Update genesis/biosecurity.py

genesis/biosecurity.py

@@ -1,70 +1,37 @@
 # genesis/biosecurity.py
 import os
 import requests
-from typing import Dict, Any
-from datetime import datetime
+from genesis.utils.neo4j_utils import run_query
 
-from .providers import pubmed_fallback_search, run_deepseek_summary
+BIOPORTAL_API_KEY = os.getenv("BIOPORTAL_API_KEY")
+BIOPORTAL_BASE_URL = "https://data.bioontology.org"
 
-OPENAI_API_KEY = os.getenv("OPENAI_API_KEY")
-NCBI_API_KEY = os.getenv("NCBI_API_KEY")
-NCBI_EMAIL = os.getenv("NCBI_EMAIL")
-
-RISK_KEYWORDS = {
-    "low": ["harmless", "biosafety level 1", "safe", "non-pathogenic"],
-    "medium": ["biosafety level 2", "BSL-2", "infectious", "containment"],
-    "high": ["BSL-3", "BSL-4", "pandemic potential", "gain-of-function", "biosecurity concern"]
-}
-
-def score_biosecurity_risk(text: str) -> int:
-    """Score risk based on keywords in AI report."""
-    text_lower = text.lower()
-    score = 0
-    for word in RISK_KEYWORDS["low"]:
-        if word in text_lower:
-            score += 10
-    for word in RISK_KEYWORDS["medium"]:
-        if word in text_lower:
-            score += 25
-    for word in RISK_KEYWORDS["high"]:
-        if word in text_lower:
-            score += 50
-    return min(score, 100)  # cap at 100
-
-def run_biosecurity_scan(entity: str) -> Dict[str, Any]:
+def search_biosecurity_terms(query, pagesize=10):
     """
-    Run AI-powered biosecurity risk scan for a given biological entity.
-    Includes AI assessment + PubMed literature.
+    Search BioPortal for biosecurity-related terms.
+    Stores results in Neo4j for knowledge graph building.
     """
-    try:
-        # AI assessment
-        prompt = f"""
-        You are a synthetic biology & biosecurity expert.
-        Assess the potential biosecurity risks of the following entity: {entity}.
-        Classify its biosafety level, potential misuse, regulatory concerns, and safe handling guidelines.
-        Respond with detailed analysis.
-        """
-        ai_report = run_deepseek_summary(prompt)
+    headers = {"Authorization": f"apikey token={BIOPORTAL_API_KEY}"}
+    params = {"q": query, "pagesize": pagesize}
 
-        # Risk score
-        score = score_biosecurity_risk(ai_report)
-
-        # PubMed citations
-        citations = pubmed_fallback_search(entity, NCBI_API_KEY, NCBI_EMAIL)
-
-        return {
-            "entity": entity,
-            "timestamp": datetime.utcnow().isoformat(),
-            "risk_score": score,
-            "report": ai_report,
-            "citations": citations
-        }
-    except Exception as e:
-        return {
-            "entity": entity,
-            "timestamp": datetime.utcnow().isoformat(),
-            "error": str(e),
-            "risk_score": 0,
-            "report": "Error running biosecurity scan.",
-            "citations": []
-        }
+    try:
+        response = requests.get(f"{BIOPORTAL_BASE_URL}/search", headers=headers, params=params)
+        response.raise_for_status()
+        results = response.json().get("collection", [])
+
+        # Store in Neo4j
+        for r in results:
+            label = r.get("prefLabel", "Unknown")
+            uri = r.get("@id", "")
+            run_query(
+                """
+                MERGE (t:BiosecurityTerm {uri: $uri})
+                SET t.label = $label, t.source = "BioPortal"
+                """,
+                {"uri": uri, "label": label}
+            )
+
+        return results
+
+    except requests.RequestException as e:
+        return {"error": str(e)}