Update genesis/providers.py

genesis/providers.py

@@ -1,55 +1,90 @@
-# genesis/graphdb.py
+# genesis/providers.py
 import os
+import requests
 from typing import List, Dict
-from neo4j import GraphDatabase
 
-NEO4J_URI = os.getenv("NEO4J_URI")
-NEO4J_USER = os.getenv("NEO4J_USER")
-NEO4J_PASSWORD = os.getenv("NEO4J_PASSWORD")
+OPENAI_API_KEY = os.getenv("OPENAI_API_KEY")
+HF_TOKEN = os.getenv("HF_TOKEN")
+GEMINI_API_KEY = os.getenv("GEMINI_API_KEY")
+NCBI_API_KEY = os.getenv("NCBI_API_KEY")
+NCBI_EMAIL = os.getenv("NCBI_EMAIL")
 
-def _get_driver():
-    if not (NEO4J_URI and NEO4J_USER and NEO4J_PASSWORD):
-        raise ValueError("[GraphDB] Missing Neo4j credentials.")
-    return GraphDatabase.driver(NEO4J_URI, auth=(NEO4J_USER, NEO4J_PASSWORD))
+# -------- DeepSeek Summary --------
+def run_deepseek_summary(prompt: str) -> str:
+    """Run a dense scientific summary using DeepSeek API."""
+    try:
+        url = "https://api.deepseek.com/v1/chat/completions"  # Example endpoint
+        headers = {"Authorization": f"Bearer {HF_TOKEN}", "Content-Type": "application/json"}
+        payload = {
+            "model": "deepseek-science",
+            "messages": [{"role": "user", "content": prompt}],
+            "temperature": 0.2
+        }
+        r = requests.post(url, headers=headers, json=payload, timeout=60)
+        r.raise_for_status()
+        data = r.json()
+        return data["choices"][0]["message"]["content"]
+    except Exception as e:
+        print(f"[DeepSeek] Failed: {e}")
+        return prompt  # fallback: return prompt
 
-def write_topic_and_papers(topic: str, citations: List[Dict], expanded_terms: List[str]):
-    """Write topic, papers, and related concepts to Neo4j."""
+# -------- Gemini Polish --------
+def run_gemini_polish(text: str) -> str:
+    """Polish the summary using Gemini for clarity and presentation."""
+    if not GEMINI_API_KEY:
+        return text
     try:
-        driver = _get_driver()
-        with driver.session() as session:
-            # Create Topic node
-            session.run(
-                "MERGE (t:Topic {name: $name})",
-                name=topic
-            )
+        url = f"https://generativelanguage.googleapis.com/v1beta/models/gemini-pro:generateContent?key={GEMINI_API_KEY}"
+        payload = {"contents": [{"parts": [{"text": f"Polish and clarify this research report:\n\n{text}"}]}]}
+        r = requests.post(url, json=payload, timeout=30)
+        r.raise_for_status()
+        data = r.json()
+        return data["candidates"][0]["content"]["parts"][0]["text"]
+    except Exception as e:
+        print(f"[Gemini] Failed: {e}")
+        return text
 
-            # Create Paper nodes and relationships
-            for cite in citations:
-                paper_id = cite.get("id", cite.get("url", ""))
-                session.run(
-                    """
-                    MERGE (p:Paper {id: $id, url: $url})
-                    ON CREATE SET p.type = $type
-                    MERGE (t:Topic {name: $topic})
-                    MERGE (t)-[:RELATED_TO]->(p)
-                    """,
-                    id=paper_id,
-                    url=cite.get("url"),
-                    type=cite.get("type"),
-                    topic=topic
-                )
+# -------- Gemini Image --------
+def run_gemini_image(query: str) -> str:
+    """Generate a research diagram using Gemini Vision/Image."""
+    if not GEMINI_API_KEY:
+        return None
+    try:
+        url = f"https://generativelanguage.googleapis.com/v1beta/models/gemini-pro-vision:generateImage?key={GEMINI_API_KEY}"
+        payload = {"prompt": f"Generate a detailed scientific diagram about: {query}"}
+        r = requests.post(url, json=payload, timeout=30)
+        r.raise_for_status()
+        data = r.json()
+        return data.get("image_url") or ""
+    except Exception as e:
+        print(f"[Gemini Image] Failed: {e}")
+        return None
 
-            # Create Concept nodes and relationships
-            for term in expanded_terms:
-                session.run(
-                    """
-                    MERGE (c:Concept {name: $term})
-                    MERGE (t:Topic {name: $topic})
-                    MERGE (t)-[:HAS_CONCEPT]->(c)
-                    """,
-                    term=term,
-                    topic=topic
-                )
-        driver.close()
+# -------- PubMed Fallback --------
+def pubmed_fallback_search(query: str, api_key: str, email: str) -> List[Dict]:
+    """Search PubMed for relevant articles if no citations found."""
+    results = []
+    if not api_key or not email:
+        return results
+    try:
+        base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
+        params = {
+            "db": "pubmed",
+            "term": query,
+            "retmax": 3,
+            "api_key": api_key,
+            "email": email,
+            "retmode": "json"
+        }
+        r = requests.get(base_url, params=params, timeout=10)
+        r.raise_for_status()
+        ids = r.json().get("esearchresult", {}).get("idlist", [])
+        for pmid in ids:
+            results.append({
+                "type": "PMID",
+                "id": pmid,
+                "url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/"
+            })
     except Exception as e:
-        print(f"[GraphDB] Failed to write data: {e}")
+        print(f"[PubMed] Failed: {e}")
+    return results