Fixes for SmartEM integration (#777)

A few things that came up in testing:

- Atlas storage folder needs to be set to the destination so it is visible from the server
- A DCG tag needs to be used to identify the correct data collection group so that the SmartEM UUID for the grid can be retrieved

Author: d-j-hatton

src/murfey/client/contexts/atlas.py

@@ -60,7 +60,14 @@ def post_transfer_serialem(
                     data={
                         "name": transferred_file.stem,
                         "acquisition_uuid": environment.acquisition_uuid,
-                        "storage_folder": str(source),
+                        "storage_folder": str(
+                            _atlas_destination(
+                                environment,
+                                source,
+                                Path(self._machine_config.get("rsync_basepath", "")),
+                            )
+                            / "atlas"
+                        ),
                     },
                 )
 

src/murfey/client/contexts/spa_metadata.py

@@ -164,6 +164,7 @@ def post_transfer(
                                 "name": f"{environment.visit}-sample-{environment.samples[images_disc].sample}",
                                 "acquisition_uuid": environment.acquisition_uuid,
                                 "register_grid": True,
+                                "tag": dcg_tag,
                             },
                         )
 

src/murfey/server/api/session_control.py

@@ -362,6 +362,7 @@ class AtlasRegistration(BaseModel):
     acquisition_uuid: str
     storage_folder: str = ""
     register_grid: bool = False
+    tag: str = ""
 
 
 @spa_router.post("/sessions/{session_id}/register_atlas")
@@ -379,14 +380,22 @@ def register_atlas(
             smartem_client = SmartEMAPIClient(
                 base_url=machine_config.smartem_api_url, logger=logger
             )
-            possible_grids = smartem_client.get_acquisition_grids(
-                atlas_registration_data.acquisition_uuid
-            )
             grid_uuid = None
-            for grid in possible_grids:
-                if grid.name == atlas_registration_data.name.replace("_atlas", ""):
-                    grid_uuid = grid.uuid
-                    break
+            if atlas_registration_data.tag:
+                dcg = murfey_db.exec(
+                    select(DataCollectionGroup)
+                    .where(DataCollectionGroup.session_id == session_id)
+                    .where(DataCollectionGroup.tag == atlas_registration_data.tag)
+                ).one_or_none()
+                grid_uuid = dcg.smartem_grid_uuid
+            else:
+                possible_grids = smartem_client.get_acquisition_grids(
+                    atlas_registration_data.acquisition_uuid
+                )
+                for grid in possible_grids:
+                    if grid.name == atlas_registration_data.name.replace("_atlas", ""):
+                        grid_uuid = grid.uuid
+                        break
             if grid_uuid is not None:
                 atlas_data = AtlasData(
                     id=atlas_registration_data.name,