Corrected database call in 'validate_and_sanitise' function; simplified LIF file registration and processing parameters; corrected 'murfey_workflow' call

Author: tieneupin

src/murfey/server/api/clem.py

@@ -23,13 +23,13 @@
     CLEMTIFFFile,
 )
 from murfey.util.db import Session as MurfeySession
-from murfey.util.models import LifFileInfo, TiffSeriesInfo
+from murfey.util.models import TiffSeriesInfo
 
 # Use backport from importlib_metadata for Python <3.10
 if sys.version_info.major == 3 and sys.version_info.minor < 10:
-    from importlib_metadata import entry_points
+    from importlib_metadata import EntryPoint, entry_points
 else:
-    from importlib.metadata import entry_points
+    from importlib.metadata import EntryPoint, entry_points
 
 # Set up logger
 logger = getLogger("murfey.server.api.clem")
@@ -52,21 +52,29 @@
 """
 
 
-def validate_and_sanitise(file: Path, session_id: int) -> Path:
+def validate_and_sanitise(
+    file: Path,
+    session_id: int,
+    db: Session,
+) -> Path:
     """
     Performs validation and sanitisation on the incoming file paths, ensuring that
     no forbidden characters are present and that the the path points only to allowed
     sections of the file server.
 
     Returns the file path as a sanitised string that can be converted into a Path
     object again.
+
+    NOTE: Due to the instrument name query, 'db' now needs to be passed as an
+    explicit variable to this function from within a FastAPI endpoint, as using the
+    instance that was imported directly won't load it in the correct state.
     """
 
     # Resolve symlinks and directory changes to get full file path
     full_path = path.normpath(path.realpath(file))
 
     instrument_name = (
-        murfey_db.exec(select(MurfeySession).where(MurfeySession.id == session_id))
+        db.exec(select(MurfeySession).where(MurfeySession.id == session_id))
         .one()
         .instrument_name
     )
@@ -144,7 +152,7 @@ def get_db_entry(
     # Validate file path if provided
     if file_path is not None:
         try:
-            file_path = validate_and_sanitise(file_path, session_id)
+            file_path = validate_and_sanitise(file_path, session_id, db)
         except Exception:
             raise Exception
 
@@ -220,7 +228,7 @@ def register_lif_file(
     # Add metadata information if provided
     if master_metadata is not None:
         try:
-            master_metadata = validate_and_sanitise(master_metadata, session_id)
+            master_metadata = validate_and_sanitise(master_metadata, session_id, db)
             clem_lif_file.master_metadata = str(master_metadata)
         except Exception:
             logger.warning(traceback.format_exc())
@@ -621,21 +629,23 @@ def register_image_stack(
 @router.post("/sessions/{session_id}/lif_to_stack")  # API posts to this URL
 def lif_to_stack(
     session_id: int,  # Used by the decorator
-    lif_info: LifFileInfo,
+    lif_file: Path,
 ):
     # Get command line entry point
     murfey_workflows = entry_points().select(
         group="murfey.workflows", name="lif_to_stack"
     )
 
     # Use entry point if found
-    if murfey_workflows:
-        murfey_workflows[0].load()(
+    if len(murfey_workflows) == 1:
+        workflow: EntryPoint = list(murfey_workflows)[0]
+        workflow.load()(
             # Match the arguments found in murfey.workflows.lif_to_stack
-            file=lif_info.name,
+            file=lif_file,
             root_folder="images",
             messenger=_transport_object,
         )
+        return True
     # Raise error if Murfey workflow not found
     else:
         raise RuntimeError("The relevant Murfey workflow was not found")
@@ -653,7 +663,8 @@ def tiff_to_stack(
 
     # Use entry point if found
     if murfey_workflows:
-        murfey_workflows[0].load()(
+        workflow: EntryPoint = list(murfey_workflows)[0]
+        workflow.load()(
             # Match the arguments found in murfey.workflows.tiff_to_stack
             file=tiff_info.tiff_files[0],  # Pass it only one file from the list
             root_folder="images",