Patch existing parents in rules

cg/services/orders/validation/models/case.py

@@ -6,6 +6,8 @@
 from cg.services.orders.validation.models.discriminators import has_internal_id
 from cg.services.orders.validation.models.existing_sample import ExistingSample
 from cg.services.orders.validation.models.sample_aliases import SampleInCase
+from cg.store.models import Sample as DbSample
+from cg.store.store import Store
 
 NewSample = Annotated[SampleInCase, Tag("new")]
 ExistingSampleType = Annotated[ExistingSample, Tag("existing")]
@@ -45,11 +47,17 @@ def enumerated_existing_samples(self) -> list[tuple[int, ExistingSample]]:
                 samples.append((sample_index, sample))
         return samples
 
-    def get_sample(self, sample_name: str) -> SampleInCase | None:
+    def get_new_sample(self, sample_name: str) -> SampleInCase | None:
         for _, sample in self.enumerated_new_samples:
             if sample.name == sample_name:
                 return sample
 
+    def get_existing_sample_from_db(self, sample_name: str, store: Store) -> DbSample | None:
+        for _, sample in self.enumerated_existing_samples:
+            db_sample: DbSample | None = store.get_sample_by_internal_id(sample.internal_id)
+            if db_sample and db_sample.name == sample_name:
+                return db_sample
+
     @model_validator(mode="before")
     def convert_empty_strings_to_none(cls, data):
         if isinstance(data, dict):

cg/services/orders/validation/rules/case/utils.py

@@ -1,3 +1,4 @@
+from cg.services.orders.validation.models.case import Case
 from cg.services.orders.validation.models.existing_case import ExistingCase
 from cg.services.orders.validation.workflows.balsamic.models.case import BalsamicCase
 from cg.services.orders.validation.workflows.balsamic_umi.models.case import BalsamicUmiCase
@@ -34,3 +35,11 @@ def is_case_not_from_collaboration(case: ExistingCase, customer_id: str, store:
     db_case: DbCase | None = store.get_case_by_internal_id(case.internal_id)
     customer: Customer | None = store.get_customer_by_internal_id(customer_id)
     return db_case and customer and db_case.customer not in customer.collaborators
+
+
+def is_sample_in_case(case: Case, sample_name: str, store: Store) -> bool:
+    if case.get_new_sample(sample_name):
+        return True
+    elif case.get_existing_sample_from_db(sample_name=sample_name, store=store):
+        return True
+    return False

cg/services/orders/validation/rules/case_sample/rules.py

@@ -292,48 +292,49 @@ def validate_sample_names_different_from_case_names(
     return errors
 
 
-def validate_fathers_are_male(order: OrderWithCases, **kwargs) -> list[InvalidFatherSexError]:
+def validate_fathers_are_male(
+    order: OrderWithCases, store: Store, **kwargs
+) -> list[InvalidFatherSexError]:
     errors: list[InvalidFatherSexError] = []
     for index, case in order.enumerated_new_cases:
         case_errors: list[InvalidFatherSexError] = get_father_sex_errors(
-            case=case, case_index=index
+            case=case, case_index=index, store=store
         )
         errors.extend(case_errors)
     return errors
 
 
 def validate_fathers_in_same_case_as_children(
-    order: OrderWithCases, **kwargs
+    order: OrderWithCases, store: Store, **kwargs
 ) -> list[FatherNotInCaseError]:
     errors: list[FatherNotInCaseError] = []
     for index, case in order.enumerated_new_cases:
         case_errors: list[FatherNotInCaseError] = get_father_case_errors(
-            case=case,
-            case_index=index,
+            case=case, case_index=index, store=store
         )
         errors.extend(case_errors)
     return errors
 
