Revise config model

src/nwb2bids/_command_line_interface/_main.py

@@ -79,13 +79,21 @@ def _run_convert_nwb_dataset(
         raise ValueError(message)
     handled_nwb_paths = [pathlib.Path(nwb_path) for nwb_path in nwb_paths]
 
-    run_config = RunConfig(
-        bids_directory=bids_directory,
-        additional_metadata_file_path=additional_metadata_file_path,
-        file_mode=file_mode,
-        cache_directory=cache_directory,
-        run_id=run_id,
-    )
+    run_config_kwargs = {
+        k: v
+        for k, v in {
+            "bids_directory": bids_directory,
+            "additional_metadata_file_path": additional_metadata_file_path,
+            "file_mode": file_mode,
+            "cache_directory": cache_directory,
+            "run_id": run_id,
+        }.items()
+        # Filter out values that indicate absence of direct user input or
+        # signal to use default
+        if (k != "file_mode" and v is not None) or (k == "file_mode" and v != "auto")
+    }
+
+    run_config = RunConfig.model_validate(run_config_kwargs)
     converter = convert_nwb_dataset(nwb_paths=handled_nwb_paths, run_config=run_config)
 
     messages = converter.messages

src/nwb2bids/_converters/_run_config.py

@@ -1,14 +1,65 @@
 import json
 import pathlib
-import tempfile
 import typing
 
 import pydantic
 
+from .._core._file_mode import _determine_file_mode
 from .._core._home import _get_home_directory
 from .._core._run_id import _generate_run_id
 
 
+def _validate_existing_directory_as_bids(directory: pathlib.Path) -> pathlib.Path:
+
+    dataset_description_file_path = directory / "dataset_description.json"
+    current_directory_contents = {path.stem for path in directory.iterdir() if not path.name.startswith(".")} - {
+        "README",
+        "CHANGES",
+        "derivatives",
+        "dandiset",
+    }
+
+    if len(current_directory_contents) == 0:
+        # The directory is considered empty, not containing any meaningful content.
+        # Populate the directory with `dataset_description.json` to make it
+        # a valid (though minimal) BIDS dataset.
+
+        default_dataset_description = {"BIDSVersion": "1.10"}
+        with dataset_description_file_path.open(mode="w") as file_stream:
+            json.dump(obj=default_dataset_description, fp=file_stream, indent=4)
+    else:
+        # The directory is considered non-empty
+
+        if not dataset_description_file_path.is_file():
+            # The directory is without `dataset_description.json` file
+            # It is an invalid BIDS dataset.
+
+            message = (
+                f"The directory ({directory}) exists and is not empty, but is not a valid BIDS dataset: "
+                "missing 'dataset_description.json' file."
+            )
+            raise ValueError(message)
+
+        with dataset_description_file_path.open(mode="r") as file_stream:
+            try:
+                dataset_description = json.load(fp=file_stream)
+            except json.JSONDecodeError as exc:
+                message = (
+                    f"The directory ({directory}) exists and contains a 'dataset_description.json' file, "
+                    "but it is not a valid JSON file."
+                )
+                raise ValueError(message) from exc
+
+        if dataset_description.get("BIDSVersion", None) is None:
+            message = (
+                f"The directory ({directory}) exists but is not a valid BIDS dataset: "
+                "missing 'BIDSVersion' in 'dataset_description.json'."
+            )
+            raise ValueError(message)
+
+    return directory
+
+
 class RunConfig(pydantic.BaseModel):
     """
     Specifies configuration options for a single run of NWB to BIDS conversion.
@@ -19,12 +70,13 @@ class RunConfig(pydantic.BaseModel):
     additional_metadata_file_path : file path, optional
         The path to a YAML file containing additional metadata not included within the NWB files
         that you wish to include in the BIDS dataset.
-    file_mode : one of "move", "copy", "symlink", or "auto", default: "auto"
+    file_mode : one of "move", "copy", or "symlink"
         Specifies how to handle the NWB files when converting to BIDS format.
             - "move": Move the files to the BIDS directory.
             - "copy": Copy the files to the BIDS directory.
             - "symlink": Create symbolic links to the files in the BIDS directory.
-            - "auto": Decides between all the above based on the system, with preference for linking when possible.
+            - if not specified, decide between all the above based on the system,
+              with preference for linking when possible.
     cache_directory : directory path
         The directory where run specific files (e.g., notifications, sanitization reports) will be stored.
         Defaults to `~/.nwb2bids`.
@@ -35,39 +87,42 @@ class RunConfig(pydantic.BaseModel):
         The default ID uses runtime timestamp information of the form "date-%Y%m%d_time-%H%M%S."
     """
 
