Cleaning up paths

ingestion_tools/scripts/importers/alignment.py

@@ -53,7 +53,7 @@ class AlignmentImporter(BaseFileImporter):
     finder_factory = MultiSourceFileFinder
     has_metadata = True
     dir_path = "{dataset_name}/{run_name}/Alignments"
-    metadata_path = "{dataset_name}/{run_name}/Alignments/{alignment_id}-alignment_metadata.json"
+    metadata_path = os.path.join(dir_path, "{alignment_id}-alignment_metadata.json")
 
     def __init__(self, *args, file_paths: dict[str, str], **kwargs):
         super().__init__(*args, **kwargs)

ingestion_tools/scripts/importers/tomogram.py

@@ -121,14 +121,13 @@ def get_alignment_metadata_path(self) -> str:
 
         for alignment in AlignmentImporter.finder(self.config, **self.parents):
             return alignment.get_metadata_path()
-        # TODO: This should be an error, but we need to fix the data first.
+        # TODO: As all tomograms need to be associated to an alignment this should be an error, but we need to fix the
+        #  data first.
         return None
 
-    def get_neuroglancer_config_path(self) -> str:
+    def get_neuroglancer_config_path(self) -> str | None:
         if self.metadata.get("is_visualization_default"):
-            # TODO: Refactor this to a method in the viz_config importer with identifier in the name
-            return self.config.resolve_output_path("viz_config", self).format(identifier=self.identifier)
-
+            return self.config.resolve_output_path("viz_config", self)
         return None
 
     @classmethod

ingestion_tools/scripts/importers/visualization_config.py

@@ -25,7 +25,7 @@ class VisualizationConfigImporter(BaseImporter):
     has_metadata = False
     dir_path = (
         "{dataset_name}/{run_name}/Reconstructions/VoxelSpacing{voxel_spacing_name}/NeuroglancerPrecompute/"
-        "{{identifier}}-neuroglancer_config.json"
+        "{tomogram_id}-neuroglancer_config.json"
     )
 
     def import_item(self) -> None:

ingestion_tools/scripts/tests/fixtures/dataset1.yaml

@@ -209,6 +209,7 @@ tomograms:
     processing: raw
     reconstruction_method: WBP
     reconstruction_software: IMOD
+    is_visualization_default: true
     tomogram_version: 1
   sources:
   - source_glob:

ingestion_tools/scripts/tests/s3_import/test_tomograms.py

@@ -145,16 +145,26 @@ def test_tomogram_import_metadata(
         item.import_metadata()
     run_name = parents["run"].name
     voxel_spacing = 13.48
-    prefix = f"output/{parents['dataset'].name}/{run_name}/Reconstructions/VoxelSpacing{voxel_spacing:.3f}/Tomograms"
+    run_path = f"output/{parents['dataset'].name}/{run_name}"
+    vs_path = f"{run_path}/Reconstructions/VoxelSpacing{voxel_spacing:.3f}"
+    prefix = f"{vs_path}/Tomograms"
     tomogram_files = get_children(s3_client, test_output_bucket, prefix)
     id_prefix = 100
     assert f"{id_prefix}-tomogram_metadata.json" in tomogram_files
+    image_path = f"{parents['dataset'].name}/{run_name}/Reconstructions/VoxelSpacing{voxel_spacing:.3f}/Images/{id_prefix}-key-photo-"
     expected = {
         "omezarr_dir": f"{id_prefix}-{run_name}.zarr",
         "mrc_files": [f"{id_prefix}-{run_name}.mrc"],
         "voxel_spacing": 13.48,
         "scales": [{"x": 6, "y": 8, "z": 10}, {"x": 3, "y": 4, "z": 5}, {"x": 2, "y": 2, "z": 3}],
         "size": {"x": 6, "y": 8, "z": 10},
+        "alignment_metadata_path": f"{test_output_bucket}/{run_path}/Alignments/100-alignment_metadata.json",
+        "neuroglancer_config_path": f"{test_output_bucket}/{vs_path}/NeuroglancerPrecompute/"
+                                    f"{id_prefix}-neuroglancer_config.json",
+        "key_photo": {
+            "snapshot": f"{image_path}snapshot.png",
+            "thumbnail": f"{image_path}thumbnail.png",
+        },
     }
     validate_metadata(expected, prefix, id_prefix)