feat: Add rsync support to BAM file detection

src/robin/utilities/bam_handler.py

@@ -38,47 +38,63 @@ class BamEventHandler(FileSystemEventHandler):
     A class to handle file system events specifically for ".bam" files.
 
     This class extends the FileSystemEventHandler from the watchdog library
-    to handle creation events for ".bam" files within a watch folder.
+    to handle creation and move events for ".bam" files within a watch folder.
 
     Attributes:
-        bam_count (DefaultDict[str, Any]): A dictionary to keep track of the number of ".bam" files
-                                           and their creation timestamps.
+        bam_count (Queue): A queue to store BAM file paths and their detection timestamps.
     """
 
     def __init__(self, bam_count: Queue):
         """
-        Initializes the BamEventHandler with a bam_count dictionary.
+        Initializes the BamEventHandler with a bam_count queue.
 
         Args:
-            bam_count (DefaultDict[str, Dict[str, Any]]): A dictionary to store the count and details of ".bam" files.
-                                                          Expected to have a "counter" key initialized to zero.
+            bam_count (Queue): A queue to store BAM file paths and their timestamps.
         """
         super().__init__()
         self.bam_count = bam_count
 
+    def _handle_bam_file(self, file_path: str) -> None:
+        """
+        Helper method to process BAM files consistently across different events.
+
+        This method checks if the file has a .bam extension and if so, adds it to
+        the processing queue with its current timestamp.
+
+        Args:
+            file_path (str): Path to the file to process
+        """
+        if file_path.endswith(".bam"):
+            self.bam_count.put((file_path, time.time()))
+            logger.info(f"New .bam file detected: {file_path}")
+
     def on_created(self, event: FileSystemEvent) -> None:
         """
         Handles the file creation event.
 
         This method is called when a new file is created in the watch folder.
-        If the created file has a ".bam" extension, it increments the counter in bam_count
-        and records the file's creation timestamp.
+        If the created file has a ".bam" extension, it processes the file.
 
         Args:
             event (FileSystemEvent): The event object representing the file system event.
         """
-        if event.is_directory:
-            return
-
-        if event.src_path.endswith(".bam"):
-            self.bam_count.put((event.src_path, time.time()))
-            logger.info(
-                # f"New .bam file detected: {event.src_path}, total count: {self.bam_count['counter']}"
-                f"New .bam file detected: {event.src_path}"  # , total count: {self.bam_count['counter']}"
-            )
-            # except Exception as e:
-            #    print("Bam error in handler.")
-            #    print(e)
+        if not event.is_directory:
+            self._handle_bam_file(event.src_path)
+
+    def on_moved(self, event: FileSystemEvent) -> None:
+        """
+        Handles file move/rename events.
+
+        This method is called when a file is moved or renamed in the watch folder,
+        which catches rsync's final move operation when copying files into the
+        watched directory.
+
+        Args:
+            event (FileSystemEvent): The event object representing the move/rename event,
+                                   containing both source and destination paths.
+        """
+        if not event.is_directory:
+            self._handle_bam_file(event.dest_path)
 
 
 def create_bam_count() -> DefaultDict[str, Dict[str, Any]]: