Rewrote 'tiff_to_stack' function to work with Zocalo wrapper

Author: tieneupin

src/murfey/server/api/clem.py

@@ -643,7 +643,7 @@ def lif_to_stack(
     )
 
     # Use entry point if found
-    if len(murfey_workflows) == 1:
+    if murfey_workflows:
 
         # Get instrument name from the database
         # This is needed in order to load the correct config file
@@ -673,6 +673,7 @@ def lif_to_stack(
 def tiff_to_stack(
     session_id: int,  # Used by the decorator
     tiff_info: TIFFSeriesInfo,
+    db: Session = murfey_db,
 ):
     # Get command line entry point
     murfey_workflows = entry_points().select(
@@ -681,14 +682,26 @@ def tiff_to_stack(
 
     # Use entry point if found
     if murfey_workflows:
+
+        # Load instrument name from database
+        row: MurfeySession = db.exec(
+            select(MurfeySession).where(MurfeySession.id == session_id)
+        ).one()
+        instrument_name = row.instrument_name
+
+        # Pass arguments to correct workflow
         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",
+            session_id=session_id,
+            instrument_name=instrument_name,
             metadata=tiff_info.series_metadata,
             messenger=_transport_object,
         )
+        return True
+
     # Raise error if Murfey workflow not found
     else:
         raise RuntimeError("The relevant Murfey workflow was not found")

src/murfey/workflows/clem/tiff_to_stack.py

@@ -6,47 +6,61 @@
 from pathlib import Path
 from typing import Optional
 
+from murfey.util.config import get_machine_config
+
 try:
     from murfey.server.ispyb import TransportManager  # Session
 except AttributeError:
     pass  # Ignore if ISPyB credentials environment variable not set
 
 
 def zocalo_cluster_request(
-    file: Path,
+    tiff_list: list[Path],
     root_folder: str,
+    session_id: int,
+    instrument_name: str,
     metadata: Optional[Path] = None,
     messenger: Optional[TransportManager] = None,
 ):
     if messenger:
         # Construct path to session directory
-        path_parts = list(file.parts)
-        new_path = []
-        for p in range(len(path_parts)):
-            part = path_parts[p]
-            # Remove leading slash for subsequent rejoining
-            if part == "/":
-                part = ""
-            # Append up to, but not including, root folder
-            if part.lower() == root_folder.lower():
-                break
-            new_path.append(part)
-        session_dir = Path("/".join(new_path))
+        path_parts = list(tiff_list[0].parts)
+        # Replace leading "/" in Unix paths
+        path_parts[0] = "" if path_parts[0] == "/" else path_parts[0]
+        try:
+            # Find the position of the root folder in the list
+            root_index = [p.lower() for p in path_parts].index(root_folder.lower())
+        except ValueError:
+            raise Exception(
+                f"Unable to find the root folder {root_folder!r} in the file path {tiff_list[0]!r}"
+            )
+        # Construct the session and job name
+        session_dir = "/".join(path_parts[:root_index])
 
         # If no metadata file provided, generate path to one
         if metadata is None:
-            series_name = file.stem.split("--")[0]
-            metadata = file.parent / "Metadata" / (series_name + ".xlif")
+            series_name = tiff_list[0].stem.split("--")[0]
+            metadata = tiff_list[0].parent / "Metadata" / (series_name + ".xlif")
+
+        # Load machine config to get the feedback queue
+        machine_config = get_machine_config()
+        feedback_queue = machine_config[instrument_name].feedback_queue
 
         messenger.send(
             "processing_recipe",
             {
                 "recipes": ["clem-tiff-to-stack"],
                 "parameters": {
-                    "session_dir": str(session_dir),
-                    "tiff_path": str(file),
-                    "root_dir": root_folder,
+                    # Job parameters
+                    "tiff_list": tiff_list,
+                    "root_folder": root_folder,
                     "metadata": str(metadata),
+                    "tiff_file": "null",
+                    # Other recipe parameters
+                    "session_dir": str(session_dir),
+                    "session_id": session_id,
+                    "job_name": series_name,
+                    "feedback_queue": feedback_queue,
                 },
             },
             new_connection=True,