(Improve order flow) Remove old case validation (#4096) (patch)

### Fixed - Removed old case order validation
Clinical-Genomics · Jan 15, 2025 · 5a253b5 · 5a253b5
1 parent 64caf0f
commit 5a253b5
Show file tree

Hide file tree

Showing 5 changed files with 73 additions and 272 deletions.
diff --git a/cg/services/orders/validate_order_services/validate_case_order.py b/cg/services/orders/validate_order_services/validate_case_order.py
diff --git a/tests/fixture_plugins/orders_fixtures/order_to_submit_fixtures.py b/tests/fixture_plugins/orders_fixtures/order_to_submit_fixtures.py
@@ -21,6 +21,7 @@
 from cg.services.order_validation_service.workflows.mutant.models.order import MutantOrder
 from cg.services.order_validation_service.workflows.pacbio_long_read.models.order import PacbioOrder
 from cg.services.order_validation_service.workflows.rml.models.order import RmlOrder
+from cg.services.order_validation_service.workflows.rna_fusion.models.order import RnaFusionOrder
 
 
 @pytest.fixture(scope="session")
@@ -156,6 +157,6 @@ def all_orders_to_submit(
         OrderType.MIP_RNA: MipRnaOrder.model_validate(mip_rna_order_to_submit),
         OrderType.PACBIO_LONG_READ: PacbioOrder.model_validate(pacbio_order_to_submit),
         OrderType.RML: RmlOrder.model_validate(rml_order_to_submit),
-        # OrderType.RNAFUSION: RnaFusionOrder.model_validate(rnafusion_order_to_submit),
+        OrderType.RNAFUSION: RnaFusionOrder.model_validate(rnafusion_order_to_submit),
         OrderType.SARS_COV_2: MutantOrder.model_validate(sarscov2_order_to_submit),
     }
diff --git a/tests/meta/orders/test_meta_orders_api.py b/tests/meta/orders/test_meta_orders_api.py
@@ -20,7 +20,6 @@
 from cg.services.order_validation_service.workflows.balsamic.models.order import BalsamicOrder
 from cg.services.order_validation_service.workflows.mip_dna.models.order import MipDnaOrder
 from cg.services.order_validation_service.workflows.mip_rna.models.order import MipRnaOrder
-from cg.services.orders.validate_order_services.validate_case_order import ValidateCaseOrderService
 from cg.store.models import Case, Customer, Pool, Sample
 from cg.store.store import Store
 from tests.store_helpers import StoreHelpers
@@ -416,131 +415,6 @@ def test_submit_unique_sample_case_name(
         # Then no exception about duplicate names should be thrown
 
 
-def test_validate_sex_inconsistent_sex(
-    orders_api: OrdersAPI, mip_dna_order_to_submit: dict, helpers: StoreHelpers
-):
-    # GIVEN we have an order with a sample that is already in the database but with different sex
-    order_data = MipDnaOrder.model_validate(mip_dna_order_to_submit)
-    store = orders_api.validation_service.store
-    customer: Customer = store.get_customer_by_internal_id(customer_internal_id=order_data.customer)
-
-    # add sample with different sex than in order
-    samples: list[Sample] = [sample for _, _, sample in order_data.enumerated_new_samples]
-    for sample in samples:
-        sample_obj: Sample = helpers.add_sample(
-            store=store,
-            customer_id=customer.internal_id,
-            sex=Sex.MALE if sample.sex == Sex.FEMALE else Sex.FEMALE,
-            name=sample.name,
-            subject_id=sample.subject_id,
-        )
-        store.session.add(sample_obj)
-        store.session.commit()
-        assert sample_obj.sex != sample.sex
-
-    validator = ValidateCaseOrderService(status_db=store)
-
-    # WHEN calling _validate_sex
-    # THEN an OrderError should be raised on non-matching sex
-    with pytest.raises(OrderError):
-        validator._validate_subject_sex(samples=samples, customer_id=order_data.customer)
-
-
-def test_validate_sex_consistent_sex(
-    orders_api: OrdersAPI, mip_dna_order_to_submit: dict, helpers: StoreHelpers
-):
-    # GIVEN we have an order with a sample that is already in the database and with same gender
-    order_data = MipDnaOrder.model_validate(mip_dna_order_to_submit)
-    store = orders_api.validation_service.store
-    customer: Customer = store.get_customer_by_internal_id(customer_internal_id=order_data.customer)
-
-    # add sample with different sex than in order
-    samples: list[Sample] = [sample for _, _, sample in order_data.enumerated_new_samples]
-    for sample in samples:
-        sample_obj: Sample = helpers.add_sample(
-            store=store,
-            customer_id=customer.internal_id,
-            sex=sample.sex,
-            name=sample.name,
-            subject_id=sample.subject_id,
-        )
-        store.session.add(sample_obj)
-        store.session.commit()
-        assert sample_obj.sex == sample.sex
-
-    validator = ValidateCaseOrderService(status_db=store)
-
-    # WHEN calling _validate_sex
-    validator._validate_subject_sex(samples=samples, customer_id=order_data.customer)
-
-    # THEN no OrderError should be raised on non-matching sex
-
-
-def test_validate_sex_unknown_existing_sex(
-    orders_api: OrdersAPI, mip_dna_order_to_submit: dict, helpers: StoreHelpers
-):
-    # GIVEN we have an order with a sample that is already in the database and with different gender but the existing is
-    # of type "unknown"
-    order_data = MipDnaOrder.model_validate(mip_dna_order_to_submit)
-    store = orders_api.validation_service.store
-    customer: Customer = store.get_customer_by_internal_id(customer_internal_id=order_data.customer)
-
-    # add sample with different sex than in order
-    samples: list[Sample] = [sample for _, _, sample in order_data.enumerated_new_samples]
-    for sample in samples:
-        sample_obj: Sample = helpers.add_sample(
-            store=store,
-            customer_id=customer.internal_id,
-            sex=Sex.UNKNOWN,
-            name=sample.name,
-            subject_id=sample.subject_id,
-        )
-        store.session.add(sample_obj)
-        store.session.commit()
-        assert sample_obj.sex != sample.sex
-
-    validator = ValidateCaseOrderService(store)
-
-    # WHEN calling _validate_sex
-    validator._validate_subject_sex(samples=samples, customer_id=order_data.customer)
-
-    # THEN no OrderError should be raised on non-matching sex
-
-
-def test_validate_sex_unknown_new_sex(
-    orders_api: OrdersAPI, mip_dna_order_to_submit: dict, helpers: StoreHelpers
-):
-    # GIVEN we have an order with a sample that is already in the database and with different gender but the new is of
-    # type "unknown"
-    order_data = MipDnaOrder.model_validate(mip_dna_order_to_submit)
-    store = orders_api.validation_service.store
-    customer: Customer = store.get_customer_by_internal_id(customer_internal_id=order_data.customer)
-
-    # add sample with different sex than in order
-    samples: list[Sample] = [sample for _, _, sample in order_data.enumerated_new_samples]
-    for sample in samples:
-        sample_obj: Sample = helpers.add_sample(
-            store=store,
-            customer_id=customer.internal_id,
-            sex=sample.sex,
-            name=sample.name,
-            subject_id=sample.subject_id,
-        )
-        sample.sex = "unknown"
-        store.session.add(sample_obj)
-        store.session.commit()
-
-    for sample in samples:
-        assert sample_obj.sex != sample.sex
-
-    validator = ValidateCaseOrderService(store)
-
-    # WHEN calling _validate_sex
-    validator._validate_subject_sex(samples=samples, customer_id=order_data.customer)
-
-    # THEN no OrderError should be raised on non-matching sex
-
-
 @pytest.mark.xfail(reason="Change in order validation")
 @pytest.mark.parametrize(
     "order_type",

