Use safe placholder atlas name if atlas XML not found (#734)

The search for an atlas XML file currently fails if no search results were returned for the atlas. This PR adjusts that logic so that it proceeds with the post to the backend server with the minimum amount of information present and safe-ish placeholder name for the atlas.

---------

Co-authored-by: yxd92326 <stephen.riggs@diamond.ac.uk>

Author: tieneupin

pyproject.toml

@@ -31,7 +31,7 @@ classifiers = [
 dependencies = [
     "aiohttp",
     "defusedxml", # For safely parsing XML files
-    "fastapi[standard-no-fastapi-cloud-cli]>=0.116.0",
+    "fastapi[standard-no-fastapi-cloud-cli]>=0.116.0,<0.128.1",
     "pydantic>=2",
     "pydantic-settings",
     "python-jose",

src/murfey/client/context.py

@@ -96,20 +96,10 @@ def ensure_dcg_exists(
         logger.info(
             f"Looking for atlas XML file in metadata directory {str((source_visit_dir / partial_path).parent)}"
         )
-        atlas_xml_path = list(
-            (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:
-            atlas_xml_data = xmltodict.parse(atlas_xml)
-            atlas_original_pixel_size = float(
-                atlas_xml_data["MicroscopeImage"]["SpatialScale"]["pixelSize"]["x"][
-                    "numericValue"
-                ]
-            )
-        # need to calculate the pixel size of the downscaled image
-        atlas_pixel_size = atlas_original_pixel_size * 7.8
-        logger.info(f"Atlas image pixel size determined to be {atlas_pixel_size}")
+
+        dcg_tag = "/".join(
+            [part for part in metadata_source.parts if part != environment.visit]
+        ).replace("//", "/")
 
         for p in partial_path.split("/"):
             if p.startswith("Sample"):
@@ -122,20 +112,39 @@ def ensure_dcg_exists(
             atlas=Path(partial_path), sample=sample
         )
 
-        dcg_tag = "/".join(
-            [part for part in metadata_source.parts if part != environment.visit]
-        ).replace("//", "/")
-        dcg_data = {
-            "experiment_type_id": experiment_type_id,
-            "tag": dcg_tag,
-            "atlas": str(
-                _atlas_destination(environment, session_file.parent, token)
-                / environment.samples[metadata_source].atlas.parent
-                / atlas_xml_path.with_suffix(".jpg").name
-            ).replace("//", "/"),
-            "sample": environment.samples[metadata_source].sample,
-            "atlas_pixel_size": atlas_pixel_size,
-        }
+        if atlas_xml_search := list(
+            (source_visit_dir / partial_path).parent.glob("Atlas_*.xml")
+        ):
+            atlas_xml_path = atlas_xml_search[0]
+            logger.info(f"Atlas XML path {str(atlas_xml_path)} found")
+            with open(atlas_xml_path, "rb") as atlas_xml:
+                atlas_xml_data = xmltodict.parse(atlas_xml)
+                atlas_original_pixel_size = float(
+                    atlas_xml_data["MicroscopeImage"]["SpatialScale"]["pixelSize"]["x"][
+                        "numericValue"
+                    ]
+                )
+            # need to calculate the pixel size of the downscaled image
+            atlas_pixel_size = atlas_original_pixel_size * 7.8
+            logger.info(f"Atlas image pixel size determined to be {atlas_pixel_size}")
+
+            dcg_data = {
+                "experiment_type_id": experiment_type_id,
+                "tag": dcg_tag,
+                "atlas": str(
+                    _atlas_destination(environment, session_file.parent, token)
+                    / environment.samples[metadata_source].atlas.parent
+                    / atlas_xml_path.with_suffix(".jpg").name
+                ).replace("//", "/"),
+                "sample": environment.samples[metadata_source].sample,
+                "atlas_pixel_size": atlas_pixel_size,
+            }
+        else:
+            dcg_data = {
+                "experiment_type_id": experiment_type_id,
+                "tag": dcg_tag,
+                "sample": environment.samples[metadata_source].sample,
+            }
     capture_post(
         base_url=str(environment.url.geturl()),
         router_name="workflow.router",