Merge branch 'improve-order-flow-main' into move-validation-service

Clinical-Genomics · Jan 17, 2025 · a7a9bef · a7a9bef
2 parents 8c013fb + f91d98e
commit a7a9bef
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diff --git a/cg/constants/orderforms.py b/cg/constants/orderforms.py
@@ -71,4 +71,5 @@ def get_current_orderform_version(order_form: str) -> str:
     "LaboratorieMedicinskt Centrum Gotland": "621 84 Visby",
     "Unilabs Eskilstuna Laboratorium": "631 88 Eskilstuna",
     "Norrland University Hospital": "901 85 Umeå",
+    "Länssjukhuset Sundsvall": "856 43 Sundsvall",
 }
diff --git a/cg/services/orders/validation/workflows/mutant/models/sample.py b/cg/services/orders/validation/workflows/mutant/models/sample.py
@@ -1,8 +1,9 @@
 from datetime import date
 
-from pydantic import BeforeValidator, PrivateAttr, field_serializer
+from pydantic import BeforeValidator, PrivateAttr, field_serializer, model_validator
 from typing_extensions import Annotated
 
+from cg.constants.orderforms import ORIGINAL_LAB_ADDRESSES, REGION_CODES
 from cg.models.orders.sample_base import ControlEnum, PriorityEnum
 from cg.services.orders.validation.constants import ElutionBuffer, ExtractionMethod
 from cg.services.orders.validation.models.sample import Sample
@@ -22,17 +23,43 @@ class MutantSample(Sample):
     control: Annotated[ControlEnum, BeforeValidator(parse_control)] = ControlEnum.not_control
     elution_buffer: Annotated[ElutionBuffer, BeforeValidator(parse_buffer)]
     extraction_method: Annotated[ExtractionMethod, BeforeValidator(parse_extraction_method)]
+    _lab_code: str = PrivateAttr(default="SE100 Karolinska")
     organism: str
     original_lab: OriginalLab
+    original_lab_address: str
     pre_processing_method: PreProcessingMethod
     primer: Primer
     priority: PriorityEnum
     quantity: int | None = None
     reference_genome: str
     region: Region
+    region_code: str
     selection_criteria: SelectionCriteria
     _verified_organism: str | None = PrivateAttr(default=None)
 
+    @model_validator(mode="before")
+    @classmethod
+    def set_original_lab_address(cls, data: any):
+        if isinstance(data, dict):
+            is_set = bool(data.get("original_lab_address"))
+            if not is_set:
+                data["original_lab_address"] = ORIGINAL_LAB_ADDRESSES[data["original_lab"]]
+        return data
+
+    @model_validator(mode="before")
+    @classmethod
+    def set_region_code(cls, data: any):
+        if isinstance(data, dict):
+            is_set = bool(data.get("region_code"))
+            if not is_set:
+                data["region_code"] = REGION_CODES[data["region"]]
+        return data
+
     @field_serializer("collection_date")
     def serialize_collection_date(self, value: date) -> str:
         return value.isoformat()
+
+    def model_dump(self, **kwargs) -> dict:
+        data = super().model_dump(**kwargs)
+        data["lab_code"] = self._lab_code
+        return data