Make scan directory manager thread safe

src/openflexure_microscope_server/scan_directories.py

@@ -5,9 +5,12 @@ import os
 import re
 import shutil
 import zipfile
+import threading
 
 from pydantic import BaseModel
 
+from openflexure_microscope_server.utilities import requires_lock
+
 IMG_DIR_NAME = "images"
 SCAN_ZERO_PAD_DIGITS = 4
 
@@ -43,6 +46,7 @@ class ScanDirectoryManager:
         self._base_scan_dir = base_scan_dir
         if not os.path.exists(self._base_scan_dir):
             os.makedirs(self._base_scan_dir)
+        self._lock = threading.RLock()
 
     @property
     def base_dir(self) -> str:
@@ -67,6 +71,7 @@ class ScanDirectoryManager:
         """
         return os.path.join(self._base_scan_dir, scan_name, IMG_DIR_NAME)
 
+    @requires_lock
     def get_file_path_from(
         self, scan_name: str, filename: str, check_exists: bool = False
     ) -> Optional[str]:
@@ -81,6 +86,7 @@ class ScanDirectoryManager:
                 return None
         return file_path
 
+    @requires_lock
     def get_file_path_from_img_dir(
         self, scan_name: str, filename: str, check_exists: bool = False
     ) -> Optional[str]:
@@ -106,10 +112,12 @@ class ScanDirectoryManager:
         return self.get_file_path_from_img_dir(scan_name, stitch_fname)
 
     @property
+    @requires_lock
     def all_scans(self) -> list[str]:
         """Return a list of the scan names in the base directory."""
         return [f.name for f in os.scandir(self._base_scan_dir) if f.is_dir()]
 
+    @requires_lock
     def all_scans_info(self) -> list[ScanInfo]:
         """Return a lists of ScanInfo objects for each scan."""
         all_info: list[ScanInfo] = []
@@ -117,6 +125,7 @@ class ScanDirectoryManager:
             all_info.append(ScanDirectory(scan_name, self.base_dir).scan_info())
         return all_info
 
+    @requires_lock
     def _unique_scan_name(self, scan_name: str) -> str:
         """Get the next unique scan name starting with the given name.
 
@@ -146,6 +155,7 @@ class ScanDirectoryManager:
 
         return f"{scan_name}_{scan_num:0{SCAN_ZERO_PAD_DIGITS}d}"
 
+    @requires_lock
     def new_scan_dir(self, scan_name: str) -> "ScanDirectory":
         """Get a unique name for this scan and create a directory for it.
 
@@ -168,10 +178,12 @@ class ScanDirectoryManager:
         os.makedirs(self.img_dir_for(full_scan_name))
         return ScanDirectory(full_scan_name, self.base_dir)
 
+    @requires_lock
     def delete_scan(self, scan_name: str) -> None:
         """Delete a scan."""
         shutil.rmtree(self.path_for(scan_name))
 
+    @requires_lock
     def zip_scan(self, scan_name: str, final_version: bool = False) -> "ScanDirectory":
         """Zips any images from the scan not yet zipped, return full path to zip.
 
@@ -181,6 +193,7 @@ class ScanDirectoryManager:
         """
         return ScanDirectory(scan_name, self.base_dir).zip_files(final_version)
 
+    @requires_lock
     def check_free_disk_space(self, min_space: int = 500000000) -> None:
         """Raise an exception if there is not enough free disk space to continue scanning.
 

src/openflexure_microscope_server/things/smart_scan.py

@@ -717,6 +717,9 @@ class SmartScanThing(lt.Thing):
         This is a wrapper around scan manager's delete_scan that logs to the
         invocation logger id there is a problem.
         """
+        if self._ongoing_scan is not None and scan_name == self._ongoing_scan.name:
+            logger.error("Attempted to delete ongoing scan.")
+            return False
         try:
             self._scan_dir_manager.delete_scan(scan_name)
             return True

src/openflexure_microscope_server/utilities.py

@@ -1,14 +1,19 @@
 """Utility functions and classes."""
 
+from typing import TypeVar, Callable, ParamSpec
 import os
 import re
 from threading import Thread
 import logging
 from importlib.metadata import version
 import tomllib
+from functools import wraps
 
 from pydantic import BaseModel
 
+T = TypeVar("T")
+P = ParamSpec("P")
+
 LOGGER = logging.getLogger(__name__)
 
 REPO_DIR = os.path.dirname(os.path.dirname(os.path.dirname(__file__)))
@@ -18,6 +23,22 @@ COMMIT_REGEX = re.compile(r"[0-9a-f]{40}")
 REF_REGEX = re.compile(r"^ref:\s(.*)$")
 
 
+def requires_lock(method: Callable[P, T]) -> Callable[P, T]:
+    """Decorate a class method so that it requires the class lock to run.
+
+    The class should have a reentrant lock with the name ``self._lock``.
+    """
+
+    @wraps(method)
+    def wrapper(self, *args: P.args, **kwargs: P.kwargs) -> T:
+        if not hasattr(self, "_lock"):
+            raise AttributeError(f"{self.__class__.__name__} has no '_lock' attribute")
+        with self._lock:
+            return method(self, *args, **kwargs)
+
+    return wrapper
+
+
 class ErrorCapturingThread(Thread):
     """Subclass of Thread that captures exceptions from the target function.