Update tools/bioportal_tool.py

tools/bioportal_tool.py

@@ -0,0 +1,41 @@
+from langchain.tools import BaseTool
+from typing import Type, Optional
+from pydantic import BaseModel, Field
+from clinical_nlp.umls_bioportal import search_bioportal_term
+from services.logger import app_logger
+from services.metrics import log_tool_usage
+
+class BioPortalInput(BaseModel):
+    term: str = Field(description="The medical term to search for.")
+    ontology: Optional[str] = Field(default="SNOMEDCT", description="The specific ontology to search within BioPortal (e.g., SNOMEDCT, ICD10, RxNorm). Defaults to SNOMEDCT.")
+
+class BioPortalLookupTool(BaseTool):
+    name: str = "bioportal_lookup"
+    description: str = (
+        "Useful for searching medical terms, codes, and definitions across various ontologies "
+        "via BioPortal. Specify the term and optionally the ontology (e.g., SNOMEDCT, ICD10CM, RxNorm)."
+    )
+    args_schema: Type[BaseModel] = BioPortalInput
+
+    def _run(self, term: str, ontology: Optional[str] = "SNOMEDCT") -> str:
+        app_logger.info(f"BioPortal Tool called with term: {term}, ontology: {ontology}")
+        log_tool_usage(self.name)
+        results = search_bioportal_term(term, ontology=ontology or "SNOMEDCT")
+        if "error" in results:
+            return f"Error from BioPortal lookup: {results['error']}"
+        
+        # Format results for LLM consumption
+        collection = results.get("collection", [])
+        if collection:
+            formatted_results = []
+            for item in collection[:3]: # Limit to 3 results
+                defs = item.get('definition', ['N/A'])
+                definition_str = "; ".join(defs) if defs else "N/A"
+                formatted_results.append(
+                    f"- Term: {item.get('prefLabel', 'N/A')}, Definition: {definition_str}, CUIs: {item.get('cui', [])}"
+                )
+            return f"BioPortal Results (Ontology: {ontology}):\n" + "\n".join(formatted_results)
+        return f"No results found in BioPortal for ontology {ontology}."
+
+    async def _arun(self, term: str, ontology: Optional[str] = "SNOMEDCT") -> str:
+        return self._run(term, ontology)