diff --git a/src/murfey/server/api/workflow.py b/src/murfey/server/api/workflow.py index 6488e2029..467989a85 100644 --- a/src/murfey/server/api/workflow.py +++ b/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"], diff --git a/src/murfey/server/feedback.py b/src/murfey/server/feedback.py index 338fc3dfe..c6331b829 100644 --- a/src/murfey/server/feedback.py +++ b/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"], diff --git a/src/murfey/util/config.py b/src/murfey/util/config.py index 80912f80e..fcf7ca243 100644 --- a/src/murfey/util/config.py +++ b/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 = "" diff --git a/src/murfey/workflows/spa/flush_spa_preprocess.py b/src/murfey/workflows/spa/flush_spa_preprocess.py index d52c18c27..e90a74bc1 100644 --- a/src/murfey/workflows/spa/flush_spa_preprocess.py +++ b/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,