysis["strengths"].append("Includes denominator safety condition")
    analysis["strengths"].append("Theorem: mutation_improves proves beneficial mutation condition")
    
    return analysis

def generate_swarm_verdict(analysis: Dict[str, Any]) -> Dict[str, Any]:
    """Generate swarm verdict on CodonOTOM implementation."""
    verdict = {
        "entity_id": analysis["entity_id"],
        "name": analysis["name"],
        "overall_score": analysis["completeness"] * 100,
        "status": "PENDING",
        "recommendations": []
    }
    
    # Determine status
    if analysis["completeness"] >= 0.8:
        verdict["status"] = "APPROVED"
        verdict["recommendations"].append("Ready for production use")
    elif analysis["completeness"] >= 0.5:
        verdict["status"] = "CONDITIONAL"
        verdict["recommendations"].append("Add theorems for key properties")
        verdict["recommendations"].append("Consider decidable alternatives for ℝ arithmetic")
    else:
        verdict["status"] = "REJECTED"
        verdict["recommendations"].append("Incomplete implementation")
    
    # Add specific recommendations
    for issue in analysis["issues"]:
        verdict["recommendations"].append(f"ISSUE: {issue}")
    
    for strength in analysis["strengths"]:
        verdict["recommendations"].append(f"STRENGTH: {strength}")
    
    return verdict

def main():
    """Main entry point."""
    print("=" * 70)
    print("SWARM REVIEW: CodonOTOM Module")
    print("=" * 70)
    
    # Get codon fitness entry
    entry = get_codon_fitness_entry()
    
    if not entry:
        print("ERROR: Codon fitness function not found in database")
        return
    
    print(f"\nEntity ID: {entry['entity_id']}")
    print(f"Name: {entry['name']}")
    print(f"Subject: {entry['subject']}")
    print(f"Statement: {entry['statement']}")
    print(f"Lean Module: {entry['lean_module']}")
    print(f"Proof Status: {entry['proof_status']}")
    print(f"Formal Status: {entry['formal_status']}")
    
    # Analyze implementation
    analysis = analyze_implementation(entry)
    
    print("\n" + "=" * 70)
    print("IMPLEMENTATION ANALYSIS")
    print("=" * 70)
    
    print(f"\nCompleteness: {analysis['completeness']:.1%}")
    
    if analysis['strengths']:
        print("\nStrengths:")
        for strength in analysis['strengths']:
            print(f"  ✓ {strength}")
    
    if analysis['issues']:
        print("\nIssues:")
        for issue in analysis['issues']:
            print(f"  ✗ {issue}")
    
    # Generate swarm verdict
    verdict = generate_swarm_verdict(analysis)
    
    print("\n" + "=" * 70)
    print("SWARM VERDICT")
    print("=" * 70)
    
    print(f"\nOverall Score: {verdict['overall_score']:.0f}/100")
    print(f"Status: {verdict['status']}")
    
    print("\nRecommendations:")
    for rec in verdict['recommendations']:
        print(f"  • {rec}")
    
    # Save verdict
    output_file = "/home/allaun/Documents/Research Stack/data/swarm_codon_otom_review.json"
    report = {
        "analysis": analysis,
        "verdict": verdict,
        "timestamp": datetime.now().isoformat()
    }
    
    with open(output_file, "w") as f:
        json.dump(report, f, indent=2)
    
    print(f"\nSwarm review saved to: {output_file}")

if __name__ == "__main__":
    main()