Update genesis/providers.py

genesis/providers.py

@@ -1,28 +1,21 @@
-# genesis/providers.py
 """
 Providers module for GENESIS-AI
-Handles:
-1. Medical/Biological APIs (PubMed, ChEMBL, BioPortal, UMLS, NCBI)
-2. AI Text Generation (Gemini, OpenAI, Claude, DeepSeek)
-3. Image Generation (Gemini Vision, OpenAI DALL·E, Hugging Face Diffusion)
-4. Text-to-Speech (ElevenLabs + fallback)
-5. Graph DB Integration (Neo4j for pathways/funding)
 """
 
 import os
 import json
 import requests
 import logging
-from neo4j import GraphDatabase
 from dotenv import load_dotenv
+from neo4j import GraphDatabase
 
 # ========================
-# SECTION 1 — SETUP & LOGGING
+# SETUP & LOGGING
 # ========================
 load_dotenv()
 logging.basicConfig(level=logging.INFO)
 
-# API KEYS from Hugging Face Secrets or local .env
+# API KEYS
 PUBMED_API_KEY = os.getenv("PUBMED_API_KEY")
 CHEMBL_API_KEY = os.getenv("CHEMBL_API_KEY")
 BIOPORTAL_API_KEY = os.getenv("BIOPORTAL_API_KEY")
@@ -40,10 +33,22 @@ NEO4J_URI = os.getenv("NEO4J_URI")
 NEO4J_USER = os.getenv("NEO4J_USER")
 NEO4J_PASSWORD = os.getenv("NEO4J_PASSWORD")
 
-# Neo4j Driver
-neo4j_driver = GraphDatabase.driver(NEO4J_URI, auth=(NEO4J_USER, NEO4J_PASSWORD))
-
+# ========================
+# OPTIONAL NEO4J CONNECTION
+# ========================
+neo4j_driver = None
+if NEO4J_URI and NEO4J_USER and NEO4J_PASSWORD:
+    try:
+        neo4j_driver = GraphDatabase.driver(NEO4J_URI, auth=(NEO4J_USER, NEO4J_PASSWORD))
+        logging.info("[Neo4j] Connected successfully.")
+    except Exception as e:
+        logging.error(f"[Neo4j] Connection failed: {e}")
+else:
+    logging.info("[Neo4j] No URI/user/password set — skipping connection.")
 
+# ========================
+# SAFE REQUEST WRAPPER
+# ========================
 def safe_request(url, headers=None, params=None, data=None, method="GET", json_data=None):
     try:
         if method == "GET":
@@ -57,11 +62,10 @@ def safe_request(url, headers=None, params=None, data=None, method="GET", json_d
         return None
 
 # ========================
-# SECTION 2 — MEDICAL & BIOLOGY API CLIENTS
+# MEDICAL & BIOLOGY API CLIENTS
 # ========================
-
 def run_pubmed_literature(query, max_results=5):
-    url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
+    url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
     params = {
         "db": "pubmed",
         "term": query,
@@ -82,35 +86,33 @@ def run_pubmed_literature(query, max_results=5):
             results.append(summary)
     return results
 
-
 def run_chembl_search(molecule_name):
-    url = f"https://www.ebi.ac.uk/chembl/api/data/molecule"
-    params = {"molecule_synonyms__icontains": molecule_name, "format": "json"}
-    return safe_request(url, params=params)
-
+    return safe_request(
+        "https://www.ebi.ac.uk/chembl/api/data/molecule",
+        params={"molecule_synonyms__icontains": molecule_name, "format": "json"}
+    )
 
 def run_bioportal_ontology(term):
-    url = f"https://data.bioontology.org/search"
-    params = {"q": term, "apikey": BIOPORTAL_API_KEY}
-    return safe_request(url, params=params)
-
+    return safe_request(
+        "https://data.bioontology.org/search",
+        params={"q": term, "apikey": BIOPORTAL_API_KEY}
+    )
 
 def run_umls_search(term):
-    url = f"https://uts-ws.nlm.nih.gov/rest/search/current"
-    params = {"string": term, "apiKey": UMLS_API_KEY}
-    return safe_request(url, params=params)
-
+    return safe_request(
+        "https://uts-ws.nlm.nih.gov/rest/search/current",
+        params={"string": term, "apiKey": UMLS_API_KEY}
+    )
 
 def run_ncbi_gene_lookup(gene_id):
-    url = f"https://api.ncbi.nlm.nih.gov/gene/{gene_id}"
-    headers = {"api-key": NCBI_API_KEY}
-    return safe_request(url, headers=headers)
-
+    return safe_request(
+        f"https://api.ncbi.nlm.nih.gov/gene/{gene_id}",
+        headers={"api-key": NCBI_API_KEY}
+    )
 
 # ========================
-# SECTION 3 — AI TEXT GENERATION PROVIDERS
+# AI TEXT GENERATION
 # ========================
-
 def ai_generate_text(prompt, model="gemini"):
     """Fallback order: Gemini → OpenAI → Claude → DeepSeek"""
     if model == "gemini" and GEMINI_API_KEY:
@@ -156,11 +158,9 @@ def ai_generate_text(prompt, model="gemini"):
 
     return "No AI provider available or all failed."
 
-
 # ========================
-# SECTION 4 — IMAGE GENERATION PROVIDERS
+# IMAGE GENERATION
 # ========================
-
 def ai_generate_image(prompt):
     """Fallback: Gemini Vision → OpenAI → Hugging Face"""
     if GEMINI_API_KEY:
@@ -181,7 +181,6 @@ def ai_generate_image(prompt):
         except Exception as e:
             logging.error(f"OpenAI Image error: {e}")
 
-    # Hugging Face fallback
     HF_TOKEN = os.getenv("HF_TOKEN")
     if HF_TOKEN:
         resp = safe_request(
@@ -195,11 +194,9 @@ def ai_generate_image(prompt):
 
     return None
 
-
 # ========================
-# SECTION 5 — TEXT-TO-SPEECH PROVIDERS
+# TEXT-TO-SPEECH
 # ========================
-
 def run_tts(text, voice="Rachel"):
     if ELEVENLABS_API_KEY:
         url = f"https://api.elevenlabs.io/v1/text-to-speech/{voice}"
@@ -209,12 +206,13 @@ def run_tts(text, voice="Rachel"):
             return resp.content
     return None
 
-
 # ========================
-# SECTION 6 — NEO4J GRAPH FUNCTIONS
+# GRAPH DB QUERIES (Optional)
 # ========================
-
 def query_funding_network(keyword):
+    if not neo4j_driver:
+        logging.warning("[Neo4j] Skipping query — no connection.")
+        return []
     with neo4j_driver.session() as session:
         result = session.run(
             """
@@ -226,8 +224,10 @@ def query_funding_network(keyword):
         )
         return [dict(record) for record in result]
 
-
 def query_pathway_graph(pathway):
+    if not neo4j_driver:
+        logging.warning("[Neo4j] Skipping query — no connection.")
+        return []
     with neo4j_driver.session() as session:
         result = session.run(
             """
@@ -238,11 +238,9 @@ def query_pathway_graph(pathway):
         )
         return [dict(record) for record in result]
 
-
 # ========================
-# SECTION 7 — EXPORTS
+# EXPORTS
 # ========================
-
 __all__ = [
     "run_pubmed_literature",
     "run_chembl_search",