Convert data_directories to a list

Author: stephen-riggs

src/murfey/cli/transfer.py

@@ -36,10 +36,8 @@ def run():
     murfey_url = urlparse(args.server, allow_fragments=False)
 
     machine_data = requests.get(f"{murfey_url.geturl()}/machine").json()
-    if Path(args.source or ".").resolve() in machine_data.data_directories.keys():
-        console.print(
-            f"[red]Source directory is the base directory for the {machine_data.data_directories[Path(args.source or '.').resolve()]}, exiting"
-        )
+    if Path(args.source or ".").resolve() in machine_data.data_directories:
+        console.print("[red]Source directory is the base directory, exiting")
         return
 
     cmd = [

src/murfey/client/analyser.py

@@ -408,8 +408,8 @@ def _xml_file(self, data_file: Path) -> Path:
         if not self._environment:
             return data_file.with_suffix(".xml")
         file_name = f"{'_'.join(p for p in data_file.stem.split('_')[:-1])}.xml"
-        data_directories = self._murfey_config.get("data_directories", {})
-        for dd in data_directories.keys():
+        data_directories = self._murfey_config.get("data_directories", [])
+        for dd in data_directories:
             if str(data_file).startswith(dd):
                 base_dir = Path(dd)
                 mid_dir = data_file.relative_to(dd).parent

src/murfey/client/contexts/spa.py

@@ -136,9 +136,9 @@ def _foil_hole_from_file(f: Path) -> int:
 
 
 def _grid_square_metadata_file(
-    f: Path, data_directories: Dict[Path, str], visit: str, grid_square: int
+    f: Path, data_directories: List[Path], visit: str, grid_square: int
 ) -> Path:
-    for dd in data_directories.keys():
+    for dd in data_directories:
         if str(f).startswith(str(dd)):
             base_dir = dd
             mid_dir = f.relative_to(dd).parent
@@ -542,7 +542,7 @@ def _position_analysis(
         grid_square = _grid_square_from_file(transferred_file)
         grid_square_metadata_file = _grid_square_metadata_file(
             transferred_file,
-            {Path(d): l for d, l in machine_config["data_directories"].items()},
+            machine_config["data_directories"],
             environment.visit,
             grid_square,
         )

src/murfey/client/tui/screens.py

@@ -89,17 +89,14 @@ def determine_default_destination(
         log.info(f"Processing only mode with sources {environment.sources}")
         _default = str(environment.sources[0].resolve()) or str(Path.cwd())
     elif machine_data.get("data_directories"):
-        for data_dir in machine_data["data_directories"].keys():
+        for data_dir in machine_data["data_directories"]:
             if source.resolve() == Path(data_dir):
                 _default = destination + f"/{visit}"
                 break
             else:
                 try:
                     mid_path = source.resolve().relative_to(data_dir)
-                    if (
-                        machine_data["data_directories"][data_dir] == "detector"
-                        and use_suggested_path
-                    ):
+                    if use_suggested_path:
                         with global_env_lock:
                             source_name = (
                                 source.name
@@ -203,10 +200,10 @@ def validate_form(form: dict, model: BaseModel) -> bool:
 class _DirectoryTree(DirectoryTree):
     valid_selection = reactive(False)
 
-    def __init__(self, *args, data_directories: dict | None = None, **kwargs):
+    def __init__(self, *args, data_directories: List[Path] | None = None, **kwargs):
         super().__init__(*args, **kwargs)
         self._selected_path = self.path
-        self._data_directories = data_directories or {}
+        self._data_directories = data_directories or []
 
     def on_tree_node_selected(self, event: Tree.NodeSelected) -> None:
         event.stop()
@@ -276,7 +273,7 @@ def compose(self):
         self._dir_tree = _DirectoryTree(
             str(self._selected_dir),
             data_directories=(
-                machine_data.get("data_directories", {}) if self.app._strict else {}
+                machine_data.get("data_directories", []) if self.app._strict else []
             ),
             id="dir-select",
         )
@@ -289,7 +286,7 @@ def compose(self):
 
