Fixes for posting metadata in the right order

Author: stephen-riggs

src/murfey/client/contexts/tomo_metadata.py

@@ -55,7 +55,7 @@ def post_transfer(
             with open(transferred_file, "r") as session_xml:
                 session_data = xmltodict.parse(session_xml.read())
 
-            windows_path = session_data["TomographySession"]["AtlasId"]["#text"]
+            windows_path = session_data["TomographySession"]["AtlasId"]
             logger.info(f"Windows path to atlas metadata found: {windows_path}")
             visit_index = windows_path.split("\\").index(environment.visit)
             partial_path = "/".join(windows_path.split("\\")[visit_index + 1 :])
@@ -97,28 +97,27 @@ def post_transfer(
             else:
                 logger.warning(f"Sample could not be identified for {transferred_file}")
                 return
-            if source:
-                environment.samples[source] = SampleInfo(
-                    atlas=Path(partial_path), sample=sample
-                )
-                url = f"{str(environment.url.geturl())}{url_path_for('workflow.router', 'register_dc_group', visit_name=environment.visit, session_id=environment.murfey_session)}"
-                dcg_tag = "/".join(
-                    p for p in transferred_file.parent.parts if p != environment.visit
-                )
-                dcg_data = {
-                    "experiment_type": "tomo",
-                    "experiment_type_id": 36,
-                    "tag": dcg_tag,
-                    "atlas": str(
-                        _atlas_destination(environment, source, transferred_file)
-                        / environment.samples[source].atlas.parent
-                        / atlas_xml_path.with_suffix(".jpg").name
-                    ),
-                    "sample": environment.samples[source].sample,
-                    "atlas_pixel_size": atlas_pixel_size,
-                    "atlas_binning": atlas_binning,
-                }
-                capture_post(url, json=dcg_data)
+            environment.samples[source] = SampleInfo(
+                atlas=Path(partial_path), sample=sample
+            )
+            url = f"{str(environment.url.geturl())}{url_path_for('workflow.router', 'register_dc_group', visit_name=environment.visit, session_id=environment.murfey_session)}"
+            dcg_tag = "/".join(
+                p for p in transferred_file.parent.parts if p != environment.visit
+            ).replace("//", "/")
+            dcg_data = {
+                "experiment_type": "tomo",
+                "experiment_type_id": 36,
+                "tag": dcg_tag,
+                "atlas": str(
+                    _atlas_destination(environment, source, transferred_file)
+                    / environment.samples[source].atlas.parent
+                    / atlas_xml_path.with_suffix(".jpg").name
+                ),
+                "sample": environment.samples[source].sample,
+                "atlas_pixel_size": atlas_pixel_size,
+                "atlas_binning": atlas_binning,
+            }
+            capture_post(url, json=dcg_data)
 
         elif transferred_file.name == "SearchMap.xml" and environment:
             logger.info("Tomography session search map xml found")

src/murfey/server/api/workflow.py

@@ -108,6 +108,9 @@ def register_dc_group(
         dcg_murfey[0].atlas_pixel_size = (
             dcg_params.atlas_pixel_size or dcg_murfey[0].atlas_pixel_size
         )
+        dcg_murfey[0].atlas_binning = (
+            dcg_params.atlas_binning or dcg_murfey[0].atlas_binning
+        )
 
         if _transport_object:
             if dcg_murfey[0].atlas_id is not None:
@@ -148,6 +151,7 @@ def register_dc_group(
             "atlas": dcg_params.atlas,
             "sample": dcg_params.sample,
             "atlas_pixel_size": dcg_params.atlas_pixel_size,
+            "atlas_binning": dcg_params.atlas_binning,
         }
 
         if _transport_object:

src/murfey/util/tomo_metadata.py

@@ -95,7 +95,8 @@ def register_search_map_in_database(
         search_map.width = search_map_params.width or search_map.width
         if _transport_object:
             _transport_object.do_update_search_map(search_map.id, search_map_params)
-    except Exception:
+    except Exception as e:
+        logger.info(f"Registering new search map due to {e}", exc_info=True)
         if _transport_object:
             sm_ispyb_response = _transport_object.do_insert_search_map(
                 dcg.atlas_id, search_map_params
@@ -140,16 +141,13 @@ def register_search_map_in_database(
             height=search_map_params.height,
             width=search_map_params.width,
         )
-    murfey_db.add(search_map)
-    murfey_db.commit()
 
     murfey_session = murfey_db.exec(
         select(MurfeySession).where(MurfeySession.id == session_id)
     ).one()
     machine_config = get_machine_config(instrument_name=murfey_session.instrument_name)[
         murfey_session.instrument_name
     ]
-
     if all(
         [
             search_map.reference_matrix_m11,
@@ -209,15 +207,22 @@ def register_search_map_in_database(
         search_map_params.width_on_atlas = int(
             search_map.width * search_map.pixel_size / dcg.atlas_pixel_size
         )
-        search_map_params.x_location = corrected_vector[0] / dcg.atlas_pixel_size + 2003
-        search_map_params.y_location = corrected_vector[1] / dcg.atlas_pixel_size + 2003
+        search_map_params.x_location = float(
+            corrected_vector[0] / dcg.atlas_pixel_size + 2003
+        )
+        search_map_params.y_location = float(
+            corrected_vector[1] / dcg.atlas_pixel_size + 2003
+        )
         search_map.x_location = search_map_params.x_location
         search_map.y_location = search_map_params.y_location
         if _transport_object:
             _transport_object.do_update_search_map(search_map.id, search_map_params)
     else:
         logger.info(
-            f"Unable to register search map {sanitise(search_map_name)} position yet"
+            f"Unable to register search map {sanitise(search_map_name)} position yet: "
+            f"stage {search_map_params.x_stage_position}, "
+            f"width {search_map_params.width}, "
+            f"atlas pixel size {dcg.atlas_pixel_size}"
         )
     murfey_db.add(search_map)
     murfey_db.commit()
@@ -327,16 +332,16 @@ def register_batch_position_in_database(
             search_map.height / 2,
         ]
         tilt_series.x_location = (
-            centre_batch_pixel[0]
-            - BatchPositionParameters.x_beamshift / search_map.pixel_size
+            centre_batch_pixel[0] - batch_parameters.x_beamshift / search_map.pixel_size
         )
         tilt_series.y_location = (
-            centre_batch_pixel[1]
-            - BatchPositionParameters.y_beamshift / search_map.pixel_size
+            centre_batch_pixel[1] - batch_parameters.y_beamshift / search_map.pixel_size
         )
     else:
         logger.warning(
-            f"No search map information available to register position of {sanitise(batch_name)}"
+            f"Incomplete search map for position of {sanitise(batch_name)}: "
+            f"stage {search_map.x_stage_position}, "
+            f"width {search_map.width}, "
         )
     murfey_db.add(tilt_series)
     murfey_db.commit()