(Improve order flow) Add metagenome rules

cg/server/endpoints/orders.py

@@ -14,7 +14,7 @@
 from cg.apps.orderform.excel_orderform_parser import ExcelOrderformParser
 from cg.apps.orderform.json_orderform_parser import JsonOrderformParser
 from cg.constants import ANALYSIS_SOURCES, METAGENOME_SOURCES
-from cg.constants.constants import FileFormat, Workflow
+from cg.constants.constants import FileFormat
 from cg.exc import (
     OrderError,
     OrderExistsError,
@@ -37,6 +37,7 @@
     db,
     delivery_message_service,
     lims,
+    metagenome_validation_service,
     microsalt_validation_service,
     mip_dna_validation_service,
     order_service,
@@ -263,17 +264,21 @@ def get_options():
     )
 
 
-@ORDERS_BLUEPRINT.route("/validate_order/<workflow>", methods=["POST"])
-def validate_order(workflow: str):
+@ORDERS_BLUEPRINT.route("/validate_order/<order_type>", methods=["POST"])
+def validate_order(order_type: OrderType):
     raw_order = request.get_json()
-    raw_order["workflow"] = workflow
+    raw_order["order_type"] = order_type
     raw_order["user_id"] = g.current_user.id
     response = {}
-    if workflow == Workflow.MICROSALT:
+    if order_type == OrderType.TOMTE:
+        response = tomte_validation_service.validate(raw_order)
+    if order_type == OrderType.MICROSALT:
         response = microsalt_validation_service.validate(raw_order)
-    if workflow == Workflow.MIP_DNA:
+    if order_type == OrderType.MIP_DNA:
         response = mip_dna_validation_service.validate(raw_order)
-    if workflow == Workflow.RNAFUSION:
+    if order_type == OrderType.METAGENOME:
+        response = metagenome_validation_service.validate(raw_order)
+    if order_type == OrderType.RNAFUSION:
         response = rna_fusion_validation_service.validate(raw_order)
     if workflow == Workflow.TOMTE:
         response = tomte_validation_service.validate(raw_order)

cg/server/ext.py

@@ -12,6 +12,9 @@
 from cg.server.app_config import app_config
 from cg.services.application.service import ApplicationsWebService
 from cg.services.delivery_message.delivery_message_service import DeliveryMessageService
+from cg.services.order_validation_service.workflows.metagenome.validation_service import (
+    MetagenomeValidationService,
+)
 from cg.services.order_validation_service.workflows.microsalt.validation_service import (
     MicroSaltValidationService,
 )
@@ -25,7 +28,9 @@
     TomteValidationService,
 )
 from cg.services.orders.order_service.order_service import OrderService
-from cg.services.orders.order_summary_service.order_summary_service import OrderSummaryService
+from cg.services.orders.order_summary_service.order_summary_service import (
+    OrderSummaryService,
+)
 from cg.services.orders.submitters.order_submitter_registry import (
     OrderSubmitterRegistry,
     setup_order_submitter_registry,
@@ -112,6 +117,7 @@ def init_app(self, app):
 tomte_validation_service = TomteValidationService(store=db)
 microsalt_validation_service = MicroSaltValidationService(store=db)
 mip_dna_validation_service = MipDnaValidationService(store=db)
+metagenome_validation_service = MetagenomeValidationService(store=db)
 rna_fusion_validation_service = RnaFusionValidationService(store=db)
 freshdesk_client = FreshdeskClient(
     base_url=app_config.freshdesk_url, api_key=app_config.freshdesk_api_key

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

@@ -4,7 +4,7 @@
 
 
 class MetagenomeSample(Sample):
-    concentration_ng_ul: float | None = None
+    concentration_sample: float | None = None
     control: ControlEnum | None = None
     elution_buffer: ElutionBuffer
     organism: str

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

@@ -0,0 +1,29 @@
+from cg.services.order_validation_service.rules.sample.rules import (
+    validate_application_compatibility,
+    validate_application_exists,
+    validate_applications_not_archived,
+    validate_container_name_required,
+    validate_required_volume,
+    validate_sample_names_available,
+    validate_sample_names_unique,
+    validate_tube_container_name_unique,
+    validate_volume_interval,
+    validate_well_position_format,
+    validate_well_positions_required,
+    validate_wells_contain_at_most_one_sample,
+)
+
+SAMPLE_RULES: list[callable] = [
+    validate_application_compatibility,
+    validate_application_exists,
+    validate_applications_not_archived,
+    validate_container_name_required,
+    validate_required_volume,
+    validate_sample_names_available,
+    validate_sample_names_unique,
+    validate_tube_container_name_unique,
+    validate_volume_interval,
+    validate_well_position_format,
+    validate_well_positions_required,
+    validate_wells_contain_at_most_one_sample,
+]

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

@@ -0,0 +1,60 @@
+from cg.services.order_validation_service.errors.order_errors import OrderError
+from cg.services.order_validation_service.errors.sample_errors import SampleError
+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_order_validation,
+    apply_sample_validation,
+)
+from cg.services.order_validation_service.workflows.metagenome.models.order import (
+    MetagenomeOrder,
+)
+from cg.services.order_validation_service.workflows.metagenome.validation_rules import (
+    SAMPLE_RULES,
+)
+from cg.services.order_validation_service.workflows.order_validation_rules import (
+    ORDER_RULES,
+)
+from cg.store.store import Store
+
+
+class MetagenomeValidationService(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=MetagenomeOrder)
+
+        if not order:
+            return field_errors
+
+        order_errors: list[OrderError] = apply_order_validation(
+            rules=ORDER_RULES,
+            order=order,
+            store=self.store,
+        )
+        sample_errors: list[SampleError] = apply_sample_validation(
+            rules=SAMPLE_RULES,
+            order=order,
+            store=self.store,
+        )
+
+        return ValidationErrors(
+            order_errors=order_errors,
+            sample_errors=sample_errors,
+        )