diff --git a/tests/services/order_validation_service/test_case_sample_rules.py b/tests/services/order_validation_service/test_case_sample_rules.py
@@ -405,6 +405,77 @@ def test_validate_sex_subject_id_clash(valid_order: OrderWithCases, sample_store
     assert isinstance(errors[0], SexSubjectIdError)
 
 
+def test_validate_sex_subject_id_no_clash(valid_order: OrderWithCases, sample_store: Store):
+    # GIVEN an existing sample
+    sample = sample_store.session.query(Sample).first()
+
+    # GIVEN an order and sample with the same customer and subject id
+    valid_order.customer = sample.customer.internal_id
+    valid_order.cases[0].samples[0].subject_id = "subject"
+    sample.subject_id = "subject"
+
+    # GIVEN that the order's sample has a matching sex to the one in StatusDB
+    valid_order.cases[0].samples[0].sex = SexEnum.female
+    sample.sex = SexEnum.female
+
+    # WHEN validating the order
+    errors: list[SexSubjectIdError] = validate_subject_sex_consistency(
+        order=valid_order,
+        store=sample_store,
+    )
+
+    # THEN no error should be returned
+    assert not errors
+
+
+def test_validate_sex_subject_id_existing_sex_unknown(
+    valid_order: OrderWithCases, sample_store: Store
+):
+    # GIVEN an existing sample
+    sample = sample_store.session.query(Sample).first()
+
+    # GIVEN an order and sample with the same customer and subject id
+    valid_order.customer = sample.customer.internal_id
+    valid_order.cases[0].samples[0].subject_id = "subject"
+    sample.subject_id = "subject"
+
+    # GIVEN a sample in the order that has a known sex and the existing sample's sex is unknown
+    valid_order.cases[0].samples[0].sex = SexEnum.female
+    sample.sex = SexEnum.unknown
+
+    # WHEN validating the order
+    errors: list[SexSubjectIdError] = validate_subject_sex_consistency(
+        order=valid_order,
+        store=sample_store,
+    )
+
+    # THEN no error should be returned
+    assert not errors
+
+
+def test_validate_sex_subject_id_new_sex_unknown(valid_order: OrderWithCases, sample_store: Store):
+    # GIVEN an existing sample
+    sample = sample_store.session.query(Sample).first()
+
+    # GIVEN an order and sample with the same customer and subject id
+    valid_order.customer = sample.customer.internal_id
+    valid_order.cases[0].samples[0].subject_id = "subject"
+    sample.subject_id = "subject"
+
+    # GIVEN a sample in the order that has an unknown sex and the existing sample's sex is known
+    valid_order.cases[0].samples[0].sex = SexEnum.unknown
+    sample.sex = SexEnum.female
+
+    # WHEN validating the order
+    errors: list[SexSubjectIdError] = validate_subject_sex_consistency(
+        order=valid_order,
+        store=sample_store,
+    )
+
+    # THEN no error should be returned
+    assert not errors
+
+
 def test_validate_sample_names_different_from_case_names(
     order_with_samples_having_same_names_as_cases: OrderWithCases,
 ):

diff --git a/tests/services/orders/test_validate_order_service/test_validate_generic_order.py b/tests/services/orders/test_validate_order_service/test_validate_generic_order.py