feat: Minor tomogram table update

apiv2/database/migrations/versions/20240923_130016_autogenerated.py

@@ -3,35 +3,52 @@
 Create Date: 2024-09-23 17:00:19.130349
 
 """
+
 import sqlalchemy as sa
 from alembic import op
 
 # revision identifiers, used by Alembic.
-revision = '20240923_130016'
-down_revision = '20240828_194323'
+revision = "20240923_130016"
+down_revision = "20240828_194323"
 branch_labels = None
 depends_on = None
 
 
 def upgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
-    op.alter_column('dataset', 'organism_name',
-               existing_type=sa.VARCHAR(),
-               nullable=True)
-    op.alter_column('tiltseries', 'microscope_manufacturer',
-               existing_type=sa.VARCHAR(length=4),
-               type_=sa.Enum('FEI', 'TFS', 'JEOL', 'SIMULATED', name='tiltseries_microscope_manufacturer_enum', native_enum=False),
-               existing_nullable=False)
+    op.alter_column("dataset", "organism_name", existing_type=sa.VARCHAR(), nullable=True)
+    op.alter_column(
+        "tiltseries",
+        "microscope_manufacturer",
+        existing_type=sa.VARCHAR(length=4),
+        type_=sa.Enum(
+            "FEI",
+            "TFS",
+            "JEOL",
+            "SIMULATED",
+            name="tiltseries_microscope_manufacturer_enum",
+            native_enum=False,
+        ),
+        existing_nullable=False,
+    )
     # ### end Alembic commands ###
 
 
 def downgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
-    op.alter_column('tiltseries', 'microscope_manufacturer',
-               existing_type=sa.Enum('FEI', 'TFS', 'JEOL', 'SIMULATED', name='tiltseries_microscope_manufacturer_enum', native_enum=False),
-               type_=sa.VARCHAR(length=4),
-               existing_nullable=False)
-    op.alter_column('dataset', 'organism_name',
-               existing_type=sa.VARCHAR(),
-               nullable=False)
+    op.alter_column(
+        "tiltseries",
+        "microscope_manufacturer",
+        existing_type=sa.Enum(
+            "FEI",
+            "TFS",
+            "JEOL",
+            "SIMULATED",
+            name="tiltseries_microscope_manufacturer_enum",
+            native_enum=False,
+        ),
+        type_=sa.VARCHAR(length=4),
+        existing_nullable=False,
+    )
+    op.alter_column("dataset", "organism_name", existing_type=sa.VARCHAR(), nullable=False)
     # ### end Alembic commands ###

apiv2/database/models/tomogram.py

@@ -87,7 +87,6 @@ class Tomogram(Base):
     tomogram_version: Mapped[float] = mapped_column(Float, nullable=True)
     processing_software: Mapped[str] = mapped_column(String, nullable=True)
     reconstruction_software: Mapped[str] = mapped_column(String, nullable=False)
-    is_canonical: Mapped[bool] = mapped_column(Boolean, nullable=True)
     s3_omezarr_dir: Mapped[str] = mapped_column(String, nullable=True)
     https_omezarr_dir: Mapped[str] = mapped_column(String, nullable=True)
     s3_mrc_file: Mapped[str] = mapped_column(String, nullable=True)

apiv2/graphql_api/helpers/tomogram.py

@@ -58,7 +58,6 @@ class TomogramGroupByOptions:
     tomogram_version: Optional[float] = None
     processing_software: Optional[str] = None
     reconstruction_software: Optional[str] = None
-    is_canonical: Optional[bool] = None
     s3_omezarr_dir: Optional[str] = None
     https_omezarr_dir: Optional[str] = None
     s3_mrc_file: Optional[str] = None