 
-def validate_mothers_are_female(order: OrderWithCases, **kwargs) -> list[InvalidMotherSexError]:
+def validate_mothers_are_female(
+    order: OrderWithCases, store: Store, **kwargs
+) -> list[InvalidMotherSexError]:
     errors: list[InvalidMotherSexError] = []
     for index, case in order.enumerated_new_cases:
         case_errors: list[InvalidMotherSexError] = get_mother_sex_errors(
-            case=case,
-            case_index=index,
+            case=case, case_index=index, store=store
         )
         errors.extend(case_errors)
     return errors
 
 
 def validate_mothers_in_same_case_as_children(
-    order: OrderWithCases, **kwargs
+    order: OrderWithCases, store: Store, **kwargs
 ) -> list[MotherNotInCaseError]:
     errors: list[MotherNotInCaseError] = []
     for index, case in order.enumerated_new_cases:
         case_errors: list[MotherNotInCaseError] = get_mother_case_errors(
-            case=case,
-            case_index=index,
+            case=case, case_index=index, store=store
         )
         errors.extend(case_errors)
     return errors

cg/services/orders/validation/rules/case_sample/utils.py

@@ -28,6 +28,7 @@
     SampleInCase,
     SampleWithRelatives,
 )
+from cg.services.orders.validation.rules.case.utils import is_sample_in_case
 from cg.services.orders.validation.rules.utils import (
     get_concentration_interval,
     has_sample_invalid_concentration,
@@ -112,21 +113,27 @@ def get_repeated_case_name_errors(order: OrderWithCases) -> list[RepeatedCaseNam
 
 
 def get_father_sex_errors(
-    case: CaseContainingRelatives, case_index: int
+    case: CaseContainingRelatives, case_index: int, store: Store
 ) -> list[InvalidFatherSexError]:
     errors: list[InvalidFatherSexError] = []
     children: list[tuple[SampleWithRelatives, int]] = case.get_samples_with_father()
     for child, child_index in children:
-        if is_father_sex_invalid(child=child, case=case):
+        if is_father_sex_invalid(child=child, case=case, store=store):
             error: InvalidFatherSexError = create_father_sex_error(
                 case_index=case_index, sample_index=child_index
             )
             errors.append(error)
     return errors
 
 
-def is_father_sex_invalid(child: SampleWithRelatives, case: CaseContainingRelatives) -> bool:
-    father: SampleWithRelatives | None = case.get_sample(child.father)
+def is_father_sex_invalid(
+    child: SampleWithRelatives, case: CaseContainingRelatives, store: Store
+) -> bool:
+    father: SampleWithRelatives | None = case.get_new_sample(child.father)
+    if not father:
+        father: DbSample | None = case.get_existing_sample_from_db(
+            sample_name=child.father, store=store
+        )
     return father and father.sex != Sex.MALE
 
 
@@ -135,14 +142,14 @@ def create_father_sex_error(case_index: int, sample_index: int) -> InvalidFather
 
 
 def get_father_case_errors(
-    case: CaseContainingRelatives,
-    case_index: int,
+    case: CaseContainingRelatives, case_index: int, store: Store
 ) -> list[FatherNotInCaseError]:
     errors: list[FatherNotInCaseError] = []
-    children: list[tuple[SampleWithRelatives, int]] = case.get_samples_with_father()
+    children: list[tuple[SampleWithRelatives | ExistingSample, int]] = (
+        case.get_samples_with_father()
+    )
     for child, child_index in children:
-        father: SampleWithRelatives | None = case.get_sample(child.father)
-        if not father:
+        if not is_sample_in_case(case=case, sample_name=child.father, store=store):
             error: FatherNotInCaseError = create_father_case_error(
                 case_index=case_index,
                 sample_index=child_index,
@@ -152,13 +159,12 @@ def get_father_case_errors(
 
 
 def get_mother_sex_errors(
-    case: CaseContainingRelatives,
-    case_index: int,
+    case: CaseContainingRelatives, case_index: int, store: Store
 ) -> list[InvalidMotherSexError]:
     errors: list[InvalidMotherSexError] = []
     children: list[tuple[SampleWithRelatives, int]] = case.get_samples_with_mother()
     for child, child_index in children:
-        if is_mother_sex_invalid(child=child, case=case):
+        if is_mother_sex_invalid(child=child, case=case, store=store):
             error: InvalidMotherSexError = create_mother_sex_error(
                 case_index=case_index,
                 sample_index=child_index,
@@ -168,14 +174,12 @@ def get_mother_sex_errors(
 
