Added function to submit cluster align-and-merge processing request to cryoemservices

Author: tieneupin

src/murfey/workflows/clem/align_and_merge.py

@@ -3,6 +3,77 @@
 from cryoemservices.
 """
 
+from __future__ import annotations
 
-def submit_cluster_request():
+from pathlib import Path
+from typing import Literal, 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 submit_cluster_request(
+    # Session parameters
+    session_id: int,
+    instrument_name: str,
+    # Processing parameters
+    series_name: str,
+    images: list[Path],
+    metadata: Path,
+    # Optional processing parameters
+    align_self: Optional[str] = None,
+    flatten: Optional[Literal["min", "max", "mean"]] = "mean",
+    align_across: Optional[str] = None,
+    # Optional session parameters
+    messenger: Optional[TransportManager] = None,
+):
+    if not messenger:
+        raise Exception("Unable to find transport manager")
+
+    # Load feedback queue
+    machine_config = get_machine_config()[instrument_name]
+    feedback_queue: str = machine_config.feedback_queue
+
+    # Work out session directory from file path
+    processed_folder = machine_config.processed_directory_name
+    if not images:
+        raise ValueError(f"No image files have been provided for {series_name!r}")
+    reference_file = images[0]
+    path_parts = list(reference_file.parts)
+    path_parts[0] = "" if path_parts[0] == "/" else path_parts[0]
+    try:
+        root_index = path_parts.index(processed_folder)
+    except ValueError:
+        raise ValueError(
+            f"The processed directory {processed_folder!r} could not be found in the "
+            f"file path for {str(reference_file)!r}"
+        )
+    session_dir = Path("/".join(path_parts[:root_index]))
+
+    # Submit message to cryoemservices
+    messenger.send(
+        "processing_recipe",
+        {
+            "recipes": ["clem-align-and-merge"],
+            "parameters": {
+                # Job parameters
+                "series_name": series_name,
+                "images": [str(file) for file in images],
+                "metadata": str(metadata),
+                "align_self": ("null" if align_self is None else align_self),
+                "flatten": ("null" if flatten is None else flatten),
+                "align_across": ("null" if align_across is None else align_across),
+                # Other recipe parameters
+                "session_dir": str(session_dir),
+                "session_id": session_id,
+                "job_name": series_name,
+                "feedback_queue": feedback_queue,
+            },
+        },
+        new_connection=True,
+    )
     return True