Update tools/bioportal_tool.py

tools/bioportal_tool.py

@@ -1,41 +1,72 @@
-from langchain.tools import BaseTool
+# /home/user/app/tools/bioportal_tool.py
+from langchain_core.tools import BaseTool
 from typing import Type, Optional
 from pydantic import BaseModel, Field
+# Assuming clinical_nlp.umls_bioportal.search_bioportal_term exists and works
 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.")
+    ontology: Optional[str] = Field(
+        default="SNOMEDCT_US", # Default to SNOMEDCT US Edition
+        description=(
+            "The specific ontology acronym to search within BioPortal (e.g., SNOMEDCT_US, ICD10CM, RXNORM, MESH, LOINC, NCIT). "
+            "Defaults to SNOMEDCT_US if not specified."
+        )
+    )
 
 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)."
+        "Use this tool to search for medical terms, codes (like ICD-10, SNOMED CT, RxNorm codes), definitions, and concept details "
+        "across a wide range of biomedical ontologies via BioPortal. "
+        "Useful when you need information from a specific ontology or want to explore different coding systems. "
+        "Input is a dictionary with 'term' and optional 'ontology'. If ontology is not specified by the user, you should default to 'SNOMEDCT_US'."
     )
     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']}"
+    def _run(self, term: str, ontology: Optional[str] = "SNOMEDCT_US") -> str:
+        # Pydantic ensures 'term' is provided. 'ontology' will have its default if not given.
+        target_ontology = ontology or "SNOMEDCT_US" # Ensure a default if None is passed
+        app_logger.info(f"BioPortal Tool called with term: '{term}', ontology: '{target_ontology}'")
+        log_tool_usage(self.name, {"query_term": term, "ontology": target_ontology})
+
+        if not term or not term.strip():
+            return "Error from BioPortal lookup: No search term provided."
+
+        try:
+            results = search_bioportal_term(term, ontology=target_ontology)
+        except Exception as e:
+            app_logger.error(f"Exception during BioPortal search for '{term}' in '{target_ontology}': {e}", exc_info=True)
+            return f"Error performing BioPortal lookup for '{term}': An unexpected error occurred during the search."
+
+        if isinstance(results, dict) and "error" in results:
+            app_logger.warning(f"BioPortal lookup for '{term}' in '{target_ontology}' returned an error: {results['error']}")
+            return f"Error from BioPortal lookup for '{term}' (Ontology: {target_ontology}): {results['error']}"
         
-        # Format results for LLM consumption
-        collection = results.get("collection", [])
+        collection = results.get("collection", []) if isinstance(results, dict) else []
         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"
+            for item in collection[:3]: # Limit to 3 results for brevity
+                pref_label = item.get('prefLabel', 'N/A')
+                defs = item.get('definition', [])
+                definition_str = ("; ".join(d for d in defs if d) if defs else "No definition available.")[:200] + "..." # Truncate long defs
+                cui_list = item.get('cui', [])
+                cui_str = ", ".join(cui_list) if cui_list else "N/A"
+                
                 formatted_results.append(
-                    f"- Term: {item.get('prefLabel', 'N/A')}, Definition: {definition_str}, CUIs: {item.get('cui', [])}"
+                    f"- Term: {pref_label} (CUIs: {cui_str}). Definition: {definition_str}"
                 )
-            return f"BioPortal Results (Ontology: {ontology}):\n" + "\n".join(formatted_results)
-        return f"No results found in BioPortal for ontology {ontology}."
+            if formatted_results:
+                return f"BioPortal Search Results for '{term}' (Ontology: {target_ontology}):\n" + "\n".join(formatted_results)
+            else: # Collection was present but no usable items after formatting
+                return f"No specific items found in BioPortal results for '{term}' (Ontology: {target_ontology}), though the query was successful."
+
+        app_logger.warning(f"No results or unexpected format from BioPortal for '{term}' in '{target_ontology}'. Raw: {str(results)[:200]}")
+        return f"No results found in BioPortal for term '{term}' in ontology '{target_ontology}'."
 
-    async def _arun(self, term: str, ontology: Optional[str] = "SNOMEDCT") -> str:
+    async def _arun(self, term: str, ontology: Optional[str] = "SNOMEDCT_US") -> str:
+        # For simplicity, using sync version. Implement true async if search_bioportal_term is async.
         return self._run(term, ontology)