Update genesis/pipeline.py

genesis/pipeline.py

@@ -1,78 +1,88 @@
 # genesis/pipeline.py
-"""
-GENESIS-AI Research Pipeline
-Coordinates ontology expansion, literature retrieval, summaries, citations, structure fetching, graphDB storage, and narration.
-"""
-
 import os
-from datetime import datetime
-
-from .ontology import expand_terms_with_ontology
-from .molecule_viewer import fetch_structure
-from .narration import narrate_text
-from .providers import (
-    run_deepseek_summary,
-    run_gemini_polish,
-    run_openai_image,
-    pubmed_fallback_search
+from genesis.providers import (
+    run_pubmed_literature,
+    run_molecule_lookup,
+    run_pathway_mapping,
+    run_funding_network,
+    run_image_analysis,
+    run_tts
 )
-from .graphdb import write_topic_and_papers
+from genesis.utils.graph_tools import render_graph_svg
+from genesis.utils.pdf_export import export_pdf_report
 
-# ENV
-ELEVEN_LABS_API_KEY = os.getenv("ELEVEN_LABS_API_KEY")
-GEMINI_API_KEY = os.getenv("GEMINI_API_KEY")
+# API Keys (already in HF secrets)
 NEO4J_URI = os.getenv("NEO4J_URI")
+NEO4J_USER = os.getenv("NEO4J_USER")
+NEO4J_PASSWORD = os.getenv("NEO4J_PASSWORD")
 
-SYNBIO_MODE = True
-
-def synthetic_biology_prompt_inject(query, expanded_terms):
-    """Injects domain-specific bias toward synthetic biology research."""
-    context = (
-        "You are an expert in synthetic biology. Focus on CRISPR, metabolic engineering, "
-        "living therapeutics, protein design, biosensors, and biosecurity. Include literature, "
-        "structures, market trends, and regulatory insights with citations."
-    )
-    return f"{context}\n\nQuery: {query}\nExpanded terms: {', '.join(expanded_terms)}"
-
-def research_once(query, graph_preview=True, narration=True):
-    """Runs the GENESIS-AI pipeline for a given research query."""
-    
-    # 1. Expand ontology
-    expanded_terms = expand_terms_with_ontology(query)
-
-    # 2. Domain injection
-    enriched_query = synthetic_biology_prompt_inject(query, expanded_terms) if SYNBIO_MODE else query
-
-    # 3. Summarize (DeepSeek)
-    summary_raw = run_deepseek_summary(enriched_query)
-
-    # 4. Polish (Gemini)
-    summary_polished = run_gemini_polish(summary_raw)
-
-    # 5. Citations
-    citations = pubmed_fallback_search(query)
-
-    # 6. Structures
-    structures = [fetch_structure(term) for term in expanded_terms]
+# ---------------------------------------------------------
+# 1 — Literature Mode
+# ---------------------------------------------------------
+def run_literature_mode(query, narration=False):
+    results = run_pubmed_literature(query)
+    output = {
+        "summary": results.get("summary"),
+        "citations": results.get("citations"),
+        "visuals": results.get("visuals")
+    }
+    if narration:
+        output["audio_url"] = run_tts(results.get("summary", ""))
+    return output
 
-    # 7. Visual (OpenAI Image)
-    image_url = run_openai_image(query)
+# ---------------------------------------------------------
+# 2 — Molecule Mode
+# ---------------------------------------------------------
+def run_molecule_mode(identifier, narration=False):
+    results = run_molecule_lookup(identifier)
+    output = {
+        "summary": results.get("summary"),
+        "structure_3d": results.get("structure_3d"),
+        "properties": results.get("properties")
+    }
+    if narration:
+        output["audio_url"] = run_tts(results.get("summary", ""))
+    return output
 
-    # 8. GraphDB
-    if graph_preview and NEO4J_URI:
-        write_topic_and_papers(query, citations, expanded_terms)
+# ---------------------------------------------------------
+# 3 — Pathway Mode
+# ---------------------------------------------------------
+def run_pathway_mode(pathway_name, narration=False):
+    results = run_pathway_mapping(pathway_name)
+    graph_svg = render_graph_svg(results.get("relationships", []))
+    output = {
+        "summary": results.get("summary"),
+        "graph_svg": graph_svg,
+        "analysis": results.get("analysis")
+    }
+    if narration:
+        output["audio_url"] = run_tts(results.get("summary", ""))
+    return output
 
-    # 9. Narration
-    audio_url = narrate_text(summary_polished) if narration and ELEVEN_LABS_API_KEY else None
+# ---------------------------------------------------------
+# 4 — Funding Mode
+# ---------------------------------------------------------
+def run_funding_mode(query, narration=False):
+    results = run_funding_network(query)
+    output = {
+        "summary": results.get("summary"),
+        "funding_graph": results.get("graph_svg"),
+        "top_investors": results.get("top_investors")
+    }
+    if narration:
+        output["audio_url"] = run_tts(results.get("summary", ""))
+    return output
 
-    # 10. Output
-    return {
-        "timestamp": datetime.utcnow().isoformat(),
-        "query": query,
-        "expanded_terms": expanded_terms,
-        "summary": summary_polished,
-        "citations": citations,
-        "structures": structures,
-        "image_url": image_url,
-        "audio_url": audio_url
+# ---------------------------------------------------------
+# 5 — Image Mode
+# ---------------------------------------------------------
+def run_image_mode(image_path, narration=False):
+    results = run_image_analysis(image_path)
+    output = {
+        "summary": results.get("summary"),
+        "annotations": results.get("annotations"),
+        "enhanced_image": results.get("enhanced_image")
     }
+    if narration:
+        output["audio_url"] = run_tts(results.get("summary", ""))
+    return output