fix: keep both tomogram.is_canonical and `tomogram.is_portal_standa…

…rd` (#303) * fix: keep both `tomogram.is_canonical` and `tomogram.is_portal_standard` to allow the frontend queries to migrate.
chanzuckerberg · Oct 7, 2024 · c65e2f6 · c65e2f6
1 parent cf8d2e0
commit c65e2f6
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Showing 13 changed files with 395 additions and 267 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/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
@@ -98,7 +98,6 @@ def get_computed_fields(self) -> dict[str, Any]:
             "fiducial_alignment_status": normalize_fiducial_alignment(self.metadata.get("fiducial_alignment_status")),
             "reconstruction_method": self.normalize_to_unknown_str(self.metadata.get("reconstruction_method")),
             "reconstruction_software": self.normalize_to_unknown_str(self.metadata.get("reconstruction_software")),
-            "is_canonical": True,  # TODO: mark this for deprecation
             "s3_omezarr_dir": self.join_path(s3_prefix, self.dir_prefix, self.metadata["omezarr_dir"]),
             "https_omezarr_dir": self.join_path(https_prefix, self.dir_prefix, self.metadata["omezarr_dir"]),
             "s3_mrc_file": self.join_path(s3_prefix, self.dir_prefix, self.metadata["mrc_files"][0]),
@@ -107,6 +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_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
@@ -236,6 +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,
         deposition_date=datetime.min,
         release_date=datetime.min,
         last_modified_date=datetime.min,
@@ -290,6 +291,7 @@ def populate_tomograms(session: sa.orm.Session) -> Tomogram:
         offset_y=0,
         offset_z=0,
         is_portal_standard=True,
+        is_canonical=True,
         deposition_date=datetime.min,
         release_date=datetime.min,
         last_modified_date=datetime.min,
@@ -323,6 +325,7 @@ def populate_stale_tomograms(session: sa.orm.Session) -> Tomogram:
         offset_y=0,
         offset_z=0,
         is_portal_standard=True,
+        is_canonical=True,
         deposition_date=datetime.min,
         release_date=datetime.min,
         last_modified_date=datetime.min,
@@ -546,7 +549,10 @@ def populate_stale_annotation_method_links(session: sa.orm.Session) -> None:
     populate_stale_annotations(session)
     session.add(
         AnnotationMethodLink(
-            annotation_id=STALE_ANNOTATION_ID, name="Stale Link 0", link_type="other", link="https://some-link.com",
+            annotation_id=STALE_ANNOTATION_ID,
+            name="Stale Link 0",
+            link_type="other",
+            link="https://some-link.com",
         ),
     )
     session.add(

diff --git a/apiv2/db_import/tests/test_db_tomo_import.py b/apiv2/db_import/tests/test_db_tomo_import.py
@@ -87,6 +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,
         "deposition_date": date(2023, 4, 2),
         "release_date": date(2024, 6, 1),
         "last_modified_date": date(2023, 9, 2),
@@ -116,6 +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,
         "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
@@ -12,6 +12,7 @@ Tomogram {
     float tomogram_version
     string processing_software
     string reconstruction_software
+    boolean is_canonical
     boolean is_portal_standard
     boolean is_author_submitted
     boolean is_visualization_default