Merge branch 'main' into safe-atlas-xml-search

Author: stephen-riggs

.github/workflows/ci.yml

@@ -69,7 +69,7 @@ jobs:
           docker container list -a
 
       - name: Get ISPyB database
-        uses: actions/download-artifact@v6
+        uses: actions/download-artifact@v7
         with:
           name: database
           path: database/

.github/workflows/publish-version.yml

@@ -78,7 +78,7 @@ jobs:
       - name: Build python package
         run: python3 -m build
       - name: Store built package artifact
-        uses: actions/upload-artifact@v5
+        uses: actions/upload-artifact@v6
         with:
           name: package-distributions
           path: dist/
@@ -100,7 +100,7 @@ jobs:
 
     steps:
       - name: Download all the dists
-        uses: actions/download-artifact@v6
+        uses: actions/download-artifact@v7
         with:
           name: package-distributions
           path: dist/
@@ -123,7 +123,7 @@ jobs:
 
     steps:
       - name: Download all the dists
-        uses: actions/download-artifact@v6
+        uses: actions/download-artifact@v7
         with:
           name: package-distributions
           path: dist/

.github/workflows/test.yml

@@ -60,7 +60,7 @@ jobs:
           mkdir database
           wget -t 3 --waitretry=20 https://github.com/DiamondLightSource/ispyb-database/releases/download/v${{ env.ISPYB_DATABASE_SCHEMA }}/ispyb-database-${{ env.ISPYB_DATABASE_SCHEMA }}.tar.gz -O database/ispyb-database.tar.gz
       - name: Store database artifact
-        uses: actions/upload-artifact@v5
+        uses: actions/upload-artifact@v6
         with:
           name: database
           path: database/

src/murfey/client/context.py

@@ -67,9 +67,9 @@ def ensure_dcg_exists(
 
     if not session_file.is_file():
         logger.warning(f"Cannot find session file {str(session_file)}")
-        dcg_tag = (
-            str(metadata_source).replace(f"/{environment.visit}", "").replace("//", "/")
-        )
+        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,
@@ -97,9 +97,9 @@ def ensure_dcg_exists(
             f"Looking for atlas XML file in metadata directory {str((source_visit_dir / partial_path).parent)}"
         )
 
-        dcg_tag = (
-            str(metadata_source).replace(f"/{environment.visit}", "").replace("//", "/")
-        )
+        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"):

src/murfey/server/feedback.py

@@ -1148,16 +1148,18 @@ def _resize_intial_model(
         logger.info(
             f"Initial model rescaling finished with code {comp_proc.returncode}"
         )
+        if comp_proc.returncode:
+            logger.error(
+                f"Resizing initial model {input_path} failed"
+                f"\n {comp_proc.stdout} \n {comp_proc.stderr}"
+            )
+            raise RuntimeError(f"Resizing initial model {input_path} failed")
         with mrcfile.open(output_path) as rescaled_mrc:
             rescaled_mrc.header.cella = (
                 downscaled_pixel_size,
                 downscaled_pixel_size,
                 downscaled_pixel_size,
             )
-        if comp_proc.returncode:
-            logger.error(
-                f"Resizing initial model {input_path} failed \n {comp_proc.stdout}"
-            )
     return None