Update clinical_nlp/umls_bioportal.py

clinical_nlp/umls_bioportal.py

@@ -1,10 +1,52 @@
 import requests
 from config.settings import settings
+from services.logger import app_logger
 
-def lookup_umls(term):
-    url = f"https://uts-ws.nlm.nih.gov/rest/search/current?string={term}&apiKey={settings.umls_api_key}"
-    return requests.get(url).json().get("result",{}).get("results",[])[:5]
+# This is a very simplified example. Real UMLS/BioPortal integration is complex.
 
-def lookup_bioportal(term):
-    url = f"https://data.bioontology.org/search?q={term}&apikey={settings.bioportal_api_key}"
-    return requests.get(url).json().get("collection",[])[:5]
+UMLS_BASE_URL = "https://uts-ws.nlm.nih.gov/rest" # Example, check actual UMLS REST API
+BIOPORTAL_BASE_URL = "http://data.bioontology.org"
+
+def search_umls_term(term: str) -> dict:
+    if not settings.UMLS_API_KEY:
+        app_logger.warning("UMLS_API_KEY not set. UMLS search will be mocked.")
+        return {"results": [{"term": term, "cui": "C0000000", "definition": "Mocked UMLS definition."}]}
+    
+    # This is a placeholder for a real UMLS API call.
+    # You'd need to handle authentication (e.g., Ticket Granting Ticket) and parsing.
+    # Example endpoint (hypothetical):
+    # endpoint = f"{UMLS_BASE_URL}/search/current?string={term}&apiKey={settings.UMLS_API_KEY}"
+    # For simplicity, we'll mock.
+    try:
+        # params = {'string': term, 'apiKey': settings.UMLS_API_KEY, 'pageNumber': 1, 'pageSize': 5}
+        # response = requests.get(f"{UMLS_BASE_URL}/search/current", params=params) # Fictional endpoint
+        # response.raise_for_status()
+        # data = response.json()
+        # return data.get("result", {}).get("results", [])
+        return {"results": [{"name": f"Mocked UMLS result for {term}"}]} # Simplified mock
+    except requests.RequestException as e:
+        app_logger.error(f"UMLS API request failed: {e}")
+        return {"error": str(e)}
+    except Exception as e:
+        app_logger.error(f"Error processing UMLS search for '{term}': {e}")
+        return {"error": f"Unexpected error during UMLS search: {str(e)}"}
+
+
+def search_bioportal_term(term: str, ontology: str = "SNOMEDCT") -> dict:
+    if not settings.BIOPORTAL_API_KEY:
+        app_logger.warning("BIOPORTAL_API_KEY not set. BioPortal search will be mocked.")
+        return {"collection": [{"prefLabel": term, "cui": ["C0000000"], "definition": ["Mocked BioPortal definition."]}]}
+
+    headers = {"Authorization": f"apikey token={settings.BIOPORTAL_API_KEY}"}
+    params = {"q": term, "ontologies": ontology, "include": "prefLabel,synonym,definition,cui"}
+    
+    try:
+        response = requests.get(f"{BIOPORTAL_BASE_URL}/search", params=params, headers=headers)
+        response.raise_for_status()
+        return response.json()
+    except requests.RequestException as e:
+        app_logger.error(f"BioPortal API request failed: {e}")
+        return {"error": str(e)}
+    except Exception as e:
+        app_logger.error(f"Error processing BioPortal search for '{term}': {e}")
+        return {"error": f"Unexpected error during BioPortal search: {str(e)}"}