Validate father in same case as child (#3492)

cg/services/order_validation_service/models/errors.py

@@ -80,6 +80,11 @@ class InvalidFatherSexError(CaseSampleError):
     message: str = "Father must be male"
 
 
+class FatherNotInCaseError(CaseSampleError):
+    field: str = "father"
+    message: str = "Father must be in the same case"
+
+
 class InvalidMotherSexError(CaseSampleError):
     field: str = "mother"
     message: str = "Mother must be female"

cg/services/order_validation_service/workflows/tomte/validation/inter_field/rules.py

@@ -1,5 +1,6 @@
 from cg.constants.subject import Sex
 from cg.services.order_validation_service.models.errors import (
+    FatherNotInCaseError,
     InvalidFatherSexError,
     InvalidMotherSexError,
     OccupiedWellError,
@@ -12,7 +13,9 @@
     _get_errors,
     _get_excess_samples,
     _get_plate_samples,
+    get_father_case_errors,
     get_father_sex_errors,
+    get_mother_sex_errors,
     get_repeated_case_name_errors,
     get_repeated_sample_name_errors,
 )
@@ -44,6 +47,14 @@ def validate_fathers_are_male(order: TomteOrder) -> list[InvalidFatherSexError]:
     return errors
 
 
+def validate_fathers_in_same_case_as_children(order: TomteOrder) -> list[FatherNotInCaseError]:
+    errors = []
+    for case in order.cases:
+        case_errors = get_father_case_errors(case)
+        errors.extend(case_errors)
+    return errors
+
+
 def validate_mothers_are_female(order: TomteOrder) -> list[InvalidMotherSexError]:
     errors: list[InvalidMotherSexError] = []
     for case in order.cases:

cg/services/order_validation_service/workflows/tomte/validation/inter_field/utils.py

@@ -2,6 +2,7 @@
 from cg.constants.subject import Sex
 from cg.models.orders.sample_base import ContainerEnum
 from cg.services.order_validation_service.models.errors import (
+    FatherNotInCaseError,
     InvalidFatherSexError,
     InvalidMotherSexError,
     OccupiedWellError,
@@ -98,6 +99,17 @@ def create_father_sex_error(case: TomteCase, sample: TomteSample) -> InvalidFath
     return InvalidFatherSexError(sample_name=sample.name, case_name=case.name)
 
 
+def get_father_case_errors(case: TomteCase) -> list[FatherNotInCaseError]:
+    errors = []
+    children: list[TomteSample] = case.get_samples_with_father()
+    for child in children:
+        father: TomteSample | None = case.get_sample(child.father)
+        if not father:
+            error = create_father_case_error(case=case, sample=child)
+            errors.append(error)
+    return errors
+
+
 def get_mother_sex_errors(case: TomteCase) -> list[InvalidMotherSexError]:
     errors = []
     children: list[TomteSample] = case.get_samples_with_mother()
@@ -108,6 +120,10 @@ def get_mother_sex_errors(case: TomteCase) -> list[InvalidMotherSexError]:
     return errors
 
 
+def create_father_case_error(case: TomteCase, sample: TomteSample) -> FatherNotInCaseError:
+    return FatherNotInCaseError(case_name=case.name, sample_name=sample.name)
+
+
 def is_mother_sex_invalid(child: TomteSample, case: TomteCase) -> bool:
     mother: TomteSample | None = case.get_sample(child.mother)
     return mother and mother.sex != Sex.FEMALE

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

@@ -10,6 +10,7 @@
 )
 from cg.services.order_validation_service.workflows.tomte.validation.inter_field.rules import (
     validate_fathers_are_male,
+    validate_fathers_in_same_case_as_children,
     validate_mothers_are_female,
     validate_no_repeated_case_names,
     validate_no_repeated_sample_names,
@@ -27,6 +28,7 @@
     validate_no_repeated_case_names,
     validate_no_repeated_sample_names,
     validate_fathers_are_male,
+    validate_fathers_in_same_case_as_children,
     validate_mothers_are_female,
     validate_application_exists,
     validate_application_compatibility,

tests/services/order_validation_service/conftest.py

@@ -98,7 +98,7 @@ def order_with_repeated_sample_names(
 @pytest.fixture
 def case() -> TomteCase:
     sample_1: TomteSample = create_sample(1)
-    sample_2: TomteSample = create_sample(1)
+    sample_2: TomteSample = create_sample(2)
     return create_case([sample_1, sample_2])
 
 
@@ -114,3 +114,12 @@ def order_with_invalid_father_sex(case: TomteCase):
     child.father = father.name
     father.sex = SexEnum.female
     return create_order([case])
+
+
+@pytest.fixture
+def order_with_father_in_wrong_case(case: TomteCase):
+    child = case.samples[0]
+    father = case.samples[1]
+    child.father = father.name
+    case.samples = [child]
+    return create_order([case])

tests/services/order_validation_service/test_tomte_inter_field_validators.py

@@ -1,4 +1,5 @@
 from cg.services.order_validation_service.models.errors import (
+    FatherNotInCaseError,
     InvalidFatherSexError,
     OccupiedWellError,
     RepeatedCaseNameError,
@@ -7,6 +8,7 @@
 from cg.services.order_validation_service.workflows.tomte.models.order import TomteOrder
 from cg.services.order_validation_service.workflows.tomte.validation.inter_field.rules import (
     validate_fathers_are_male,
+    validate_fathers_in_same_case_as_children,
     validate_no_repeated_case_names,
     validate_no_repeated_sample_names,
     validate_wells_contain_at_most_one_sample,
@@ -85,3 +87,17 @@ def test_no_father_sex_error_when_no_father_present(valid_order: TomteOrder):
 
     # THEN no errors are returned
     assert not errors
+
+
+def test_father_in_wrong_case(order_with_father_in_wrong_case: TomteOrder):
+
+    # GIVEN an order with the father sample in the wrong case
+
+    # WHEN validating the order
+    errors = validate_fathers_in_same_case_as_children(order_with_father_in_wrong_case)
+
+    # THEN an error is returned
+    assert errors
+
+    # THEN the error is about the father being in the wrong case
+    assert isinstance(errors[0], FatherNotInCaseError)