chore: checkpoint local changes

Author: iamh2o

bloom_lims/api/v1/beta_lab.py

@@ -29,6 +29,10 @@
     BetaRunCreateRequest,
     BetaRunResolutionResponse,
     BetaRunResponse,
+    BetaTubeCreateRequest,
+    BetaTubeResponse,
+    BetaSpecimenUpdateRequest,
+    BetaTubeUpdateRequest,
 )
 
 logger = logging.getLogger(__name__)
@@ -82,6 +86,75 @@ async def register_accepted_material(
         service.close()
 
 
+@router.post("/tubes", response_model=BetaTubeResponse)
+async def create_empty_tube(
+    payload: BetaTubeCreateRequest,
+    user: APIUser = Depends(require_external_write),
+    idempotency_key: str | None = Header(None, alias="Idempotency-Key"),
+):
+    service = BetaLabService(app_username=user.email)
+    try:
+        return service.create_empty_tube(
+            payload=payload,
+            idempotency_key=idempotency_key,
+        )
+    except ValueError as exc:
+        raise HTTPException(
+            status_code=_status_for_value_error(exc), detail=str(exc)
+        ) from exc
+    except Exception as exc:
+        logger.exception("Failed creating empty Bloom tube")
+        raise HTTPException(status_code=500, detail=str(exc)) from exc
+    finally:
+        service.close()
+
+
+@router.patch("/tubes/{container_euid}", response_model=BetaTubeResponse)
+async def update_tube(
+    container_euid: str,
+    payload: BetaTubeUpdateRequest,
+    user: APIUser = Depends(require_external_write),
+):
+    service = BetaLabService(app_username=user.email)
+    try:
+        return service.update_tube(
+            container_euid=container_euid,
+            payload=payload,
+        )
+    except ValueError as exc:
+        raise HTTPException(
+            status_code=_status_for_value_error(exc), detail=str(exc)
+        ) from exc
+    except Exception as exc:
+        logger.exception("Failed updating Bloom tube")
+        raise HTTPException(status_code=500, detail=str(exc)) from exc
+    finally:
+        service.close()
+
+
+@router.patch("/specimens/{specimen_euid}", response_model=BetaMaterialResponse)
+async def update_specimen(
+    specimen_euid: str,
+    payload: BetaSpecimenUpdateRequest,
+    user: APIUser = Depends(require_external_write),
+):
+    service = BetaLabService(app_username=user.email)
+    try:
+        return service.update_specimen(
+            specimen_euid=specimen_euid,
+            payload=payload,
+        )
+    except ValueError as exc:
+        raise HTTPException(
+            status_code=_status_for_value_error(exc), detail=str(exc)
+        ) from exc
+    except Exception as exc:
+        logger.exception("Failed updating Bloom specimen")
+        raise HTTPException(status_code=500, detail=str(exc)) from exc
+    finally:
+        service.close()
+
+
 @router.post(
     "/queues/{queue_name}/items/{material_euid}",
     response_model=BetaQueueTransitionResponse,

bloom_lims/domain/beta_actions.py

@@ -23,6 +23,18 @@
         "name": "Register Accepted Material",
         "description": "Creates accepted Bloom beta material and links Atlas process-item references.",
     },
+    "create_empty_tube": {
+        "name": "Create Empty Tube",
+        "description": "Creates a Bloom beta tube/container with Atlas linkage references.",
+    },
+    "update_tube": {
+        "name": "Update Tube",
+        "description": "Updates a Bloom beta tube/container status and Atlas linkage references.",
+    },
+    "update_specimen": {
+        "name": "Update Specimen",
+        "description": "Updates Bloom beta specimen Atlas collection-event reference metadata.",
+    },
     "move_material_to_queue": {
         "name": "Move Material To Queue",
         "description": "Moves Bloom beta material into a canonical beta queue.",