Do not make processed directories in murfey (#807)

Author: stephen-riggs

src/murfey/server/api/workflow.py

@@ -1,5 +1,4 @@
 import asyncio
-import os
 from datetime import datetime
 from logging import getLogger
 from pathlib import Path
@@ -609,10 +608,6 @@ async def request_spa_preprocessing(
 
         db.close()
 
-        if not mrc_out.parent.exists():
-            mrc_out_dir = Path(secure_filename(str(mrc_out))).parent
-            mrc_out_dir.mkdir(parents=True, exist_ok=True)
-            os.chmod(mrc_out_dir, mode=machine_config.mkdir_chmod)
         recipe_name = machine_config.recipes.get(
             "em-spa-preprocess", "em-spa-preprocess"
         )
@@ -837,9 +832,6 @@ async def request_tomography_preprocessing(
         dcid = data_collection[0][1].id
         appid = data_collection[0][3].id
         murfey_ids = _murfey_id(appid, db, number=1, close=False)
-        if not mrc_out.parent.exists():
-            mrc_out.parent.mkdir(parents=True, exist_ok=True)
-            os.chmod(mrc_out.parent, mode=machine_config.mkdir_chmod)
 
         session_processing_parameters = db.exec(
             select(SessionProcessingParameters).where(
@@ -990,9 +982,6 @@ def register_completed_tilt_series(
                 / "tomograms"
                 / f"{ts.tag}_stack.mrc"
             )
-            if not stack_file.parent.exists():
-                stack_file.parent.mkdir(parents=True)
-                os.chmod(stack_file.parent, mode=machine_config.mkdir_chmod)
             tilt_offset = midpoint([float(get_angle(t)) for t in tilts])
             zocalo_message = {
                 "recipes": ["em-tomo-align"],

src/murfey/server/feedback.py

@@ -9,7 +9,6 @@
 
 import logging
 import math
-import os
 import subprocess
 import time
 from datetime import datetime
@@ -1409,10 +1408,6 @@ def _flush_tomography_preprocessing(message: dict, _db):
         detached_ids = [c.id for c in collected_ids]
 
         murfey_ids = _murfey_id(detached_ids[3], _db, number=1, close=False)
-        p = Path(f.mrc_out)
-        if not p.parent.exists():
-            p.parent.mkdir(parents=True)
-            os.chmod(p.parent, mode=machine_config.mkdir_chmod)
         movie = db.Movie(
             murfey_id=murfey_ids[0],
             data_collection_id=detached_ids[1],
@@ -1886,9 +1881,6 @@ def feedback_callback(header: dict, message: dict, _db=murfey_db) -> None:
                     / "tomograms"
                     / f"{relevant_tilt_series.tag}_stack.mrc"
                 )
-                if not stack_file.parent.exists():
-                    stack_file.parent.mkdir(parents=True)
-                    os.chmod(stack_file.parent, machine_config.mkdir_chmod)
                 tilt_offset = midpoint([float(get_angle(t)) for t in tilts])
                 zocalo_message = {
                     "recipes": ["em-tomo-align"],

src/murfey/util/config.py

@@ -59,7 +59,7 @@ class MachineConfig(BaseModel):  # type: ignore
         "directories": [],
         "files": [],
     }
-    mkdir_chmod: int = 0o750
+    mkdir_chmod: int = 0o2750
 
     # Rsync setup
     rsync_url: str = ""

src/murfey/workflows/spa/flush_spa_preprocess.py

@@ -1,5 +1,4 @@
 import logging
-import os
 from pathlib import Path
 from typing import Optional
 
@@ -544,11 +543,7 @@ def flush_spa_preprocess(message: dict, murfey_db: Session) -> dict[str, bool]:
             )
             foil_hole_id = None
 
-        mrcp = Path(f.mrc_out)
         ppath = Path(f.file_path)
-        if not mrcp.parent.exists():
-            mrcp.parent.mkdir(parents=True)
-            os.chmod(mrcp.parent, mode=machine_config.mkdir_chmod)
         movie = Movie(
             murfey_id=murfey_ids[2 * i],
             data_collection_id=collected_ids[1].id,