         text_log.write("Selected directories:\n")
         btn_disabled = True
-        for d in machine_data.get("data_directories", {}).keys():
+        for d in machine_data.get("data_directories", []):
             if (
                 Path(self._dir_tree._selected_path).resolve().is_relative_to(d)
                 or self.app._environment.processing_only_mode
@@ -718,11 +715,7 @@ def on_button_pressed(self, event: Button.Pressed):
         if self._switch_status:
             self.app.install_screen(
                 DirectorySelection(
-                    [
-                        p[0]
-                        for p in machine_data.get("data_directories", {}).items()
-                        if p[1] == "detector" and Path(p[0]).exists()
-                    ]
+                    [p for p in machine_data.get("data_directories", []) if p.exists()]
                 ),
                 "directory-select",
             )
@@ -784,11 +777,7 @@ def on_button_pressed(self, event: Button.Pressed):
 
         self.app.install_screen(
             DirectorySelection(
-                [
-                    p[0]
-                    for p in machine_data.get("data_directories", {}).items()
-                    if p[1] == "detector" and Path(p[0]).exists()
-                ]
+                [p for p in machine_data.get("data_directories", []) if p.exists()]
             ),
             "directory-select",
         )

src/murfey/server/api/instrument.py

@@ -92,9 +92,7 @@ async def start_multigrid_watcher(
         _config = {
             "acquisition_software": machine_config.acquisition_software,
             "calibrations": machine_config.calibrations,
-            "data_directories": {
-                str(k): v for k, v in machine_config.data_directories.items()
-            },
+            "data_directories": [str(k) for k in machine_config.data_directories],
             "rsync_basepath": str(machine_config.rsync_basepath),
             "visit": visit,
             "default_model": str(machine_config.default_model),

src/murfey/util/config.py

@@ -14,7 +14,7 @@
 class MachineConfig(BaseModel, extra=Extra.allow):  # type: ignore
     acquisition_software: List[str]
     calibrations: Dict[str, Dict[str, Union[dict, float]]]
-    data_directories: Dict[Path, str]
+    data_directories: List[Path]
     rsync_basepath: Path
     default_model: Path
     display_name: str = ""
@@ -148,7 +148,7 @@ def get_machine_config(instrument_name: str = "") -> Dict[str, MachineConfig]:
         "": MachineConfig(
             acquisition_software=[],
             calibrations={},
-            data_directories={},
+            data_directories=[],
             rsync_basepath=Path("dls/tmp"),
             murfey_db_credentials="",
             default_model="/tmp/weights.h5",

src/murfey/util/dummy_setup.py

@@ -17,21 +17,15 @@
 def initialise(dummy_location: Path) -> Path:
     base = dummy_location / "murfey_dummy"
     base.mkdir()
-    microscope_dir = base / "M"
     detector_dir = base / "Data"
-    microscope_dir.mkdir()
-    (microscope_dir / "Supervisor").mkdir()
     detector_dir.mkdir()
     (detector_dir / "Supervisor").mkdir()
     with open(base / "config.yaml", "w") as yaml_out:
         yaml.dump(
             {
                 "m12": {
                     "acquisition_software": ["epu", "tomo", "serialem"],
-                    "data_directories": {
-                        str(detector_dir): "detector",
-                        str(microscope_dir): "microscope",
-                    },
+                    "data_directories": [str(detector_dir)],
                     "rsync_basepath": str(dummy_location),
                     "calibrations": {"dummy": 0},
                 }
@@ -99,7 +93,7 @@ def generate_data(base_path: Path, timeout: int | None = None, pause: int = 10):
                         base_path,
                         "Supervisor",
                         f"Position_{tilt}.mrc",
-                        data_dir="M",
+                        data_dir="Data",
                         size=(128, 128),
                     )
                 except ValueError: