Various atlas fixes

Author: stephen-riggs

src/murfey/client/contexts/spa_metadata.py

@@ -117,12 +117,10 @@ def post_transfer(
             source_visit_dir = source.parent
 
             logger.info(
-                f"Looking for atlas XML file in metadata directory {str((source_visit_dir / environment.visit / partial_path).parent)}"
+                f"Looking for atlas XML file in metadata directory {str((source_visit_dir / partial_path).parent)}"
             )
             atlas_xml_path = list(
-                (source_visit_dir / environment.visit / partial_path).parent.glob(
-                    "Atlas_*.xml"
-                )
+                (source_visit_dir / partial_path).parent.glob("Atlas_*.xml")
             )[0]
             logger.info(f"Atlas XML path {str(atlas_xml_path)} found")
             with open(atlas_xml_path, "rb") as atlas_xml:
@@ -150,8 +148,10 @@ def post_transfer(
                     atlas=Path(partial_path), sample=sample
                 )
                 url = f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/register_data_collection_group"
-                dcg_search_dir = "/".join(
-                    p for p in transferred_file.parent.parts if p != environment.visit
+                dcg_search_dir = "/" + "/".join(
+                    p
+                    for p in transferred_file.parent.parts[1:]
+                    if p != environment.visit
                 )
                 dcg_images_dirs = sorted(
                     Path(dcg_search_dir).glob("Images-Disc*"),
@@ -174,7 +174,7 @@ def post_transfer(
                 }
                 capture_post(url, json=dcg_data)
                 gs_pix_positions = get_grid_square_atlas_positions(
-                    source_visit_dir / environment.visit / partial_path
+                    source_visit_dir / partial_path
                 )
                 for gs, pos_data in gs_pix_positions.items():
                     if pos_data:

src/murfey/server/__init__.py

@@ -2569,6 +2569,7 @@ def feedback_callback(header: dict, message: dict) -> None:
                     message["atlas_pixel_size"],
                     message["sample"],
                 )
+                _transport_object.transport.ack(header)
             return None
         elif message["register"] == "data_collection":
             murfey_session_id = message["session_id"]

src/murfey/server/ispyb.py

@@ -213,7 +213,8 @@ def do_update_grid_square(
                         grid_square_parameters.readout_area_x
                         / grid_square_parameters.thumbnail_size_x
                     )
-                grid_square.gridSquareImage = grid_square_parameters.image
+                if grid_square_parameters.image:
+                    grid_square.gridSquareImage = grid_square_parameters.image
                 grid_square.pixelLocationX = (
                     int(grid_square_parameters.x_location / 7.8)
                     if grid_square_parameters.x_location
@@ -296,7 +297,7 @@ def do_insert_foil_hole(
             with Session() as db:
                 db.add(record)
                 db.commit()
-                log.info(f"Created FoilHole {record.gridSquareId}")
+                log.info(f"Created FoilHole {record.foilHoleId}")
                 return {"success": True, "return_value": record.foilHoleId}
         except ispyb.ISPyBException as e:
             log.error(