Tests.

chanzuckerberg · Oct 21, 2024 · b8cea01 · b8cea01
1 parent 1aa878a
commit b8cea01
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Showing 4 changed files with 29 additions and 20 deletions.
diff --git a/ingestion_tools/scripts/tests/db_import/populate_db.py b/ingestion_tools/scripts/tests/db_import/populate_db.py
@@ -192,6 +192,7 @@ def populate_stale_tomogram_voxel_spacing(run_id: int = RUN1_ID) -> None:
     TomogramAuthor.create(tomogram_id=stale_tomogram.id, name="John John", author_list_order=2)
     stale_annotation = Annotation.create(
         tomogram_voxel_spacing_id=stale_voxel_spacing.id,
+        deposition_id=DEPOSITION_ID2,
         s3_metadata_path="foo",
         https_metadata_path="foo",
         deposition_date="2025-04-01",
@@ -342,14 +343,15 @@ def populate_annotations() -> None:
     Annotation.create(
         id=ANNOTATION_ID,
         tomogram_voxel_spacing_id=TOMOGRAM_VOXEL_ID1,
+        deposition_id=DEPOSITION_ID2,
         s3_metadata_path="s3://test-public-bucket/30001/RUN1/Tomograms/VoxelSpacing12.300/Annotations/100-foo-1.0.json",
         https_metadata_path="foo",
         deposition_date="2025-04-01",
         release_date="2025-06-01",
         last_modified_date="2025-06-01",
-        annotation_method="",
+        annotation_method="2D CNN predictions",
         ground_truth_status=False,
-        object_name="bar",
+        object_name="foo",
         object_count=0,
         object_id="invalid-id",
         annotation_software="bar",
@@ -360,6 +362,7 @@ def populate_stale_annotations() -> None:
     Annotation.create(
         id=STALE_ANNOTATION_ID,
         tomogram_voxel_spacing_id=TOMOGRAM_VOXEL_ID1,
+        deposition_id=DEPOSITION_ID2,
         s3_metadata_path="foo",
         https_metadata_path="foo",
         deposition_date="2025-04-01",

diff --git a/ingestion_tools/scripts/tests/db_import/test_db_annotation_import.py b/ingestion_tools/scripts/tests/db_import/test_db_annotation_import.py
@@ -19,7 +19,7 @@
 
 @pytest.fixture
 def expected_annotations(http_prefix: str) -> list[dict[str, Any]]:
-    path = f"{DATASET_ID}/RUN1/Tomograms/VoxelSpacing12.300/Annotations/100-foo-1.0.json"
+    path = f"{DATASET_ID}/RUN1/Reconstructions/VoxelSpacing12.300/Annotations/100/foo-1.0.json"
     return [
         {
             "id": ANNOTATION_ID,
@@ -43,12 +43,12 @@ def expected_annotations(http_prefix: str) -> list[dict[str, Any]]:
                 {
                     "link": "https://fake-link.com/resources/100-foo-1.0_method.pdf",
                     "link_type": "documentation",
-                    "name": "Method Documentation",
+                    "custom_name": "Method Documentation",
                 },
                 {
                     "link": "https://another-link.com/100-foo-1.0_code.zip",
                     "link_type": "source_code",
-                    "name": "Source Code",
+                    "custom_name": "Source Code",
                 },
             ],
         },
@@ -57,7 +57,7 @@ def expected_annotations(http_prefix: str) -> list[dict[str, Any]]:
 
 @pytest.fixture
 def expected_annotation_files(http_prefix: str) -> list[dict[str, Any]]:
-    path = f"{DATASET_ID}/RUN1/Tomograms/VoxelSpacing12.300/Annotations/"
+    path = f"{DATASET_ID}/RUN1/Reconstructions/VoxelSpacing12.300/Annotations/"
     return [
         {
             "id": ANNOTATION_FILE_ID,