apiv2/graphql_api/types/tomogram.py

@@ -230,7 +230,6 @@ class TomogramWhereClause(TypedDict):
     tomogram_version: Optional[FloatComparators] | None
     processing_software: Optional[StrComparators] | None
     reconstruction_software: Optional[StrComparators] | None
-    is_canonical: Optional[BoolComparators] | None
     s3_omezarr_dir: Optional[StrComparators] | None
     https_omezarr_dir: Optional[StrComparators] | None
     s3_mrc_file: Optional[StrComparators] | None
@@ -276,7 +275,6 @@ class TomogramOrderByClause(TypedDict):
     tomogram_version: Optional[orderBy] | None
     processing_software: Optional[orderBy] | None
     reconstruction_software: Optional[orderBy] | None
-    is_canonical: Optional[orderBy] | None
     s3_omezarr_dir: Optional[orderBy] | None
     https_omezarr_dir: Optional[orderBy] | None
     s3_mrc_file: Optional[orderBy] | None
@@ -341,9 +339,6 @@ class Tomogram(EntityInterface):
         description="Processing software used to derive the tomogram", default=None,
     )
     reconstruction_software: str = strawberry.field(description="Name of software used for reconstruction")
-    is_canonical: Optional[bool] = strawberry.field(
-        description="whether this tomogram is canonical for the run", default=None,
-    )
     s3_omezarr_dir: Optional[str] = strawberry.field(
         description="S3 path to this tomogram in multiscale OME-Zarr format", default=None,
     )
@@ -467,7 +462,6 @@ class TomogramCountColumns(enum.Enum):
     tomogramVersion = "tomogram_version"
     processingSoftware = "processing_software"
     reconstructionSoftware = "reconstruction_software"
-    isCanonical = "is_canonical"
     s3OmezarrDir = "s3_omezarr_dir"
     httpsOmezarrDir = "https_omezarr_dir"
     s3MrcFile = "s3_mrc_file"
@@ -552,9 +546,6 @@ class TomogramCreateInput:
         description="Processing software used to derive the tomogram", default=None,
     )
     reconstruction_software: str = strawberry.field(description="Name of software used for reconstruction")
-    is_canonical: Optional[bool] = strawberry.field(
-        description="whether this tomogram is canonical for the run", default=None,
-    )
     s3_omezarr_dir: Optional[str] = strawberry.field(
         description="S3 path to this tomogram in multiscale OME-Zarr format", default=None,
     )
@@ -620,9 +611,6 @@ class TomogramUpdateInput:
         description="Processing software used to derive the tomogram", default=None,
     )
     reconstruction_software: Optional[str] = strawberry.field(description="Name of software used for reconstruction")
-    is_canonical: Optional[bool] = strawberry.field(
-        description="whether this tomogram is canonical for the run", default=None,
-    )
     s3_omezarr_dir: Optional[str] = strawberry.field(
         description="S3 path to this tomogram in multiscale OME-Zarr format", default=None,
     )

apiv2/schema/schema.yaml

@@ -2326,11 +2326,6 @@ classes:
         range: string
         required: true
         description: Name of software used for reconstruction
-      is_canonical:
-        name: is_canonical
-        description: whether this tomogram is canonical for the run
-        from_schema: cdp-dataset-config
-        range: boolean
       s3_omezarr_dir:
         name: s3_omezarr_dir
         description: S3 path to this tomogram in multiscale OME-Zarr format

apiv2/test_infra/factories/tomogram.py

@@ -55,7 +55,6 @@ class Meta:
     tomogram_version = fuzzy.FuzzyFloat(1, 100)
     processing_software = fuzzy.FuzzyText()
     reconstruction_software = fuzzy.FuzzyText()
-    is_canonical = factory.Faker("boolean")
     s3_omezarr_dir = fuzzy.FuzzyText()
     https_omezarr_dir = fuzzy.FuzzyText()
     s3_mrc_file = fuzzy.FuzzyText()

apiv2/validators/tomogram.py

@@ -68,7 +68,6 @@ class TomogramCreateInputValidator(BaseModel):
             strip_whitespace=True,
         ),
     ]
-    is_canonical: Annotated[bool | None, Field()]
     s3_omezarr_dir: Annotated[
         str | None,
         StringConstraints(
@@ -190,7 +189,6 @@ class TomogramUpdateInputValidator(BaseModel):
             strip_whitespace=True,
         ),
     ]
-    is_canonical: Annotated[bool | None, Field()]
     s3_omezarr_dir: Annotated[
         str | None,
         StringConstraints(