Sanitised file paths in logs

Author: tieneupin

src/murfey/server/api/session_control.py

@@ -352,7 +352,9 @@ def get_foil_hole(
 def make_atlas_jpg(
     session_id: MurfeySessionID, atlas_mrc: StringOfPathModel, db=murfey_db
 ):
-    logger.debug(f"Received request to create JPG image of atlas {atlas_mrc.path!r}")
+    logger.debug(
+        f"Received request to create JPG image of atlas {sanitise(atlas_mrc.path)!r}"
+    )
     session = db.exec(select(Session).where(Session.id == session_id)).one()
     return atlas_jpg_from_mrc(
         session.instrument_name, session.visit, Path(atlas_mrc.path)

src/murfey/workflows/spa/atlas.py

@@ -5,13 +5,16 @@
 import PIL.Image
 from werkzeug.utils import secure_filename
 
+from murfey.util import sanitise
 from murfey.util.config import get_machine_config
 
 logger = logging.getLogger("murfey.workflows.spa.atlas")
 
 
 def atlas_jpg_from_mrc(instrument_name: str, visit_name: str, atlas_mrc: Path):
-    logger.debug(f"Starting workflow to create JPG image of atlas {atlas_mrc}")
+    logger.debug(
+        f"Starting workflow to create JPG image of atlas {sanitise(str(atlas_mrc))}"
+    )
     with mrcfile.open(atlas_mrc) as mrc:
         data = mrc.data