Update genesis/pipeline.py

genesis/pipeline.py

@@ -1,31 +1,29 @@
 # genesis/pipeline.py
 import os
 import re
-import json
-from typing import Dict, Any, List, Optional
+from typing import Dict, Any, List
 from datetime import datetime
 
 from .ontology import expand_terms_with_ontology
 from .structures import fetch_structures_for_terms
 from .narration import narrate_text
 from .graphdb import write_topic_and_papers
-from .providers import run_deepseek_summary, run_gemini_polish, run_gemini_image
-from .providers import pubmed_fallback_search
+from .providers import run_deepseek_summary, run_gemini_polish, run_openai_image, pubmed_fallback_search
 
+# ===== ENV VARIABLES =====
 OPENAI_API_KEY = os.getenv("OPENAI_API_KEY")
 UMLS_API_KEY = os.getenv("UMLS_API_KEY")
 BIOPORTAL_API_KEY = os.getenv("BIOPORTAL_API_KEY")
 NCBI_API_KEY = os.getenv("NCBI_API_KEY")
 NCBI_EMAIL = os.getenv("NCBI_EMAIL")
 ELEVEN_LABS_API_KEY = os.getenv("ELEVEN_LABS_API_KEY")
-GEMINI_API_KEY = os.getenv("GEMINI_API_KEY")
 NEO4J_USER = os.getenv("NEO4J_USER")
 NEO4J_PASSWORD = os.getenv("NEO4J_PASSWORD")
 NEO4J_URI = os.getenv("NEO4J_URI")
 
-SYNBIO_MODE = True  # force synthetic biology bias
+SYNBIO_MODE = True  # force synthetic biology bias for demo
 
-# Preloaded killer queries for tomorrow's demo
+# ===== DEMO PRESETS =====
 DEMO_QUERIES = [
     "Map all CRISPR-based living therapeutics in clinical trials since 2020",
     "Graph metabolic engineering pathways for bio-based drug production",
@@ -87,20 +85,20 @@ def research_once(query: str, graph_preview: bool = True, narration: bool = True
         fallback_cites = pubmed_fallback_search(query, NCBI_API_KEY, NCBI_EMAIL)
         citations.extend(fallback_cites)
 
-    # 6. Fetch molecular structures for any mentioned terms
+    # 6. Fetch molecular structures
     structures = fetch_structures_for_terms(expanded_terms)
 
-    # 7. Generate visual diagram with Gemini
-    visual_image_url = run_gemini_image(query) if GEMINI_API_KEY else None
+    # 7. Generate visual diagram with OpenAI image model
+    visual_image_url = run_openai_image(query) if OPENAI_API_KEY else None
 
-    # 8. Write to Neo4j
+    # 8. Write to Neo4j graph
     if graph_preview and NEO4J_URI:
         write_topic_and_papers(query, citations, expanded_terms)
 
     # 9. Narrate executive summary
     audio_url = narrate_text(polished_summary) if narration and ELEVEN_LABS_API_KEY else None
 
-    # 10. Build output
+    # 10. Build output package
     report = {
         "timestamp": datetime.utcnow().isoformat(),
         "query": query,