Allow local path = uri; update volume building

Author: kaitj

src/neuromaps_prime/graph/builder.py

@@ -10,7 +10,6 @@
 
 from __future__ import annotations
 
-from pathlib import Path
 from typing import TYPE_CHECKING, Any, cast
 
 import yaml
@@ -30,6 +29,8 @@
 from neuromaps_prime.resources import NEUROMAPSPRIME_GRAPH
 
 if TYPE_CHECKING:
+    from pathlib import Path
+
     import networkx as nx
 
 
@@ -201,10 +202,6 @@ def _build_volume_edge(
     # Generic resource parsers                                             #
     # ------------------------------------------------------------------ #
 
-    def _resolve_path(self, path: str) -> Path:
-        """Prepend data_dir to path when set, otherwise return as-is."""
-        return (self.data_dir / path) if self.data_dir else Path(path)
-
     def _parse_surface_annotations(
         self, prefix: str, space: str, density: str, annots: dict[str, Any]
     ) -> list[SurfaceAnnotation]:
@@ -402,24 +399,28 @@ def _parse_volume_resources(
                 for vol_type, vol_value in types.items():
                     if vol_type == "annotation":
                         for annot_key, annot_dict in vol_value.items():
+                            name = f"{prefix}_{res}_{annot_key}.nii.gz"
                             annotations.append(
                                 VolumeAnnotation(
-                                    name=f"{prefix}_{res}_{annot_key}",
+                                    name=name,
                                     space=space,
                                     label=annot_key,
                                     resolution=res,
-                                    file_path=self._resolve_path(annot_dict.get("uri")),
+                                    uri=annot_dict.get("uri"),
+                                    file_path=self.data_dir / name,
                                     references=annot_dict.get("references"),
                                     notes=annot_dict.get("notes"),
                                 )
                             )
                         continue
 
                     extra = {"provider": provider} if is_transform else {}
+                    name = f"{prefix}_{res}_{vol_type}"
                     result.append(
                         cls(
-                            name=f"{prefix}_{res}_{vol_type}",
-                            file_path=self._resolve_path(vol_value),
+                            name=name,
+                            uri=vol_value,
+                            file_path=self.data_dir / name,
                             resolution=res,
                             resource_type=vol_type,
                             references=transform_refs,

src/neuromaps_prime/graph/models.py

@@ -31,9 +31,13 @@ def fetch(self) -> Path:
         Raises:
             FileNotFoundError: if file cannot be fetched
         """
-        if not self.file_path.exists():
-            if self.uri is None:
-                raise FileNotFoundError("File does not exist and cannot be fetched.")
+        if self.file_path.exists():
+            return self.file_path
+        if self.uri is None:
+            raise FileNotFoundError("File does not exist and cannot be fetched.")
+        if (local_file := Path(self.uri)).exists():
+            self.file_path = local_file
+        else:
             _logger.info(f"Fetching {self.file_path.name} from remote server.")
             download_and_validate(uri=self.uri, dest=self.file_path)
             if not self.file_path.exists():

tests/unit/graph/test_model.py

@@ -2,6 +2,7 @@
 
 from __future__ import annotations
 
+from pathlib import Path
 from typing import TYPE_CHECKING, Any, Protocol
 from unittest.mock import MagicMock, patch
 
@@ -11,7 +12,6 @@
 
 if TYPE_CHECKING:
     from collections.abc import Callable
-    from pathlib import Path
 
 
 @pytest.fixture
@@ -108,9 +108,25 @@ def test_validate_and_fetch(
         obj = model_cls(
             name="test",
             description="testing description",
-            file_path=tmp_file,
+            uri=str(tmp_file),
+            file_path=Path("abc"),
             **extra_kwargs,
         )
+        assert obj.file_path.name == "abc"
+        assert obj.fetch() == tmp_file
+        assert obj.file_path == tmp_file
+
+    def test_fetch_existing_file_path(self, tmp_file: Path) -> None:
+        """Test resource instantiation and fetching."""
+        obj = models.SurfaceAtlas(
+            name="test",
+            description="testing description",
+            space="Yerkes19",
+            density="32k",
+            hemisphere="left",
+            resource_type="surf_atlas",
+            file_path=tmp_file,
+        )
         assert obj.file_path == tmp_file
         assert obj.fetch() == tmp_file