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
@@ -68,10 +68,10 @@ def expected_tomograms_by_run(http_prefix: str) -> dict[str, dict[float, list[di
         "processing_software": "tomo3D",
         "tomogram_version": "1",
         "is_canonical": True,
-        "s3_omezarr_dir": f"s3://test-public-bucket/{run1_vs_path}CanonicalTomogram/RUN1.zarr",
-        "https_omezarr_dir": f"{http_prefix}/{run1_vs_path}CanonicalTomogram/RUN1.zarr",
-        "s3_mrc_scale0": f"s3://test-public-bucket/{run1_vs_path}CanonicalTomogram/RUN1.mrc",
-        "https_mrc_scale0": f"{http_prefix}/{run1_vs_path}CanonicalTomogram/RUN1.mrc",
+        "s3_omezarr_dir": f"s3://test-public-bucket/{run1_vs_path}Tomograms/100/RUN1.zarr",
+        "https_omezarr_dir": f"{http_prefix}/{run1_vs_path}Tomograms/100/RUN1.zarr",
+        "s3_mrc_scale0": f"s3://test-public-bucket/{run1_vs_path}Tomograms/100/RUN1.mrc",
+        "https_mrc_scale0": f"{http_prefix}/{run1_vs_path}Tomograms/100/RUN1.mrc",
         "scale0_dimensions": "980,1016,500",
         "scale1_dimensions": "490,508,250",
         "scale2_dimensions": "245,254,125",
@@ -85,11 +85,11 @@ def expected_tomograms_by_run(http_prefix: str) -> dict[str, dict[float, list[di
             [0, 0, 1, 0],
             [0, 0, 0, 1],
         ],
-        "key_photo_url": f"{http_prefix}/{run1_vs_path}KeyPhotos/key-photo-snapshot.png",
-        "key_photo_thumbnail_url": f"{http_prefix}/{run1_vs_path}KeyPhotos/key-photo-thumbnail.png",
+        "key_photo_url": f"{http_prefix}/{run1_vs_path}Images/key-photo-snapshot.png",
+        "key_photo_thumbnail_url": f"{http_prefix}/{run1_vs_path}Images/key-photo-thumbnail.png",
         "neuroglancer_config": '{"foo":"bar","baz":"test"}',
         "type": "CANONICAL",
-        "deposition_id": 301,
+        "deposition_id": 300,
     }
     run2_tomo = {
         "name": "RUN2",
@@ -102,19 +102,25 @@ def expected_tomograms_by_run(http_prefix: str) -> dict[str, dict[float, list[di
         "reconstruction_software": "Unknown",
         "processing": "filtered",
         "tomogram_version": "1",
+        "affine_transformation_matrix": [
+            [1, 0, 0, 0],
+            [0, 1, 0, 0],
+            [0, 0, 1, 0],
+            [0, 0, 0, 1],
+        ],
         "is_canonical": True,
-        "s3_omezarr_dir": f"s3://test-public-bucket/{run2_vs_path}CanonicalTomogram/RUN2.zarr",
-        "https_omezarr_dir": f"{http_prefix}/{run2_vs_path}CanonicalTomogram/RUN2.zarr",
-        "s3_mrc_scale0": f"s3://test-public-bucket/{run2_vs_path}CanonicalTomogram/RUN2.mrc",
-        "https_mrc_scale0": f"{http_prefix}/{run2_vs_path}CanonicalTomogram/RUN2.mrc",
+        "s3_omezarr_dir": f"s3://test-public-bucket/{run2_vs_path}Tomograms/100/RUN2.zarr",
+        "https_omezarr_dir": f"{http_prefix}/{run2_vs_path}Tomograms/100/RUN2.zarr",
+        "s3_mrc_scale0": f"s3://test-public-bucket/{run2_vs_path}Tomograms/100/RUN2.mrc",
+        "https_mrc_scale0": f"{http_prefix}/{run2_vs_path}Tomograms/100/RUN2.mrc",
         "scale0_dimensions": "800,800,400",
         "scale1_dimensions": "400,400,200",
         "scale2_dimensions": "200,200,100",
         "ctf_corrected": False,
         "offset_x": 0,
         "offset_y": 0,
         "offset_z": 0,
-        "neuroglancer_config": "{}",
+        "neuroglancer_config": '{"foo":"bar","baz":"test"}',
         "type": "CANONICAL",
         "deposition_id": 300,
     }

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
@@ -70,7 +70,7 @@
     "last_modified_date": "2022-09-02",
     "release_date": "2022-06-01"
   },
-  "alignment_metadata_path": "test-public-bucket/30001/RUN2/Alignments/100/alignment_metadata.json",
-  "neuroglancer_config_path": "test-public-bucket/30001/RUN2/Reconstructions/VoxelSpacing13.480/NeuroglancerPrecompute/100-neuroglancer_config.json",
+  "alignment_metadata_path": null,
+  "neuroglancer_config_path": null,
   "last_updated_at": 1728676818
 }