Add application validation

cg/services/order_validation_service/models/errors.py

@@ -53,3 +53,8 @@ class OrderNameRequiredError(OrderError):
 class OccupiedWellError(CaseSampleError):
     field: str = "well_position"
     message: str = "Well is already occupied"
+
+
+class ApplicationNotValidError(SampleError):
+    field: str = "application"
+    message: str = "Application is not valid"

cg/services/order_validation_service/utils.py

@@ -5,6 +5,7 @@
 from cg.services.order_validation_service.models.errors import (
     CaseSampleError,
     OrderError,
+    SampleError,
     ValidationErrors,
 )
 from cg.services.order_validation_service.models.order import Order
@@ -20,11 +21,19 @@ def apply_order_validation(rules: list[Callable], order: Order, store: Store) ->
 
 
 def apply_case_sample_validation(
-    rules: list[Callable], case, store: Store
+    rules: list[Callable], order: Order, store: Store
 ) -> list[CaseSampleError]:
     errors: list[CaseSampleError] = []
     for rule in rules:
-        rule_errors: list[CaseSampleError] = rule(case=case, store=store)
+        rule_errors: list[CaseSampleError] = rule(order=order, store=store)
+        errors.extend(rule_errors)
+    return errors
+
+
+def apply_sample_validation(rules: list[Callable], order: Order, store: Store) -> list[SampleError]:
+    errors: list[SampleError] = []
+    for rule in rules:
+        rule_errors: list[CaseSampleError] = rule(order=order, store=store)
         errors.extend(rule_errors)
     return errors
 

cg/services/order_validation_service/validators/data/rules.py

@@ -1,8 +1,10 @@
 from cg.services.order_validation_service.models.errors import (
+    ApplicationNotValidError,
     CustomerCannotSkipReceptionControlError,
     CustomerDoesNotExistError,
-    UserNotAssociatedWithCustomerError,
     OrderError,
+    SampleError,
+    UserNotAssociatedWithCustomerError,
 )
 from cg.services.order_validation_service.models.order import Order
 from cg.store.store import Store
@@ -41,3 +43,13 @@ def validate_customer_exists(order: Order, store: Store, **kwargs) -> list[Order
         error = CustomerDoesNotExistError()
         errors.append(error)
     return errors
+
+
+def validate_application_exists(order: Order, store: Store, **kwargs) -> list[SampleError]:
+    errors: list[SampleError] = []
+    for case in order.cases:
+        for sample in case.samples:
+            if not store.get_application_by_tag(sample.application):
+                error = ApplicationNotValidError(sample_name=sample.name)
+                errors.append(error)
+    return errors

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

@@ -1,4 +1,5 @@
 from cg.services.order_validation_service.validators.data.rules import (
+    validate_application_exists,
     validate_customer_can_skip_reception_control,
     validate_customer_exists,
     validate_user_belongs_to_customer,
@@ -18,3 +19,5 @@
 ]
 
 TOMTE_CASE_SAMPLE_RULES = [validate_wells_contain_at_most_one_sample]
+
+TOMTE_SAMPLE_RULES = [validate_application_exists]

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

@@ -1,6 +1,7 @@
 from cg.services.order_validation_service.models.errors import (
     CaseSampleError,
     OrderError,
+    SampleError,
     ValidationErrors,
 )
 from cg.services.order_validation_service.order_validation_service import (
@@ -9,13 +10,15 @@
 from cg.services.order_validation_service.utils import (
     apply_case_sample_validation,
     apply_order_validation,
+    apply_sample_validation,
 )
 from cg.services.order_validation_service.workflows.tomte.validation.field.model_validator import (
     TomteModelValidator,
 )
 from cg.services.order_validation_service.workflows.tomte.validation_rules import (
     TOMTE_CASE_SAMPLE_RULES,
     TOMTE_ORDER_RULES,
+    TOMTE_SAMPLE_RULES,
 )
 from cg.store.store import Store
 
@@ -36,6 +39,14 @@ def validate(self, order_json: str) -> ValidationErrors:
             rules=TOMTE_ORDER_RULES, order=order, store=self.store
         )
         case_sample_errors: list[CaseSampleError] = apply_case_sample_validation(
-            rules=TOMTE_CASE_SAMPLE_RULES, case=order.cases, store=self.store
+            rules=TOMTE_CASE_SAMPLE_RULES, order=order, store=self.store
+        )
+        sample_errors: list[SampleError] = apply_sample_validation(
+            rules=TOMTE_SAMPLE_RULES, order=order, store=self.store
+        )
+
+        return ValidationErrors(
+            order_errors=order_errors,
+            case_sample_errors=case_sample_errors,
+            sample_errors=sample_errors,
         )
-        return ValidationErrors(order_errors=order_errors, case_sample_errors=case_sample_errors)

tests/services/order_validation_service/conftest.py

@@ -15,7 +15,7 @@
 def create_sample(id: int) -> TomteSample:
     return TomteSample(
         name=f"name{id}",
-        application="application",
+        application="WGSPCFC030",
         container=ContainerEnum.plate,
         require_qc_ok=True,
         reference_genome=GenomeVersion.hg19,

tests/services/order_validation_service/test_data_validators.py

@@ -0,0 +1,21 @@
+from cg.services.order_validation_service.models.errors import ApplicationNotValidError
+from cg.services.order_validation_service.models.order import Order
+from cg.services.order_validation_service.validators.data.rules import (
+    validate_application_exists,
+)
+from cg.store.store import Store
+
+
+def test_applications_exist(valid_order: Order, base_store: Store):
+    # GIVEN an order where one of the samples has an invalid application
+    for case in valid_order.cases:
+        case.samples[0].application = "Invalid application"
+
+    # WHEN validating the order
+    errors = validate_application_exists(order=valid_order, store=base_store)
+
+    # THEN an error should be returned
+    assert errors
+
+    # THEN the error should be about the ticket number
+    assert isinstance(errors[0], ApplicationNotValidError)