Test case where ng config path is not present.

chanzuckerberg · Oct 22, 2024 · 6e34538 · 6e34538
1 parent e592a59
commit 6e34538
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Showing 6 changed files with 4 additions and 7 deletions.
diff --git a/ingestion_tools/scripts/importers/db/tomogram.py b/ingestion_tools/scripts/importers/db/tomogram.py
@@ -74,8 +74,7 @@ def get_tomogram_type(self) -> str:
 
     def generate_neuroglancer_data(self, config_path) -> str:
         if not config_path:
-            return {}
-        tomogram_id = self.dir_prefix.split("/").pop()
+            return "{}"
         config = self.config.load_key_json(config_path, is_file_required=True)
         # TODO: Log warning
         return json.dumps(config, separators=(",", ":")) if config else "{}"

diff --git a/ingestion_tools/scripts/tests/db_import/test_db_tomo_import.py b/ingestion_tools/scripts/tests/db_import/test_db_tomo_import.py
@@ -120,7 +120,7 @@ def expected_tomograms_by_run(http_prefix: str) -> dict[str, dict[float, list[di
         "offset_x": 0,
         "offset_y": 0,
         "offset_z": 0,
-        "neuroglancer_config": '{"foo":"bar","baz":"test"}',
+        "neuroglancer_config": "{}",
         "type": "CANONICAL",
         "deposition_id": 300,
     }

diff --git a/...erPrecompute/100-neuroglancer_config.json → ...erPrecompute/100/neuroglancer_config.json b/...erPrecompute/100-neuroglancer_config.json → ...erPrecompute/100/neuroglancer_config.json
diff --git a/..._files/30001/RUN1/Reconstructions/VoxelSpacing12.300/Tomograms/100/tomogram_metadata.json b/..._files/30001/RUN1/Reconstructions/VoxelSpacing12.300/Tomograms/100/tomogram_metadata.json
@@ -94,7 +94,7 @@
     "last_modified_date": "2023-09-02",
     "release_date": "2024-06-01"
   },
-  "alignment_metadata_path": "test-public-bucket/30001/RUN1/Alignments/100/alignment_metadata.json",
-  "neuroglancer_config_path": "test-public-bucket/30001/RUN1/Reconstructions/VoxelSpacing12.300/NeuroglancerPrecompute/100-neuroglancer_config.json",
+  "alignment_metadata_path": "30001/RUN1/Alignments/100/alignment_metadata.json",
+  "neuroglancer_config_path": "30001/RUN1/Reconstructions/VoxelSpacing12.300/NeuroglancerPrecompute/100/neuroglancer_config.json",
   "last_updated_at": 1728676818
 }
diff --git a/...UN2/Reconstructions/VoxelSpacing3.456/NeuroglancerPrecompute/100-neuroglancer_config.json b/...UN2/Reconstructions/VoxelSpacing3.456/NeuroglancerPrecompute/100-neuroglancer_config.json
diff --git a/...t_files/30001/RUN2/Reconstructions/VoxelSpacing3.456/Tomograms/100/tomogram_metadata.json b/...t_files/30001/RUN2/Reconstructions/VoxelSpacing3.456/Tomograms/100/tomogram_metadata.json
@@ -71,6 +71,5 @@
     "release_date": "2022-06-01"
   },
   "alignment_metadata_path": "foo",
-  "neuroglancer_config_path": "test-public-bucket/30001/RUN2/Reconstructions/VoxelSpacing3.456/NeuroglancerPrecompute/100-neuroglancer_config.json",
   "last_updated_at": 1728676818
 }