-    bids_directory: pydantic.DirectoryPath | None = None
+    bids_directory: typing.Annotated[
+        pydantic.DirectoryPath,
+        pydantic.Field(default_factory=pathlib.Path.cwd),
+        pydantic.AfterValidator(_validate_existing_directory_as_bids),
+    ]
     additional_metadata_file_path: pydantic.FilePath | None = None
-    file_mode: typing.Literal["move", "copy", "symlink", "auto"] = "auto"
-    cache_directory: pydantic.DirectoryPath | None = None
-    run_id: str | None = None
-    _parent_run_directory: pathlib.Path | None = pydantic.PrivateAttr(default=None)
-    _run_directory: pathlib.Path | None = pydantic.PrivateAttr(default=None)
+    file_mode: typing.Annotated[
+        typing.Literal["move", "copy", "symlink"], pydantic.Field(default_factory=_determine_file_mode)
+    ]
+    cache_directory: typing.Annotated[pydantic.DirectoryPath, pydantic.Field(default_factory=_get_home_directory)]
+    run_id: typing.Annotated[str, pydantic.Field(default_factory=_generate_run_id)]
 
     model_config = pydantic.ConfigDict(
         validate_assignment=True,  # Re-validate model on mutation
+        validate_default=True,  # Validate default values as well
     )
 
     def model_post_init(self, context: typing.Any, /) -> None:
-        """Ensure the various run directories and files are created."""
-        if self.run_id is None:
-            self.run_id = _generate_run_id()
-
-        if self.bids_directory is None:
-            self.bids_directory = pathlib.Path.cwd()
-
-        self._validate_existing_directory_as_bids()
-        self._determine_file_mode()
 
-        if self.cache_directory is None:
-            self.cache_directory = _get_home_directory()
-        self._parent_run_directory = self.cache_directory / "runs"
+        # Ensure run directory and its parent exist
         self._parent_run_directory.mkdir(exist_ok=True)
-        self._run_directory = self._parent_run_directory / self.run_id
         self._run_directory.mkdir(exist_ok=True)
 
         self.notifications_file_path.touch()
         self.notifications_json_file_path.touch()
 
+    @property
+    def _parent_run_directory(self) -> pathlib.Path:
+        """The parent directory where all run-specific directories are stored."""
+        return self.cache_directory / "runs"
+
+    @property
+    def _run_directory(self) -> pathlib.Path:
+        """The directory specific to this run."""
+        return self._parent_run_directory / self.run_id
+
     @pydantic.computed_field
     @property
     def notifications_file_path(self) -> pathlib.Path:
@@ -81,55 +136,3 @@ def notifications_json_file_path(self) -> pathlib.Path:
         """The file path leading to a JSON dump of the notifications."""
         notifications_file_path = self._run_directory / f"{self.run_id}_notifications.json"
         return notifications_file_path
-
-    def _validate_existing_directory_as_bids(self) -> None:
-        bids_directory = self.bids_directory
-
-        dataset_description_file_path = bids_directory / "dataset_description.json"
-        current_directory_contents = {
-            path.stem for path in bids_directory.iterdir() if not path.name.startswith(".")
-        } - {"README", "CHANGES", "derivatives", "dandiset"}
-        if len(current_directory_contents) == 0:
-            default_dataset_description = {"BIDSVersion": "1.10"}
-            with dataset_description_file_path.open(mode="w") as file_stream:
-                json.dump(obj=default_dataset_description, fp=file_stream, indent=4)
-            return
-
-        if not dataset_description_file_path.exists():
-            message = (
-                f"The directory ({bids_directory}) exists and is not empty, but is not a valid BIDS dataset: "
-                "missing 'dataset_description.json'."
-            )
-            raise ValueError(message)
-
-        with dataset_description_file_path.open(mode="r") as file_stream:
-            dataset_description = json.load(fp=file_stream)
-        if dataset_description.get("BIDSVersion", None) is None:
-            message = (
-                f"The directory ({bids_directory}) exists but is not a valid BIDS dataset: "
-                "missing 'BIDSVersion' in 'dataset_description.json'."
-            )
-            raise ValueError(message)
-
-    def _determine_file_mode(self) -> None:
-        if self.file_mode != "auto":
-            return
-
-        with tempfile.TemporaryDirectory(prefix="nwb2bids-") as temp_dir_str:
-            temp_dir_path = pathlib.Path(temp_dir_str)
-
-            # Create a test file to determine if symlinks are supported
-            test_file_path = temp_dir_path / "test_file.txt"
-            test_file_path.touch()
-
-            try:
-                # Create a symlink to the test file
-                (temp_dir_path / "test_symlink.txt").symlink_to(target=test_file_path)
-            except (OSError, PermissionError, NotImplementedError):  # Windows can sometimes have trouble with symlinks
-                # TODO: log a INFO message here when logging is set up
-                self.file_mode = "copy"
-                return
-            else:
-                # If symlink creation was successful, return "symlink"
-                self.file_mode = "symlink"
-                return

src/nwb2bids/_core/_file_mode.py

@@ -0,0 +1,25 @@
+import pathlib
+import tempfile
+import typing
+
+
+def _determine_file_mode() -> typing.Literal["symlink", "copy"]:
+    """
+    Determine what file mode to use in creating a BIDS dataset based on the system
+    """
+    with tempfile.TemporaryDirectory(prefix="nwb2bids-") as temp_dir_str:
+        temp_dir_path = pathlib.Path(temp_dir_str)
+
+        # Create a test file to determine if symlinks are supported
+        test_file_path = temp_dir_path / "test_file.txt"
+        test_file_path.touch()
+
+        try:
+            # Create a symlink to the test file
+            (temp_dir_path / "test_symlink.txt").symlink_to(target=test_file_path)
+        except (OSError, PermissionError, NotImplementedError):  # Windows can sometimes have trouble with symlinks
+            # TODO: log a INFO message here when logging is set up
+            return "copy"
+        else:
+            # If symlink creation was successful, return "symlink"
+            return "symlink"