Update genesis/pipeline.py

genesis/pipeline.py

@@ -1,17 +1,20 @@
 # genesis/pipeline.py
+"""
+GENESIS-AI — Multimodal Synthetic Biology Research Pipeline
+Coordinates ontology expansion, literature review, AI summarization, image generation,
+funding intelligence, safety/biosecurity checks, and report export.
+"""
+
 import os
 import re
 from datetime import datetime
 from typing import Dict, Any, List
 
-# API client imports
+# API clients
 from genesis.api_clients.pubmed_api import search_pubmed_literature
 from genesis.api_clients.bioportal_api import expand_with_bioportal
 from genesis.api_clients.umls_api import expand_with_umls
-from genesis.api_clients.chembl_api import get_molecule_data
-from genesis.api_clients.ncbi_api import fetch_ncbi_structure
-from genesis.utils.pdf_export import export_report_to_pdf
-
+from genesis.structures import fetch_structures_for_terms
 
 # Core logic providers
 from genesis.providers import (
@@ -23,26 +26,29 @@ from genesis.providers import (
     run_hf_image,
     narrate_text_elevenlabs
 )
+
+# Utility modules
 from genesis.utils.pdf_export import export_report_to_pdf
+from genesis.utils.graph_tools import write_topic_and_papers
+
+# Visualizations
 from genesis.visualization import generate_pathway_graph, generate_funding_network
+
+# Data sources
 from genesis.funding import fetch_funding_data
 from genesis.trials import fetch_clinical_trials
 from genesis.biosecurity import analyze_biosecurity_risks
 from genesis.regulation import fetch_regulatory_info
 from genesis.safety import analyze_safety_concerns
-from genesis.structures import fetch_structures_for_terms
 from genesis.ontology import merge_ontology_terms
-from genesis.utils.graph_tools import write_topic_and_papers
 
 # Environment vars
 ELEVEN_LABS_API_KEY = os.getenv("ELEVEN_LABS_API_KEY")
 NEO4J_URI = os.getenv("NEO4J_URI")
-NEO4J_USER = os.getenv("NEO4J_USER")
-NEO4J_PASSWORD = os.getenv("NEO4J_PASSWORD")
 
 SYNBIO_MODE = True  # Bias towards synthetic biology context
 
-# Demo queries for UI preload
+# Demo queries
 DEMO_QUERIES = [
     "CRISPR living therapeutics in clinical trials since 2020",
     "AI-designed enzymes for plastic degradation — literature + pathways",
@@ -51,9 +57,10 @@ DEMO_QUERIES = [
     "Oncolytic virus engineering — biosecurity risk analysis"
 ]
 
+# ---------- Helper Functions ----------
 
 def extract_citations(text: str) -> List[Dict[str, str]]:
-    """Extract citations (DOI, PMID, URLs) from text."""
+    """Extract DOI, PMID, and URLs from text."""
     citations = []
     doi_pattern = r"(10\.\d{4,9}/[-._;()/:A-Z0-9]+)"
     pmid_pattern = r"PMID:\s*(\d+)"
@@ -66,12 +73,10 @@ def extract_citations(text: str) -> List[Dict[str, str]]:
     for match in re.finditer(url_pattern, text, re.IGNORECASE):
         if not any(c["url"] == match.group(1) for c in citations):
             citations.append({"type": "URL", "id": "", "url": match.group(1)})
-
     return citations
 
-
 def inject_synbio_context(query: str, expanded_terms: List[str]) -> str:
-    """Injects synthetic biology expertise into the prompt."""
+    """Inject synthetic biology expertise into the prompt."""
     context = (
         "You are an expert in synthetic biology, biosecurity, and regulatory affairs. "
         "Provide literature review, molecular insights, market trends, and policy implications. "
@@ -80,9 +85,14 @@ def inject_synbio_context(query: str, expanded_terms: List[str]) -> str:
     )
     return f"{context}\n\nQuery: {query}\nExpanded terms: {', '.join(expanded_terms)}"
 
