Add balsamic

cg/services/order_validation_service/workflows/balsamic/models/case.py

@@ -0,0 +1,8 @@
+from cg.services.order_validation_service.models.case import Case
+from cg.services.order_validation_service.workflows.balsamic.models.sample import BalsamicSample
+
+
+class BalsamicCase(Case):
+    samples: list[BalsamicSample]
+    cohorts: list[str] | None = None
+    synopsis: str | None = None

cg/services/order_validation_service/workflows/balsamic/models/order.py

@@ -0,0 +1,6 @@
+from cg.services.order_validation_service.models.order_with_cases import OrderWithCases
+from cg.services.order_validation_service.workflows.balsamic.models.case import BalsamicCase
+
+
+class BalsamicOrder(OrderWithCases):
+    cases: list[BalsamicCase]

cg/services/order_validation_service/workflows/balsamic/models/sample.py

@@ -0,0 +1,26 @@
+from pydantic import Field
+from cg.constants.constants import GenomeVersion
+from cg.models.orders.sample_base import NAME_PATTERN, ControlEnum, SexEnum, StatusEnum
+from cg.services.order_validation_service.constants import ElutionBuffer, TissueBlockEnum
+from cg.services.order_validation_service.models.sample import Sample
+
+
+class BalsamicSample(Sample):
+    age_at_sampling: float | None = None
+    capture_kit: str | None = None
+    comment: str | None = None
+    concentration_ng_ul: float | None = None
+    control: ControlEnum | None = None
+    elution_buffer: ElutionBuffer
+    formalin_fixation_time: int | None = None
+    is_tumour: bool
+    phenotype_groups: list[str] | None = None
+    phenotype_terms: list[str] | None = None
+    post_formalin_fixation_time: int | None = None
+    reference_genome: GenomeVersion
+    sex: SexEnum
+    source: str
+    status: StatusEnum | None = None
+    subject_id: str = Field(pattern=NAME_PATTERN, max_length=128)
+    tissue_block_size: TissueBlockEnum | None = None
+    tumour_purity: int | None = None

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

@@ -0,0 +1,2 @@
+CASE_RULES = []
+CASE_SAMPLE_RULES = []

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

@@ -0,0 +1,56 @@
+from cg.services.order_validation_service.errors.case_errors import CaseError
+from cg.services.order_validation_service.errors.case_sample_errors import CaseSampleError
+from cg.services.order_validation_service.errors.order_errors import OrderError
+from cg.services.order_validation_service.errors.validation_errors import ValidationErrors
+from cg.services.order_validation_service.model_validator.model_validator import ModelValidator
+from cg.services.order_validation_service.order_validation_service import OrderValidationService
+from cg.services.order_validation_service.response_mapper import create_order_validation_response
+from cg.services.order_validation_service.utils import (
+    apply_case_sample_validation,
+    apply_case_validation,
+    apply_order_validation,
+)
+from cg.services.order_validation_service.workflows.balsamic.validation_rules import (
+    CASE_RULES,
+    CASE_SAMPLE_RULES,
+)
+from cg.services.order_validation_service.workflows.order_validation_rules import ORDER_RULES
+from cg.store.store import Store
+
+
+class MicroSaltValidationService(OrderValidationService):
+
+    def __init__(self, store: Store):
+        self.store = store
+
+    def validate(self, raw_order: dict) -> dict:
+        errors: ValidationErrors = self._get_errors(raw_order)
+        return create_order_validation_response(raw_order=raw_order, errors=errors)
+
+    def _get_errors(self, raw_order: dict) -> ValidationErrors:
+        order, field_errors = ModelValidator.validate(order=raw_order, model=BalsamicOrder)
+
+        if field_errors:
+            return field_errors
+
+        order_errors: list[OrderError] = apply_order_validation(
+            rules=ORDER_RULES,
+            order=order,
+            store=self.store,
+        )
+        case_errors: list[CaseError] = apply_case_validation(
+            rules=CASE_RULES,
+            order=order,
+            store=self.store,
+        )
+        case_sample_errors: list[CaseSampleError] = apply_case_sample_validation(
+            rules=CASE_SAMPLE_RULES,
+            order=order,
+            store=self.store,
+        )
+
+        return ValidationErrors(
+            order_errors=order_errors,
+            case_errors=case_errors,
+            case_sample_errors=case_sample_errors,
+        )

cg/services/order_validation_service/workflows/mip_dna/models/sample.py

@@ -1,5 +1,4 @@
 from pydantic import Field
-from cg.constants.constants import GenomeVersion
 from cg.models.orders.sample_base import NAME_PATTERN, ControlEnum, SexEnum, StatusEnum
 from cg.services.order_validation_service.constants import TissueBlockEnum
 from cg.services.order_validation_service.models.sample import Sample