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)