The client needs to read metadata from the original location, not the destination

Author: d-j-hatton

src/murfey/client/contexts/spa_metadata.py

@@ -61,23 +61,18 @@ def post_transfer(
             ]["#text"]
             visit_index = windows_path.split("\\").index(environment.visit)
             partial_path = "/".join(windows_path.split("\\")[visit_index + 1 :])
-            visitless_path = Path(
-                str(transferred_file).replace(f"/{environment.visit}", "")
-            )
-            visit_index_of_transferred_file = transferred_file.parts.index(
-                environment.visit
-            )
+
+            source = _get_source(transferred_file, environment)
+            if not source:
+                logger.warning(
+                    f"Source could not be indentified for {str(transferred_file)}"
+                )
+                return
+
+            source_visit_dir = source.parent
+
             atlas_xml_path = list(
-                (
-                    Path(
-                        "/".join(
-                            transferred_file.parts[
-                                : visit_index_of_transferred_file + 1
-                            ]
-                        )
-                    )
-                    / partial_path
-                ).parent.glob("Atlas_*.xml")
+                (source_visit_dir / partial_path).parent.glob("Atlas_*.xml")
             )[0]
             with open(atlas_xml_path, "rb") as atlas_xml:
                 atlas_xml_data = xmltodict.parse(atlas_xml)
@@ -88,10 +83,6 @@ def post_transfer(
             # need to calculate the pixel size of the downscaled image
             atlas_pixel_size = atlas_original_pixel_size * 7.8
 
-            source = _get_source(
-                visitless_path.parent / "Images-Disc1" / visitless_path.name,
-                environment,
-            )
             sample = None
             for p in partial_path.split("/"):
                 if p.startswith("Sample"):
@@ -126,8 +117,7 @@ def post_transfer(
                 )
                 if registered_grid_squares:
                     gs_pix_positions = _get_grid_square_atlas_positions(
-                        _atlas_destination(environment, source, transferred_file)
-                        / environment.samples[source].atlas
+                        source_visit_dir / partial_path
                     )
                     for gs in registered_grid_squares:
                         pos_data = gs_pix_positions.get(str(gs["name"]))