fix(041): lint fixes — ruff format backend, line length compliance

T051: All ruff check + format passes for library/ and backend/.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: satra

backend/src/auth/dependencies.py

@@ -147,9 +147,9 @@ def _check(user: dict | None) -> dict:
             raise HTTPException(
                 status_code=403,
                 detail=(
-                f"Role '{role}' required. "
-                f"Your roles: {user.get('realm_access', {}).get('roles', [])}"
-            ),
+                    f"Role '{role}' required. "
+                    f"Your roles: {user.get('realm_access', {}).get('roles', [])}"
+                ),
             )
         return user
 

backend/src/graphql/resolvers.py

@@ -410,18 +410,19 @@ async def resolve_search(
                         )
                         sem_result = await session.execute(
                             sem_stmt,
-                            {"qvec": str(query_vec if isinstance(query_vec, list) else query_vec.tolist()), "lim": first},
+                            {
+                                "qvec": str(
+                                    query_vec if isinstance(query_vec, list) else query_vec.tolist()
+                                ),
+                                "lim": first,
+                            },
                         )
                         for row in sem_result:
                             sim = round(float(row.similarity), 4)
                             sem_scores[row.sha256] = sim
                             if row.sha256 in seen_sha:
                                 continue  # Will update score below
-                            prov = (
-                                (row.provenance or [{}])[0]
-                                if row.provenance
-                                else {}
-                            )
+                            prov = (row.provenance or [{}])[0] if row.provenance else {}
                             results.append(
                                 t.SearchResultType(
                                     entity_type=etype,
@@ -431,8 +432,7 @@ async def resolve_search(
                                         row.file_name or row.sha256[:12],
                                     ),
                                     source=prov.get("source"),
-                                    description=row.description
-                                    or prov.get("description", ""),
+                                    description=row.description or prov.get("description", ""),
                                     score=sim,
                                 )
                             )
@@ -471,12 +471,14 @@ async def resolve_search(
                             )
                         )
                         if existing.scalar_one_or_none() is None:
-                            session.add(AlignmentCandidate(
-                                entity_a=sha_a,
-                                entity_b=sha_b,
-                                similarity=min(a.score, b.score),
-                                source="search",
-                            ))
+                            session.add(
+                                AlignmentCandidate(
+                                    entity_a=sha_a,
+                                    entity_b=sha_b,
+                                    similarity=min(a.score, b.score),
+                                    source="search",
+                                )
+                            )
                 await session.flush()
         except Exception as exc:
             logger.debug("Failed to record alignment candidates: %s", exc)
@@ -1585,9 +1587,7 @@ async def resolve_ontology_store_info(session: AsyncSession) -> list[dict]:
     from src.db.models import OntologySource
 
     stmt = (
-        select(OntologySource)
-        .where(OntologySource.active.is_(True))
-        .order_by(OntologySource.name)
+        select(OntologySource).where(OntologySource.active.is_(True)).order_by(OntologySource.name)
     )
     rows = (await session.execute(stmt)).scalars().all()
     return [

backend/src/services/chat_service.py

@@ -49,8 +49,7 @@ def _get_model() -> str:
         "function": {
             "name": "lookup_ontology_term",
             "description": (
-                "Search the ontology store for a term."
-                " Use this instead of guessing URIs."
+                "Search the ontology store for a term. Use this instead of guessing URIs."
             ),
             "parameters": {
                 "type": "object",
@@ -162,9 +161,7 @@ async def chat_completion(
     system = SYSTEM_PROMPT
     if entity_context:
         ctx = json.dumps(entity_context, indent=2, default=str)
-        system += (
-            f"\n\nCurrent entity context:\n```json\n{ctx}\n```"
-        )
+        system += f"\n\nCurrent entity context:\n```json\n{ctx}\n```"
 
     full_messages = [{"role": "system", "content": system}] + messages
 

backend/src/tools/enrichment_tools.py

@@ -114,8 +114,7 @@
                     "adapter_type": {
                         "type": "string",
                         "description": (
-                            "Adapter to use (bids, dandi,"
-                            " reproschema, csv, json-schema)"
+                            "Adapter to use (bids, dandi, reproschema, csv, json-schema)"
                         ),
                     },
                 },

specs/041-cross-source-alignment/tasks.md

@@ -130,7 +130,7 @@
 - [ ] T048 Run full pipeline across all 8 sources with alignment enabled — record entity counts before/after alignment in eval-record.md per constitution
 - [ ] T049 Verify alignment report: confirm known cross-source pairs (age↔interview_age, sex↔gender) aligned; confirm no false merges for entities with different ranges
 - [ ] T050 Performance validation: time full alignment of registry and verify <30 minutes; document in eval-record.md
-- [ ] T051 Fix any ruff lint/format issues across all modified files — run `uv run ruff check --fix` and `uv run ruff format` in library/ and backend/
+- [X] T051 Fix any ruff lint/format issues across all modified files — run `uv run ruff check --fix` and `uv run ruff format` in library/ and backend/
 - [ ] T052 Verify frontend builds cleanly — run `pnpm lint && pnpm build` in frontend/
 - [X] T053 Update library/src/undata_library/cli.py pipeline command to include alignment as default post-commit step — `pipeline --source X` runs extract→enrich→commit→align→transform