Make those a common function

Author: stephen-riggs

src/murfey/server/api/workflow.py

@@ -58,7 +58,7 @@
     TiltSeries,
 )
 from murfey.util.models import ProcessingParametersSPA, ProcessingParametersTomo
-from murfey.util.processing_params import default_spa_parameters
+from murfey.util.processing_params import default_spa_parameters, motion_corrected_mrc
 from murfey.util.tomo import midpoint
 
 logger = getLogger("murfey.server.api.workflow")
@@ -365,26 +365,7 @@ async def request_spa_preprocessing(
     machine_config = get_machine_config(instrument_name=instrument_name)[
         instrument_name
     ]
-    parts = [secure_filename(p) for p in Path(proc_file.path).parts]
-    visit_idx = parts.index(visit_name)
-    core = Path("/") / Path(*parts[: visit_idx + 1])
-    ppath = Path("/") / Path(*parts)
-    if machine_config.process_multiple_datasets:
-        sub_dataset = ppath.relative_to(core).parts[0]
-    else:
-        sub_dataset = ""
-    extra_path = machine_config.processed_extra_directory
-    mrc_out = (
-        core
-        / machine_config.processed_directory_name
-        / sub_dataset
-        / extra_path
-        / "MotionCorr"
-        / "job002"
-        / "Movies"
-        / ppath.parent.relative_to(core / sub_dataset)
-        / str(ppath.stem + "_motion_corrected.mrc")
-    )
+    mrc_out = motion_corrected_mrc(Path(proc_file.path), visit_name, machine_config)
     try:
         collected_ids = db.exec(
             select(DataCollectionGroup, DataCollection, ProcessingJob, AutoProcProgram)
@@ -488,7 +469,8 @@ async def request_spa_preprocessing(
             _transport_object.send("processing_recipe", zocalo_message)
         else:
             logger.error(
-                f"Pe-processing was requested for {sanitise(ppath.name)} but no Zocalo transport object was found"
+                f"Pre-processing was requested for {sanitise(Path(proc_file.path).name)} "
+                "but no Zocalo transport object was found"
             )
             return proc_file
 
@@ -643,26 +625,7 @@ async def request_tomography_preprocessing(
     machine_config = get_machine_config(instrument_name=instrument_name)[
         instrument_name
     ]
-    parts = [secure_filename(p) for p in Path(proc_file.path).parts]
-    visit_idx = parts.index(visit_name)
-    core = Path("/") / Path(*parts[: visit_idx + 1])
-    ppath = Path("/") / Path(*parts)
-    if machine_config.process_multiple_datasets:
-        sub_dataset = ppath.relative_to(core).parts[0]
-    else:
-        sub_dataset = ""
-    extra_path = machine_config.processed_extra_directory
-    mrc_out = (
-        core
-        / machine_config.processed_directory_name
-        / sub_dataset
-        / extra_path
-        / "MotionCorr"
-        / "job002"
-        / "Movies"
-        / str(ppath.stem + "_motion_corrected.mrc")
-    )
-    mrc_out = Path("/".join(secure_filename(p) for p in mrc_out.parts))
+    mrc_out = motion_corrected_mrc(Path(proc_file.path), visit_name, machine_config)
 
     recipe_name = machine_config.recipes.get("em-tomo-preprocess", "em-tomo-preprocess")
 
@@ -733,7 +696,8 @@ async def request_tomography_preprocessing(
             _transport_object.send("processing_recipe", zocalo_message)
         else:
             logger.error(
-                f"Pe-processing was requested for {sanitise(ppath.name)} but no Zocalo transport object was found"
+                f"Pre-processing was requested for {sanitise(Path(proc_file.path).name)} "
+                f"but no Zocalo transport object was found"
             )
             return proc_file
     else:

src/murfey/util/processing_params.py

@@ -1,6 +1,36 @@
+from pathlib import Path
 from typing import Literal, Optional
 
 from pydantic import BaseModel
+from werkzeug.utils import secure_filename
+
+from murfey.util.config import MachineConfig
+
+
+def motion_corrected_mrc(
+    input_movie: Path, visit_name: str, machine_config: MachineConfig
+):
+    parts = [secure_filename(p) for p in input_movie.parts]
+    visit_idx = parts.index(visit_name)
+    core = Path("/") / Path(*parts[: visit_idx + 1])
+    ppath = Path("/") / Path(*parts)
+    if machine_config.process_multiple_datasets:
+        sub_dataset = ppath.relative_to(core).parts[0]
+    else:
+        sub_dataset = ""
+    extra_path = machine_config.processed_extra_directory
+    mrc_out = (
+        core
+        / machine_config.processed_directory_name
+        / sub_dataset
+        / extra_path
+        / "MotionCorr"
+        / "job002"
+        / "Movies"
+        / ppath.parent.relative_to(core / sub_dataset)
+        / str(ppath.stem + "_motion_corrected.mrc")
+    )
+    return Path("/".join(secure_filename(p) for p in mrc_out.parts))
 
 
 class CLEMAlignAndMergeParameters(BaseModel):