 
 def get_mother_case_errors(
-    case: CaseContainingRelatives,
-    case_index: int,
+    case: CaseContainingRelatives, case_index: int, store: Store
 ) -> list[MotherNotInCaseError]:
     errors: list[MotherNotInCaseError] = []
     children: list[tuple[SampleWithRelatives, int]] = case.get_samples_with_mother()
     for child, child_index in children:
-        mother: SampleWithRelatives | None = case.get_sample(child.mother)
-        if not mother:
+        if not is_sample_in_case(case=case, sample_name=child.mother, store=store):
             error: MotherNotInCaseError = create_mother_case_error(
                 case_index=case_index, sample_index=child_index
             )
@@ -191,8 +195,14 @@ def create_mother_case_error(case_index: int, sample_index: int) -> MotherNotInC
     return MotherNotInCaseError(case_index=case_index, sample_index=sample_index)
 
 
-def is_mother_sex_invalid(child: SampleWithRelatives, case: CaseContainingRelatives) -> bool:
-    mother: SampleWithRelatives | None = case.get_sample(child.mother)
+def is_mother_sex_invalid(
+    child: SampleWithRelatives, case: CaseContainingRelatives, store: Store
+) -> bool:
+    mother: SampleWithRelatives | None = case.get_new_sample(child.mother)
+    if not mother:
+        mother: DbSample | None = case.get_existing_sample_from_db(
+            sample_name=child.mother, store=store
+        )
     return mother and mother.sex != Sex.FEMALE
 
 

cg/services/orders/validation/workflows/mip_dna/models/case.py

@@ -16,8 +16,8 @@ class MipDnaCase(Case):
     synopsis: str | None = None
     samples: list[Annotated[NewSample | OldSample, Discriminator(has_internal_id)]]
 
-    def get_samples_with_father(self) -> list[tuple[MipDnaSample, int]]:
+    def get_samples_with_father(self) -> list[tuple[MipDnaSample | ExistingSample, int]]:
         return [(sample, index) for index, sample in self.enumerated_samples if sample.father]
 
-    def get_samples_with_mother(self) -> list[tuple[MipDnaSample, int]]:
+    def get_samples_with_mother(self) -> list[tuple[MipDnaSample | ExistingSample, int]]:
         return [(sample, index) for index, sample in self.enumerated_samples if sample.mother]

cg/services/orders/validation/workflows/tomte/models/case.py

@@ -16,8 +16,8 @@ class TomteCase(Case):
     synopsis: str | None = None
     samples: list[Annotated[NewSample | OldSample, Discriminator(has_internal_id)]]
 
-    def get_samples_with_father(self) -> list[tuple[TomteSample, int]]:
+    def get_samples_with_father(self) -> list[tuple[TomteSample | ExistingSample, int]]:
         return [(sample, index) for index, sample in self.enumerated_samples if sample.father]
 
-    def get_samples_with_mother(self) -> list[tuple[TomteSample, int]]:
+    def get_samples_with_mother(self) -> list[tuple[TomteSample | ExistingSample, int]]:
         return [(sample, index) for index, sample in self.enumerated_samples if sample.mother]

tests/services/orders/validation_service/workflows/tomte/test_case_sample_rules.py

@@ -1,3 +1,4 @@
+from cg.constants import Sex
 from cg.models.orders.sample_base import StatusEnum
 from cg.services.orders.validation.errors.case_errors import (
     InvalidGenePanelsError,
@@ -7,6 +8,7 @@
     DescendantAsFatherError,
     FatherNotInCaseError,
     InvalidFatherSexError,
+    InvalidMotherSexError,
     PedigreeError,
     SampleIsOwnFatherError,
 )
@@ -16,9 +18,11 @@
     validate_fathers_are_male,
     validate_fathers_in_same_case_as_children,
     validate_gene_panels_exist,
+    validate_mothers_are_female,
     validate_pedigree,
 )
 from cg.services.orders.validation.workflows.tomte.models.order import TomteOrder
+from cg.store.models import Sample
 from cg.store.store import Store
 from tests.store_helpers import StoreHelpers
 
