(Improve order flow) Override microbial dump (#4127) (patch)

### Fixed

- MutantSample and MicrosaltSample dumps the verified_organism value

cg/services/orders/lims_service/service.py

@@ -4,8 +4,6 @@
 from cg.constants import DataDelivery, Workflow
 from cg.models.lims.sample import LimsSample
 from cg.services.orders.validation.models.sample import Sample
-from cg.services.orders.validation.workflows.microsalt.models.sample import MicrosaltSample
-from cg.services.orders.validation.workflows.mutant.models.sample import MutantSample
 
 LOG = logging.getLogger(__name__)
 
@@ -28,8 +26,6 @@ def _build_lims_sample(
             dict_sample["data_analysis"] = workflow
             dict_sample["data_delivery"] = delivery_type
             dict_sample["family_name"] = sample._case_name
-            if isinstance(sample, MutantSample | MicrosaltSample):
-                dict_sample["verified_organism"] = sample._verified_organism
             lims_sample: LimsSample = LimsSample.parse_obj(dict_sample)
             samples_lims.append(lims_sample)
         return samples_lims

cg/services/orders/storing/implementations/microbial_order_service.py

@@ -89,7 +89,7 @@ def _fill_in_sample_verified_organism(self, samples: list[MicrobialSample]):
             organism_id = sample.organism
             reference_genome = sample.reference_genome
             organism: Organism = self.status.get_organism_by_internal_id(internal_id=organism_id)
-            is_verified = (
+            is_verified: bool = (
                 organism and organism.reference_genome == reference_genome and organism.verified
             )
             sample._verified_organism = is_verified

cg/services/orders/validation/workflows/microsalt/models/sample.py

@@ -14,4 +14,9 @@ class MicrosaltSample(Sample):
     organism: str
     priority: PriorityEnum
     reference_genome: str = Field(max_length=255)
-    _verified_organism: str | None = PrivateAttr(default=None)
+    _verified_organism: bool | None = PrivateAttr(default=None)
+
+    def model_dump(self, **kwargs) -> dict:
+        data = super().model_dump(**kwargs)
+        data["verified_organism"] = self._verified_organism
+        return data

cg/services/orders/validation/workflows/mutant/models/sample.py

@@ -35,7 +35,7 @@ class MutantSample(Sample):
     region: Region
     region_code: str
     selection_criteria: SelectionCriteria
-    _verified_organism: str | None = PrivateAttr(default=None)
+    _verified_organism: bool | None = PrivateAttr(default=None)
 
     @model_validator(mode="before")
     @classmethod
@@ -62,4 +62,5 @@ def serialize_collection_date(self, value: date) -> str:
     def model_dump(self, **kwargs) -> dict:
         data = super().model_dump(**kwargs)
         data["lab_code"] = self._lab_code
+        data["verified_organism"] = self._verified_organism
         return data