Path logic fixes for MSYS2 Windows-style paths (#517)

* Replaced Path().resolve() with Path().absolute() in client-side modules

* Fixed path logic in '_xml_file' function and '_grid_square_metadata_file'; added catch to _analyse for ValueError

Author: tieneupin

src/murfey/client/__init__.py

@@ -239,7 +239,7 @@ def run():
 
     if args.remove_files:
         remove_prompt = Confirm.ask(
-            f"Are you sure you want to remove files from {args.source or Path('.').resolve()}?"
+            f"Are you sure you want to remove files from {args.source or Path('.').absolute()}?"
         )
         if not remove_prompt:
             exit("Exiting")

src/murfey/client/analyser.py

@@ -302,6 +302,10 @@ def _analyse(self):
                                         f"Metadata gathering failed with a key error for key: {e.args[0]}"
                                     )
                                     raise e
+                                except ValueError as e:
+                                    logger.error(
+                                        f"Metadata gathering failed with a value error: {e}"
+                                    )
                             if not dc_metadata or not self._force_mdoc_metadata:
                                 self._unseen_xml.append(transferred_file)
                             else:
@@ -406,16 +410,16 @@ def _xml_file(self, data_file: Path) -> Path:
         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
+                base_dir = Path(dd).absolute()
+                mid_dir = data_file.relative_to(base_dir).parent
                 break
         else:
             return data_file.with_suffix(".xml")
         return base_dir / self._environment.visit / mid_dir / file_name
 
     def enqueue(self, rsyncer: RSyncerUpdate):
         if not self._stopping and rsyncer.outcome == TransferResult.SUCCESS:
-            absolute_path = (self._basepath / rsyncer.file_path).resolve()
+            absolute_path = (self._basepath / rsyncer.file_path).absolute()
             self.queue.put(absolute_path)
 
     def start(self):

src/murfey/client/contexts/spa.py

@@ -61,8 +61,8 @@ def _grid_square_metadata_file(
 ) -> Path:
     for dd in data_directories:
         if str(f).startswith(str(dd)):
-            base_dir = dd
-            mid_dir = f.relative_to(dd).parent
+            base_dir = dd.absolute()
+            mid_dir = f.relative_to(base_dir).parent
             break
     else:
         raise ValueError(f"Could not determine grid square metadata path for {f}")

src/murfey/client/rsync.py

@@ -199,7 +199,7 @@ def finalise(self, thread: bool = True):
 
     def enqueue(self, file_path: Path):
         if not self._stopping:
-            absolute_path = (self._basepath / file_path).resolve()
+            absolute_path = self._basepath / file_path
             self.queue.put(absolute_path)
 
     def _process(self):

src/murfey/client/tui/screens.py

@@ -88,15 +88,15 @@ def determine_default_destination(
     _default = ""
     if environment.processing_only_mode and environment.sources:
         log.info(f"Processing only mode with sources {environment.sources}")
-        _default = str(environment.sources[0].resolve()) or str(Path.cwd())
+        _default = str(environment.sources[0].absolute()) or str(Path.cwd())
     elif machine_data.get("data_directories"):
         for data_dir in machine_data["data_directories"]:
-            if source.resolve() == Path(data_dir):
+            if source.absolute() == Path(data_dir).absolute():
                 _default = f"{destination}/{visit}"
                 break
             else:
                 try:
-                    mid_path = source.resolve().relative_to(data_dir)
+                    mid_path = source.absolute().relative_to(Path(data_dir).absolute())
                     if use_suggested_path:
                         with global_env_lock:
                             source_name = (
@@ -221,7 +221,7 @@ def on_tree_node_selected(self, event: Tree.NodeSelected) -> None:
                 self.valid_selection = True
                 return
             for d in self._data_directories:
-                if Path(self._selected_path).resolve().is_relative_to(d):
+                if Path(self._selected_path).absolute().is_relative_to(d.absolute()):
                     self.valid_selection = True
                     break
             else:
@@ -282,7 +282,9 @@ def compose(self):
         btn_disabled = True
         for d in machine_data.get("data_directories", []):
             if (
-                Path(self._dir_tree._selected_path).resolve().is_relative_to(d)
+                Path(self._dir_tree._selected_path)
+                .absolute()
+                .is_relative_to(Path(d).absolute())
                 or self.app._environment.processing_only_mode
             ):
                 btn_disabled = False
@@ -306,7 +308,7 @@ def _check_valid_selection(self, valid: bool):
                 self._add_btn.disabled = True
 
     def _add_directory(self, directory: str, add_destination: bool = True):
-        source = Path(self._dir_tree.path).resolve() / directory
+        source = Path(self._dir_tree.path).absolute() / directory
         if add_destination:
             for s in self.app._environment.sources:
                 if source.is_relative_to(s):
@@ -705,9 +707,9 @@ def on_button_pressed(self, event: Button.Pressed):
             self.app.install_screen(
                 DirectorySelection(
                     [
-                        p
-                        for p in machine_data.get("data_directories", [])
-                        if Path(p).exists()
+                        path
+                        for path in machine_data.get("data_directories", [])
+                        if Path(path).exists()
                     ]
                 ),
                 "directory-select",
@@ -771,9 +773,9 @@ def on_button_pressed(self, event: Button.Pressed):
         self.app.install_screen(
             DirectorySelection(
                 [
-                    p
-                    for p in machine_data.get("data_directories", [])
-                    if Path(p).exists()
+                    path
+                    for path in machine_data.get("data_directories", [])
+                    if Path(path).exists()
                 ]
             ),
             "directory-select",
@@ -941,7 +943,7 @@ def __init__(self, directories: List[str], *args, **kwargs):
 
     def on_button_pressed(self, event: Button.Pressed):
         self.app._multigrid = self._switch_status
-        visit_dir = Path(str(event.button.label)) / self.app._visit
+        visit_dir = Path(str(event.button.label)).absolute() / self.app._visit
         visit_dir.mkdir(exist_ok=True)
         self.app._set_default_acquisition_directories(visit_dir)
         machine_config = get_machine_config_client(