Remove action field from StainingJsonSchema (#151)

imi-bigpicture · Feb 12, 2024 · 4645777 · 4645777
1 parent 6e7533b
commit 4645777
Showing 1 changed file with 33 additions and 35 deletions.
diff --git a/wsidicom/metadata/schema/json/sample/schema.py b/wsidicom/metadata/schema/json/sample/schema.py
@@ -33,44 +33,44 @@
     SpecimenSamplingProcedureCode,
     SpecimenStainsCode,
 )
-from wsidicom.metadata.schema.common import DataclassLoadingSchema, LoadingSchema
-from wsidicom.metadata.schema.json.fields import (
-    CodeJsonField,
-    JsonFieldFactory,
-    MeasurementJsonField,
-    SpecimenIdentifierJsonField,
-    UidJsonField,
-)
-from wsidicom.metadata.schema.json.sample.model import (
-    SpecimenJsonModel,
-    PreparationAction,
-    SampleJsonModel,
-    SamplingConstraintJsonModel,
-    SamplingJsonModel,
-    SlideSampleJsonModel,
-    BaseSpecimenJsonModel,
-)
-from wsidicom.metadata.schema.json.sample.parser import SpecimenJsonParser
 from wsidicom.metadata.sample import (
+    BaseSpecimen,
     Collection,
     Embedding,
-    Specimen,
     Fixation,
     PreparationStep,
     Processing,
     Receiving,
     Sample,
     SampledSpecimen,
+    SampleLocalization,
     Sampling,
     SamplingLocation,
     SlideSample,
-    BaseSpecimen,
+    Specimen,
     SpecimenIdentifier,
-    SampleLocalization,
     Staining,
     Storage,
     UnknownSampling,
 )
+from wsidicom.metadata.schema.common import DataclassLoadingSchema, LoadingSchema
+from wsidicom.metadata.schema.json.fields import (
+    CodeJsonField,
+    JsonFieldFactory,
+    MeasurementJsonField,
+    SpecimenIdentifierJsonField,
+    UidJsonField,
+)
+from wsidicom.metadata.schema.json.sample.model import (
+    BaseSpecimenJsonModel,
+    PreparationAction,
+    SampleJsonModel,
+    SamplingConstraintJsonModel,
+    SamplingJsonModel,
+    SlideSampleJsonModel,
+    SpecimenJsonModel,
+)
+from wsidicom.metadata.schema.json.sample.parser import SpecimenJsonParser
 
 
 class SamplingLocationJsonSchema(LoadingSchema[SamplingLocation]):
@@ -173,19 +173,6 @@ def load_type(self) -> Type[Fixation]:
         return Fixation
 
 
-class StainingJsonSchema(DataclassLoadingSchema[Staining]):
-    action = fields.Constant(PreparationAction.STAINING.value, dump_only=True)
-    substances = fields.List(
-        JsonFieldFactory.concept_code(SpecimenStainsCode)(), allow_none=True
-    )
-    date_time = fields.DateTime(allow_none=True)
-    description = fields.String(allow_none=True)
-
-    @property
-    def load_type(self) -> Type[Staining]:
-        return Staining
-
-
 class ReceivingJsonSchema(DataclassLoadingSchema[Receiving]):
     action = fields.Constant(PreparationAction.RECEIVING.value, dump_only=True)
     date_time = fields.DateTime(allow_none=True)
@@ -228,7 +215,6 @@ class PreparationStepJsonSchema(Schema):
         PreparationAction.PROCESSING: ProcessingJsonSchema,
         PreparationAction.EMBEDDING: EmbeddingJsonSchema,
         PreparationAction.FIXATION: FixationJsonSchema,
-        PreparationAction.STAINING: StainingJsonSchema,
         PreparationAction.RECEIVING: ReceivingJsonSchema,
         PreparationAction.STORAGE: StorageJsonSchema,
     }
@@ -270,6 +256,18 @@ def _subschema_dump(self, step: PreparationStep):
         return schema().dump(step, many=False)
 
 
+class StainingJsonSchema(DataclassLoadingSchema[Staining]):
+    substances = fields.List(
+        JsonFieldFactory.concept_code(SpecimenStainsCode)(), allow_none=True
+    )
+    date_time = fields.DateTime(allow_none=True)
+    description = fields.String(allow_none=True)
+
+    @property
+    def load_type(self) -> Type[Staining]:
+        return Staining
+
+
 class SpecimenJsonSchema(LoadingSchema[Specimen]):
     """Schema for extracted specimen that has not been sampled from other specimen."""