+# ---------- Main Pipeline ----------
+
+def research_once(topic: str) -> Dict[str, Any]:
+    """Alias to multimodal_research for compatibility."""
+    return multimodal_research(topic)
 
 def multimodal_research(query: str, narration: bool = False, generate_pdf: bool = False) -> Dict[str, Any]:
-    """Main multi-modal synthetic biology pipeline."""
+    """Main research pipeline for GENESIS-AI."""
     print(f"[Pipeline] Starting research for query: {query}")
 
     # 1 — Expand query with ontology
@@ -93,10 +103,10 @@ def multimodal_research(query: str, narration: bool = False, generate_pdf: bool
     )
     print(f"[Pipeline] Expanded terms: {expanded_terms}")
 
-    # 2 — Inject domain-specific context
+    # 2 — Enrich query with domain-specific context
     enriched_query = inject_synbio_context(query, expanded_terms) if SYNBIO_MODE else query
 
-    # 3 — Summarization with fallback
+    # 3 — Summarization (fallback order)
     summary = None
     for summarizer in [run_deepseek_summary, run_gemini_summary, run_openai_summary]:
         try:
@@ -110,13 +120,13 @@ def multimodal_research(query: str, narration: bool = False, generate_pdf: bool
     if not summary:
         summary = "No summary generated — please refine your query."
 
-    # 4 — Citations extraction & PubMed fallback
+    # 4 — Extract citations, fallback to PubMed if none found
     citations = extract_citations(summary)
     if not citations:
         print("[Pipeline] No citations in summary, querying PubMed...")
         citations = search_pubmed_literature(query)
 
-    # 5 — Structures (NCBI, ChEMBL)
+    # 5 — Fetch related structures (NCBI, ChEMBL)
     structures = fetch_structures_for_terms(expanded_terms)
 
     # 6 — Image generation with fallback
@@ -130,7 +140,7 @@ def multimodal_research(query: str, narration: bool = False, generate_pdf: bool
         except Exception as e:
             print(f"[Pipeline] {img_fn.__name__} failed: {e}")
 
-    # 7 — Funding, Trials, Regulation, Safety, Biosecurity
+    # 7 — Funding, trials, regulations, safety, biosecurity
     funding_data = fetch_funding_data(query) or []
     trial_data = fetch_clinical_trials(query) or []
     regulation_data = fetch_regulatory_info(query) or []
@@ -141,7 +151,7 @@ def multimodal_research(query: str, narration: bool = False, generate_pdf: bool
     pathway_graph = generate_pathway_graph(query, expanded_terms) if expanded_terms else None
     funding_graph = generate_funding_network(query, funding_data) if funding_data else None
 
-    # 9 — Save to Neo4j
+    # 9 — Save to Neo4j if configured
     if NEO4J_URI:
         try:
             write_topic_and_papers(query, citations, expanded_terms)
@@ -149,7 +159,7 @@ def multimodal_research(query: str, narration: bool = False, generate_pdf: bool
         except Exception as e:
             print(f"[Pipeline] Neo4j save failed: {e}")
 
-    # 10 — Optional narration
+    # 10 — Narration (optional)
     audio_url = None
     if narration and ELEVEN_LABS_API_KEY:
         try:
@@ -158,7 +168,7 @@ def multimodal_research(query: str, narration: bool = False, generate_pdf: bool
         except Exception as e:
             print(f"[Pipeline] Narration failed: {e}")
 
-    # 11 — Optional PDF export
+    # 11 — PDF export (optional)
     pdf_path = None
     if generate_pdf:
         try:
@@ -167,7 +177,6 @@ def multimodal_research(query: str, narration: bool = False, generate_pdf: bool
         except Exception as e:
             print(f"[Pipeline] PDF generation failed: {e}")
 
-    # 12 — Build output
     return {
         "timestamp": datetime.utcnow().isoformat(),
         "query": query,