remove directory for balsamic specific rules

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

@@ -8,6 +8,7 @@
     ApplicationNotCompatibleError,
     ApplicationNotValidError,
     BufferMissingError,
+    CaptureKitMissingError,
     ConcentrationRequiredIfSkipRCError,
     ContainerNameMissingError,
     ContainerNameRepeatedError,
@@ -52,6 +53,7 @@
     is_concentration_missing,
     is_container_name_missing,
     is_invalid_plate_well_format,
+    is_sample_missing_capture_kit,
     is_sample_tube_name_reused,
     is_well_position_missing,
     validate_concentration_in_case,
@@ -62,6 +64,7 @@
     is_volume_invalid,
     is_volume_missing,
 )
+from cg.services.orders.validation.workflows.balsamic.models.order import BalsamicOrder
 from cg.store.models import Sample as DbSample
 from cg.store.store import Store
 
@@ -438,3 +441,19 @@ def validate_buffer_required(order: OrderWithCases, **kwargs) -> list[BufferMiss
             error = BufferMissingError(case_index=case_index, sample_index=sample_index)
             errors.append(error)
     return errors
+
+
+def validate_capture_kit_panel_requirement(
+    order: BalsamicOrder, store: Store
+) -> list[CaptureKitMissingError]:
+    """
+    Return an error for each new sample missing a capture kit, if its application requires one.
+    Applicable to Balsamic orders only.
+    """
+    errors: list[CaptureKitMissingError] = []
+    for case_index, case in order.enumerated_new_cases:
+        for sample_index, sample in case.enumerated_new_samples:
+            if is_sample_missing_capture_kit(sample=sample, store=store):
+                error = CaptureKitMissingError(case_index=case_index, sample_index=sample_index)
+                errors.append(error)
+    return errors

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

@@ -2,6 +2,7 @@
 from collections import Counter
 
 from cg.constants.constants import StatusOptions
+from cg.constants.sequencing import SeqLibraryPrepCategory
 from cg.constants.subject import Sex
 from cg.models.orders.sample_base import ContainerEnum, SexEnum
 from cg.services.orders.validation.errors.case_errors import RepeatedCaseNameError
@@ -33,6 +34,8 @@
     is_sample_on_plate,
     is_volume_within_allowed_interval,
 )
+from cg.services.orders.validation.workflows.balsamic.models.sample import BalsamicSample
+from cg.store.models import Application
 from cg.store.store import Store
 
 
@@ -283,3 +286,13 @@ def is_buffer_missing(sample: SampleInCase) -> bool:
         sample.application.startswith(tuple(applications_requiring_buffer))
         and not sample.elution_buffer
     )
+
+
+def is_sample_missing_capture_kit(sample: BalsamicSample, store: Store) -> bool:
+    """Returns whether a TGS sample has an application and is missing a capture kit."""
+    application: Application | None = store.get_application_by_tag(sample.application)
+    return (
+        application
+        and application.prep_category == SeqLibraryPrepCategory.TARGETED_GENOME_SEQUENCING
+        and not sample.capture_kit
+    )

cg/services/orders/validation/workflows/balsamic/validation_rules.py

@@ -11,6 +11,7 @@
     validate_application_not_archived,
     validate_buffer_required,
     validate_buffer_skip_rc_condition,
+    validate_capture_kit_panel_requirement,
     validate_concentration_interval_if_skip_rc,
     validate_concentration_required_if_skip_rc,
     validate_container_name_required,
@@ -27,9 +28,6 @@
     validate_well_positions_required,
     validate_wells_contain_at_most_one_sample,
 )
-from cg.services.orders.validation.workflows.balsamic.rules import (
-    validate_capture_kit_panel_requirement,
-)
 
 BALSAMIC_CASE_RULES: list[callable] = [
     validate_at_most_two_samples_per_case,

tests/services/orders/validation_service/workflows/balsamic/test_rules.py

@@ -9,11 +9,11 @@
     validate_at_most_two_samples_per_case,
     validate_number_of_normal_samples,
 )
-from cg.services.orders.validation.workflows.balsamic.models.order import BalsamicOrder
-from cg.services.orders.validation.workflows.balsamic.models.sample import BalsamicSample
-from cg.services.orders.validation.workflows.balsamic.rules import (
+from cg.services.orders.validation.rules.case_sample.rules import (
     validate_capture_kit_panel_requirement,
 )
+from cg.services.orders.validation.workflows.balsamic.models.order import BalsamicOrder
+from cg.services.orders.validation.workflows.balsamic.models.sample import BalsamicSample
 from cg.store.models import Application
 from cg.store.store import Store