fix: add is_standardized back temporarily (#304)

fix: use is_standardized rather than is_canonical
chanzuckerberg · Oct 7, 2024 · dfe9a8b · dfe9a8b
1 parent c65e2f6
commit dfe9a8b
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Showing 14 changed files with 52 additions and 54 deletions.
diff --git a/apiv2/database/migrations/versions/20241002_152402_autogenerated.py b/apiv2/database/migrations/versions/20241002_152402_autogenerated.py
diff --git a/apiv2/database/migrations/versions/20241003_144355_autogenerated.py b/apiv2/database/migrations/versions/20241003_144355_autogenerated.py
diff --git a/apiv2/database/models/tomogram.py b/apiv2/database/models/tomogram.py
diff --git a/apiv2/db_import/importers/tomogram.py b/apiv2/db_import/importers/tomogram.py
@@ -106,7 +106,7 @@ def get_computed_fields(self) -> dict[str, Any]:
             "key_photo_thumbnail_url": None,
             "neuroglancer_config": self.generate_neuroglancer_data(),
             "type": self.get_tomogram_type(),
-            "is_canonical": self.metadata.get("is_standardized") or False,
+            "is_standardized": self.metadata.get("is_standardized") or False,
             "is_portal_standard": self.metadata.get("is_standardized") or False,
         }
         date_fields = ["deposition_date", "release_date", "last_modified_date"]

diff --git a/apiv2/db_import/tests/populate_db.py b/apiv2/db_import/tests/populate_db.py
@@ -236,7 +236,7 @@ def populate_stale_tomogram_voxel_spacing(session: sa.orm.Session, run_id: int =
         offset_y=0,
         offset_z=0,
         is_portal_standard=True,
-        is_canonical=True,
+        is_standardized=True,
         deposition_date=datetime.min,
         release_date=datetime.min,
         last_modified_date=datetime.min,
@@ -291,7 +291,7 @@ def populate_tomograms(session: sa.orm.Session) -> Tomogram:
         offset_y=0,
         offset_z=0,
         is_portal_standard=True,
-        is_canonical=True,
+        is_standardized=True,
         deposition_date=datetime.min,
         release_date=datetime.min,
         last_modified_date=datetime.min,
@@ -325,7 +325,7 @@ def populate_stale_tomograms(session: sa.orm.Session) -> Tomogram:
         offset_y=0,
         offset_z=0,
         is_portal_standard=True,
-        is_canonical=True,
+        is_standardized=True,
         deposition_date=datetime.min,
         release_date=datetime.min,
         last_modified_date=datetime.min,

diff --git a/apiv2/db_import/tests/test_db_tomo_import.py b/apiv2/db_import/tests/test_db_tomo_import.py
@@ -87,7 +87,7 @@ def expected_tomograms_by_run(http_prefix: str) -> dict[str, dict[float, list[di
         "neuroglancer_config": '{"foo":"bar","baz":"test"}',
         "deposition_id": 301,
         "is_portal_standard": False,
-        "is_canonical": False,
+        "is_standardized": False,
         "deposition_date": date(2023, 4, 2),
         "release_date": date(2024, 6, 1),
         "last_modified_date": date(2023, 9, 2),
@@ -117,7 +117,7 @@ def expected_tomograms_by_run(http_prefix: str) -> dict[str, dict[float, list[di
         "neuroglancer_config": "{}",
         "deposition_id": 300,
         "is_portal_standard": False,
-        "is_canonical": False,
+        "is_standardized": False,
         "deposition_date": date(2022, 4, 2),
         "release_date": date(2022, 6, 1),
         "last_modified_date": date(2022, 9, 2),

diff --git a/apiv2/graphql_api/helpers/tomogram.py b/apiv2/graphql_api/helpers/tomogram.py
diff --git a/apiv2/graphql_api/schema.graphql b/apiv2/graphql_api/schema.graphql
diff --git a/apiv2/graphql_api/schema.json b/apiv2/graphql_api/schema.json
diff --git a/apiv2/graphql_api/types/tomogram.py b/apiv2/graphql_api/types/tomogram.py
diff --git a/apiv2/schema/README.md b/apiv2/schema/README.md
@@ -12,7 +12,7 @@ Tomogram {
     float tomogram_version
     string processing_software
     string reconstruction_software
-    boolean is_canonical
+    boolean is_standardized
     boolean is_portal_standard
     boolean is_author_submitted
     boolean is_visualization_default

diff --git a/apiv2/schema/schema.yaml b/apiv2/schema/schema.yaml
@@ -2383,10 +2383,11 @@ classes:
         range: string
         required: true
         description: Name of software used for reconstruction
-      is_canonical:
+      is_standardized:
         description: whether this tomogram adheres to portal standards
         range: boolean
         ifabsent: false
+        required: true
       is_portal_standard:
         description: whether this tomogram adheres to portal standards
         range: boolean

diff --git a/apiv2/test_infra/factories/tomogram.py b/apiv2/test_infra/factories/tomogram.py
diff --git a/apiv2/validators/tomogram.py b/apiv2/validators/tomogram.py