refactor: resolve pylint errors and warnings across api and src routers

- Enforced explicit exception chaining (raise from exc) in ask/search/analyze routes
- Fixed dynamic method call references pointing to llm_config missing members
- Patched missing explicit utf-8 encodings in file handlers via BiomarkerValidator

api/app/routes/biomarkers.py

@@ -34,7 +34,7 @@ async def list_biomarkers():
         # Load biomarker references
         config_path = Path(__file__).parent.parent.parent.parent / "config" / "biomarker_references.json"
 
-        with open(config_path) as f:
+        with open(config_path, encoding="utf-8") as f:
             config_data = json.load(f)
 
         biomarkers_data = config_data.get("biomarkers", {})
@@ -73,8 +73,8 @@ async def list_biomarkers():
             biomarkers=biomarkers_list, total_count=len(biomarkers_list), timestamp=datetime.now().isoformat()
         )
 
-    except FileNotFoundError:
-        raise HTTPException(status_code=500, detail="Biomarker configuration file not found")
+    except FileNotFoundError as exc:
+        raise HTTPException(status_code=500, detail="Biomarker configuration file not found") from exc
 
     except Exception as e:
         raise HTTPException(status_code=500, detail=f"Failed to load biomarkers: {e!s}") from e

src/biomarker_validator.py

@@ -15,7 +15,7 @@ class BiomarkerValidator:
     def __init__(self, reference_file: str = "config/biomarker_references.json"):
         """Load biomarker reference ranges from JSON file"""
         ref_path = Path(__file__).parent.parent / reference_file
-        with open(ref_path) as f:
+        with open(ref_path, encoding="utf-8") as f:
             self.references = json.load(f)["biomarkers"]
 
     def validate_biomarker(

src/main.py

@@ -101,12 +101,12 @@ async def lifespan(app: FastAPI):
 
     # --- Agentic RAG service ---
     try:
-        from src.llm_config import get_llm
+        from src.llm_config import get_chat_model
         from src.services.agents.agentic_rag import AgenticRAGService
         from src.services.agents.context import AgenticContext
 
         if app.state.opensearch_client and app.state.embedding_service:
-            llm = get_llm()
+            llm = get_chat_model()
             ctx = AgenticContext(
                 llm=llm,
                 embedding_service=app.state.embedding_service,
@@ -136,11 +136,11 @@ async def lifespan(app: FastAPI):
 
     # --- Extraction service (for natural language input) ---
     try:
-        from src.llm_config import get_llm
+        from src.llm_config import get_chat_model
         from src.services.extraction.service import make_extraction_service
 
         try:
-            llm = get_llm()
+            llm = get_chat_model()
         except Exception as e:
             logger.warning("Failed to get LLM for extraction, will use fallback: %s", e)
             llm = None

src/routers/analyze.py

@@ -124,7 +124,7 @@ async def _run_guild_analysis(
         raise HTTPException(
             status_code=500,
             detail=f"Analysis pipeline error: {exc}",
-        )
+        ) from exc
 
     elapsed = (time.time() - t0) * 1000
 
@@ -159,7 +159,7 @@ async def analyze_natural(body: NaturalAnalysisRequest, request: Request):
         extracted = await extraction_svc.extract_biomarkers(body.message)
     except Exception as exc:
         logger.exception("Biomarker extraction failed: %s", exc)
-        raise HTTPException(status_code=422, detail=f"Could not extract biomarkers: {exc}")
+        raise HTTPException(status_code=422, detail=f"Could not extract biomarkers: {exc}") from exc
 
     patient_ctx = body.patient_context.model_dump(exclude_none=True) if body.patient_context else {}
     return await _run_guild_analysis(request, extracted, patient_ctx, extracted_biomarkers=extracted)

src/routers/ask.py

@@ -41,7 +41,7 @@ async def ask_medical_question(body: AskRequest, request: Request):
         )
     except Exception as exc:
         logger.exception("Agentic RAG failed: %s", exc)
-        raise HTTPException(status_code=500, detail=f"RAG pipeline error: {exc}")
+        raise HTTPException(status_code=500, detail=f"RAG pipeline error: {exc}") from exc
 
     elapsed = (time.time() - t0) * 1000
 

src/routers/search.py

@@ -48,7 +48,7 @@ async def hybrid_search(body: SearchRequest, request: Request):
         raise
     except Exception as exc:
         logger.exception("Search failed: %s", exc)
-        raise HTTPException(status_code=500, detail=f"Search error: {exc}")
+        raise HTTPException(status_code=500, detail=f"Search error: {exc}") from exc
 
     elapsed = (time.time() - t0) * 1000