Add balsamic sample sex validation

cg/services/order_validation_service/errors/case_sample_errors.py

@@ -143,3 +143,8 @@ class InvalidVolumeError(CaseSampleError):
 class InvalidBufferError(CaseSampleError):
     field: str = "elution_buffer"
     message: str = "The chosen buffer is not allowed when skipping reception control"
+
+
+class SubjectIdGenderError(CaseSampleError):
+    field: str = "subject_id"
+    message: str = "Another sample with the same subject id has a different gender"

cg/services/order_validation_service/workflows/balsamic/rules/case_sample/rules.py

@@ -0,0 +1,30 @@
+from cg.services.order_validation_service.errors.case_sample_errors import SubjectIdGenderError
+from cg.services.order_validation_service.workflows.balsamic.models.order import BalsamicOrder
+from cg.services.order_validation_service.workflows.balsamic.rules.case_sample.utils import (
+    has_sex_and_subject,
+)
+from cg.store.store import Store
+
+
+def validate_subject_sex_consistency(
+    order: BalsamicOrder,
+    store: Store,
+) -> list[SubjectIdGenderError]:
+    errors: list[SubjectIdGenderError] = []
+
+    for case_index, case in order.enumerated_new_cases:
+        for sample_index, sample in case.enumerated_new_samples:
+            if not has_sex_and_subject(sample):
+                continue
+
+            if store.sample_exists_with_different_sex(
+                customer_internal_id=order.customer,
+                subject_id=sample.subject_id,
+                sex=sample.sex,
+            ):
+                error = SubjectIdGenderError(
+                    case_index=case_index,
+                    sample_index=sample_index,
+                )
+                errors.append(error)
+    return errors

cg/services/order_validation_service/workflows/balsamic/rules/case_sample/utils.py

@@ -0,0 +1,5 @@
+from cg.services.order_validation_service.workflows.balsamic.models.sample import BalsamicSample
+
+
+def has_sex_and_subject(sample: BalsamicSample) -> bool:
+    return sample.subject_id and sample.sex

cg/services/order_validation_service/workflows/balsamic/validation_rules.py

@@ -20,6 +20,10 @@
     validate_volume_interval,
     validate_wells_contain_at_most_one_sample,
 )
+from cg.services.order_validation_service.workflows.balsamic.rules.case_sample.rules import (
+    validate_subject_sex_consistency,
+)
+
 
 CASE_RULES: list[callable] = [
     validate_case_internal_ids_exist,
@@ -43,4 +47,5 @@
     validate_subject_ids_different_from_sample_names,
     validate_volume_interval,
     validate_wells_contain_at_most_one_sample,
+    validate_subject_sex_consistency,
 ]

cg/store/crud/read.py

@@ -1562,3 +1562,16 @@ def get_case_ids_for_samples(self, sample_ids: list[int]) -> list[str]:
         for sample_id in sample_ids:
             case_ids.extend(self.get_case_ids_with_sample(sample_id))
         return list(set(case_ids))
+
+    def sample_exists_with_different_sex(
+        self,
+        customer_internal_id: str,
+        subject_id: str,
+        sex: str,
+    ) -> bool:
+        samples: list[Sample] = self.get_samples_by_customer_and_subject_id(
+            customer_internal_id=customer_internal_id,
+            subject_id=subject_id,
+        )
+        existing_sex: set[str] = {sample.sex for sample in samples}
+        return bool(samples) and sex not in existing_sex