Merged recent changes from 'main' branch

Author: tieneupin

.bumpclient.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.19.4"
+current_version = "0.19.5"
 commit = true
 tag = false
 

.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.19.4"
+current_version = "0.19.5"
 commit = true
 tag = true
 

Helm/Chart.yaml

@@ -1,7 +1,7 @@
 apiVersion: v1
 name: murfey-services
 description: Umbrella Helm chart for deploying the servers and daemons needed to enable Murfey to transfer and process data
-version: 0.19.4
+version: 0.19.5
 dependencies:
   - name: murfey-instrument-server-clem
   - name: murfey-instrument-server-tem

Helm/charts/murfey-instrument-server-clem/Chart.yaml

@@ -1,4 +1,4 @@
 apiVersion: v1
 name: murfey-instrument-server-clem
 description: Helm chart for deploying a Murfey instrument server, which executes orders to detect, modify, and transfer files on the instrument PC, and notifies the backend server about transferred files
-version: 0.19.4
+version: 0.19.5

Helm/charts/murfey-instrument-server-tem/Chart.yaml

@@ -1,4 +1,4 @@
 apiVersion: v1
 name: murfey-instrument-server-tem
 description: Helm chart for deploying a Murfey instrument server, which executes orders to detect, modify, and transfer files on the instrument PC, and notifies the backend server about transferred files
-version: 0.19.4
+version: 0.19.5

Helm/charts/murfey-rsync/Chart.yaml

@@ -1,4 +1,4 @@
 apiVersion: v1
 name: murfey-rsync
 description: Helm chart for deploying an rsync daemon, which is responsible for executing the transfer of files from the client storage directory to the server storage system
-version: 0.19.4
+version: 0.19.5

Helm/charts/murfey-server/Chart.yaml

@@ -1,4 +1,4 @@
 apiVersion: v1
 name: murfey-server
 description: Helm chart for deploying a Murfey backend server, which is responsible for orchestrating the data transfer and processing workflow between the client PC and the storage system
-version: 0.19.4
+version: 0.19.5

pyproject.toml

@@ -7,7 +7,7 @@ requires = [
 
 [project]
 name = "murfey"
-version = "0.19.4"
+version = "0.19.5"
 description = "Client-Server architecture hauling Cryo-EM data"
 readme = "README.md"
 keywords = [

src/murfey/__init__.py

@@ -1,4 +1,4 @@
 from __future__ import annotations
 
-__version__ = "0.19.4"
-__supported_client_version__ = "0.19.4"
+__version__ = "0.19.5"
+__supported_client_version__ = "0.19.5"

src/murfey/client/analyser.py

@@ -15,6 +15,7 @@
 from typing import Type
 
 from murfey.client.context import Context
+from murfey.client.contexts.atlas import AtlasContext
 from murfey.client.contexts.clem import CLEMContext
 from murfey.client.contexts.spa import SPAModularContext
 from murfey.client.contexts.spa_metadata import SPAMetadataContext
@@ -135,7 +136,7 @@ def _find_context(self, file_path: Path) -> bool:
 
         # Tomography and SPA workflow checks
         if "atlas" in file_path.parts:
-            self._context = SPAMetadataContext("epu", self._basepath)
+            self._context = AtlasContext("epu", self._basepath)
             return True
 
         if "Metadata" in file_path.parts or file_path.name == "EpuSession.dm":
@@ -266,7 +267,7 @@ def _analyse(self):
                             )
                         except Exception as e:
                             logger.error(f"Exception encountered: {e}")
-                        if "atlas" not in transferred_file.parts:
+                        if not isinstance(self._context, AtlasContext):
                             if not dc_metadata:
                                 try:
                                     dc_metadata = self._context.gather_metadata(
@@ -308,6 +309,10 @@ def _analyse(self):
                     )
                     self.post_transfer(transferred_file)
 
+                elif isinstance(self._context, AtlasContext):
+                    logger.debug(f"File {transferred_file.name!r} is part of the atlas")
+                    self.post_transfer(transferred_file)
+
                 # Handle files with tomography and SPA context differently
                 elif not self._extension or self._unseen_xml:
                     valid_extension = self._find_extension(transferred_file)
@@ -325,36 +330,35 @@ def _analyse(self):
                             )
                         except Exception as e:
                             logger.error(f"Exception encountered: {e}")
-                        if "atlas" not in transferred_file.parts:
-                            if not dc_metadata:
-                                try:
-                                    dc_metadata = self._context.gather_metadata(
-                                        mdoc_for_reading
-                                        or self._xml_file(transferred_file),
-                                        environment=self._environment,
-                                    )
-                                except KeyError as e:
-                                    logger.error(
-                                        f"Metadata gathering failed with a key error for key: {e.args[0]}"
-                                    )
-                                    raise e
-                            if not dc_metadata or not self._force_mdoc_metadata:
-                                mdoc_for_reading = None
-                                self._unseen_xml.append(transferred_file)
-                            if dc_metadata:
-                                self._unseen_xml = []
-                                if dc_metadata.get("file_extension"):
-                                    self._extension = dc_metadata["file_extension"]
-                                else:
-                                    dc_metadata["file_extension"] = self._extension
-                                dc_metadata["acquisition_software"] = (
-                                    self._context._acquisition_software
+                        if not dc_metadata:
+                            try:
+                                dc_metadata = self._context.gather_metadata(
+                                    mdoc_for_reading
+                                    or self._xml_file(transferred_file),
+                                    environment=self._environment,
                                 )
-                                self.notify(
-                                    {
-                                        "form": dc_metadata,
-                                    }
+                            except KeyError as e:
+                                logger.error(
+                                    f"Metadata gathering failed with a key error for key: {e.args[0]}"
                                 )
+                                raise e
+                        if not dc_metadata or not self._force_mdoc_metadata:
+                            mdoc_for_reading = None
+                            self._unseen_xml.append(transferred_file)
+                        if dc_metadata:
+                            self._unseen_xml = []
+                            if dc_metadata.get("file_extension"):
+                                self._extension = dc_metadata["file_extension"]
+                            else:
+                                dc_metadata["file_extension"] = self._extension
+                            dc_metadata["acquisition_software"] = (
+                                self._context._acquisition_software
+                            )
+                            self.notify(
+                                {
+                                    "form": dc_metadata,
+                                }
+                            )
                 elif isinstance(
                     self._context,
                     (
@@ -370,6 +374,7 @@ def _analyse(self):
                     )
                     self.post_transfer(transferred_file)
             self.queue.task_done()
+        logger.debug("Analyer thread has stopped analysing incoming files")
         self.notify(final=True)
 
     def _xml_file(self, data_file: Path) -> Path:
@@ -403,6 +408,12 @@ def request_stop(self):
         self._stopping = True
         self._halt_thread = True
 
+    def is_safe_to_stop(self):
+        """
+        Checks that the analyser thread is safe to stop
+        """
+        return self._stopping and self._halt_thread and not self.queue.qsize()
+
     def stop(self):
         logger.debug("Analyser thread stop requested")
         self._stopping = True
@@ -412,5 +423,8 @@ def stop(self):
                 self.queue.put(None)
                 self.thread.join()
         except Exception as e:
-            logger.error(f"Exception encountered while stopping analyser: {e}")
+            logger.error(
+                f"Exception encountered while stopping Analyser: {e}",
+                exc_info=True,
+            )
         logger.debug("Analyser thread stop completed")