add other organism to microbial sample models

Clinical-Genomics · Jan 22, 2025 · bfb4fba · bfb4fba
1 parent e72ecee
commit bfb4fba
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 1 deletion.
diff --git a/cg/services/orders/validation/workflows/microsalt/models/sample.py b/cg/services/orders/validation/workflows/microsalt/models/sample.py
@@ -12,6 +12,7 @@ class MicrosaltSample(Sample):
     elution_buffer: Annotated[ElutionBuffer, BeforeValidator(parse_buffer)]
     extraction_method: Annotated[ExtractionMethod, BeforeValidator(parse_extraction_method)]
     organism: str
+    other_organism: str | None = Field(alias="organism_other", default=None)
     priority: PriorityEnum
     reference_genome: str = Field(max_length=255)
     _verified_organism: bool | None = PrivateAttr(default=None)

diff --git a/cg/services/orders/validation/workflows/mutant/models/sample.py b/cg/services/orders/validation/workflows/mutant/models/sample.py
@@ -1,6 +1,6 @@
 from datetime import date
 
-from pydantic import BeforeValidator, PrivateAttr, field_serializer, model_validator
+from pydantic import BeforeValidator, Field, PrivateAttr, field_serializer, model_validator
 from typing_extensions import Annotated
 
 from cg.constants.orderforms import ORIGINAL_LAB_ADDRESSES, REGION_CODES
@@ -25,6 +25,7 @@ class MutantSample(Sample):
     extraction_method: Annotated[ExtractionMethod, BeforeValidator(parse_extraction_method)]
     _lab_code: str = PrivateAttr(default="SE100 Karolinska")
     organism: str
+    other_organism: str | None = Field(alias="organism_other", default=None)
     original_lab: OriginalLab
     original_lab_address: str
     pre_processing_method: PreProcessingMethod