Add a config key to allow transfer to a single raw directory

Author: stephen-riggs

src/murfey/client/watchdir_multigrid.py

@@ -49,12 +49,12 @@ def stop(self):
             self.thread.join()
         log.debug("MultigridDirWatcher thread stop completed")
 
-    def _handle_metadata(self, directory: Path, extra_directory: str):
+    def _handle_metadata(self, directory: Path, extra_directory: str, limited=True):
         self.notify(
             directory,
             extra_directory=extra_directory,
             analyse=self._analyse,
-            limited=True,
+            limited=limited,
             tag="metadata",
         )
         self._seen_dirs.append(directory)
@@ -122,6 +122,12 @@ def _process(self):
                                     / f"{sample.parent.name}_{sample.name}",
                                 )
 
+                    elif self._machine_config["single_data_directory"]:
+                        if d.is_dir() and d not in self._seen_dirs:
+                            self._handle_metadata(
+                                d, extra_directory=f"{d.name}", limited=False
+                            )
+
                     else:
                         if d.is_dir() and d not in self._seen_dirs:
                             self._handle_metadata(

src/murfey/server/api/file_io_instrument.py

@@ -85,15 +85,16 @@ def suggest_path(
             raise FileNotFoundError(log_message)
 
     check_path_name = check_path.name
-    while check_path.exists():
-        count = count + 1 if count else 2
-        check_path = check_path.parent / f"{check_path_name}{count}"
+    if not machine_config.single_data_directory:
+        while check_path.exists():
+            count = count + 1 if count else 2
+            check_path = check_path.parent / f"{check_path_name}{count}"
     if params.touch:
-        check_path.mkdir()
+        check_path.mkdir(exist_ok=True)
         os.chmod(check_path, mode=machine_config.mkdir_chmod)
         if params.extra_directory:
             extra_dir = check_path / secure_filename(params.extra_directory)
-            extra_dir.mkdir()
+            extra_dir.mkdir(exist_ok=True)
             os.chmod(extra_dir, mode=machine_config.mkdir_chmod)
     return {"suggested_path": check_path.relative_to(rsync_basepath)}
 

src/murfey/util/config.py

@@ -50,6 +50,7 @@ class MachineConfig(BaseModel):  # type: ignore
     analyse_created_directories: list[str] = []
     gain_reference_directory: Optional[Path] = None
     eer_fractionation_file_template: str = ""
+    single_data_directory: bool = False
 
     # Data transfer setup -------------------------------------------------------------
     # General setup