@@ -55,11 +59,13 @@ def test_repeated_gene_panels(valid_order: TomteOrder, store_with_panels: Store)
     assert isinstance(errors[0], RepeatedGenePanelsError)
 
 
-def test_father_must_be_male(order_with_invalid_father_sex: TomteOrder):
+def test_father_must_be_male(order_with_invalid_father_sex: TomteOrder, base_store: Store):
     # GIVEN an order with an incorrectly specified father
 
     # WHEN validating the order
-    errors: list[InvalidFatherSexError] = validate_fathers_are_male(order_with_invalid_father_sex)
+    errors: list[InvalidFatherSexError] = validate_fathers_are_male(
+        order=order_with_invalid_father_sex, store=base_store
+    )
 
     # THEN errors are returned
     assert errors
@@ -68,13 +74,73 @@ def test_father_must_be_male(order_with_invalid_father_sex: TomteOrder):
     assert isinstance(errors[0], InvalidFatherSexError)
 
 
-def test_father_in_wrong_case(order_with_father_in_wrong_case: TomteOrder):
+def test_existing_father_must_be_male(
+    valid_order: TomteOrder, store_with_multiple_cases_and_samples: Store
+):
+    """Tests that an order with a father which is a female sample in StatusDB gives an error."""
+
+    # GIVEN a sample in StatusDB with female sex
+    father_db_sample: Sample = store_with_multiple_cases_and_samples.session.query(Sample).first()
+    father_db_sample.sex = Sex.FEMALE
+    store_with_multiple_cases_and_samples.commit_to_store()
+
+    # GIVEN that an order has a corresponding existing sample in one of its cases
+    father_sample = ExistingSample(internal_id=father_db_sample.internal_id)
+    valid_order.cases[0].samples.append(father_sample)
+
+    # GIVEN that another sample in the order specifies the sample as its father
+    father_name = father_db_sample.name
+    valid_order.cases[0].samples[0].father = father_name
+
+    # WHEN validating the order
+    errors: list[InvalidFatherSexError] = validate_fathers_are_male(
+        order=valid_order, store=store_with_multiple_cases_and_samples
+    )
+
+    # THEN errors are returned
+    assert errors
+
+    # THEN the errors are about the father's sex
+    assert isinstance(errors[0], InvalidFatherSexError)
+
+
+def test_existing_mother_must_be_female(
+    valid_order: TomteOrder, store_with_multiple_cases_and_samples: Store
+):
+    """Tests that an order with a mother which is a male sample in StatusDB gives an error."""
+
+    # GIVEN a sample in StatusDB with male sex
+    mother_db_sample: Sample = store_with_multiple_cases_and_samples.session.query(Sample).first()
+    mother_db_sample.sex = Sex.MALE
+    store_with_multiple_cases_and_samples.commit_to_store()
+
+    # GIVEN that an order has a corresponding existing sample in one of its cases
+    mother_sample = ExistingSample(internal_id=mother_db_sample.internal_id)
+    valid_order.cases[0].samples.append(mother_sample)
+
+    # GIVEN that another sample in the order specifies the sample as its mother
+    mother_name = mother_db_sample.name
+    valid_order.cases[0].samples[0].mother = mother_name
+
+    # WHEN validating the order
+    errors: list[InvalidMotherSexError] = validate_mothers_are_female(
+        order=valid_order, store=store_with_multiple_cases_and_samples
+    )
+
+    # THEN errors are returned
+    assert errors
+
+    # THEN the errors are about the father's sex
+    assert isinstance(errors[0], InvalidMotherSexError)
+
+
+def test_father_in_wrong_case(order_with_father_in_wrong_case: TomteOrder, base_store: Store):
 
     # GIVEN an order with the father sample in the wrong case
 
     # WHEN validating the order
     errors: list[FatherNotInCaseError] = validate_fathers_in_same_case_as_children(
-        order_with_father_in_wrong_case
+        order=order_with_father_in_wrong_case, store=base_store
     )
 
     # THEN an error is returned