(Improve order flow) Fix delivery types

cg/services/orders/storing/implementations/fastq_order_service.py

@@ -5,6 +5,7 @@
 from cg.constants.constants import CustomerId
 from cg.constants.sequencing import SeqLibraryPrepCategory
 from cg.models.orders.sample_base import SexEnum, StatusEnum
+from cg.services.orders.constants import ORDER_TYPE_WORKFLOW_MAP
 from cg.services.orders.lims_service.service import OrderLimsService
 from cg.services.orders.storing.constants import MAF_ORDER_ID
 from cg.services.orders.storing.service import StoreOrderService
@@ -82,8 +83,8 @@ def _create_db_case(self, order: FastqOrder, db_order: Order) -> Case:
         """Return a Case database object."""
         priority: str = order.samples[0].priority
         case: Case = self.status_db.add_case(
-            data_analysis=Workflow.RAW_DATA,
-            data_delivery=DataDelivery.FASTQ,
+            data_analysis=ORDER_TYPE_WORKFLOW_MAP[order.order_type],
+            data_delivery=DataDelivery(order.delivery_type),
             name=str(db_order.ticket_id),
             priority=priority,
             ticket=str(db_order.ticket_id),
@@ -104,7 +105,7 @@ def _create_db_sample(
             comment=sample.comment,
             internal_id=sample._generated_lims_id,
             ordered=datetime.now(),
-            original_ticket=str(ticket_id),
+            original_ticket=ticket_id,
             priority=sample.priority,
             tumour=sample.tumour,
             capture_kit=sample.capture_kit,

cg/services/orders/storing/implementations/microbial_fastq_order_service.py

@@ -2,6 +2,7 @@
 
 from cg.constants import DataDelivery, SexOptions, Workflow
 from cg.models.orders.sample_base import StatusEnum
+from cg.services.orders.constants import ORDER_TYPE_WORKFLOW_MAP
 from cg.services.orders.lims_service.service import OrderLimsService
 from cg.services.orders.storing.service import StoreOrderService
 from cg.services.orders.validation.workflows.microbial_fastq.models.order import MicrobialFastqOrder
@@ -46,7 +47,7 @@ def store_order_data_in_status_db(self, order: MicrobialFastqOrder) -> list[Samp
         with self.status_db.session.no_autoflush:
             for sample in order.samples:
                 case: Case = self._create_db_case_for_sample(
-                    sample=sample, customer=db_order.customer, ticket_id=str(db_order.ticket_id)
+                    sample=sample, customer=db_order.customer, order=order
                 )
                 db_sample: Sample = self._create_db_sample(
                     sample=sample,
@@ -73,16 +74,16 @@ def _create_db_order(self, order: MicrobialFastqOrder) -> Order:
         return self.status_db.add_order(customer=customer, ticket_id=ticket_id)
 
     def _create_db_case_for_sample(
-        self, sample: MicrobialFastqSample, customer: Customer, ticket_id: str
+        self, sample: MicrobialFastqSample, customer: Customer, order: MicrobialFastqOrder
     ) -> Case:
         """Return a Case database object for a MicrobialFastqSample."""
         case_name: str = f"{sample.name}-case"
         case: Case = self.status_db.add_case(
-            data_analysis=Workflow.RAW_DATA,
-            data_delivery=DataDelivery.FASTQ,
+            data_analysis=ORDER_TYPE_WORKFLOW_MAP[order.order_type],
+            data_delivery=DataDelivery(order.delivery_type),
             name=case_name,
             priority=sample.priority,
-            ticket=ticket_id,
+            ticket=str(order._generated_ticket_id),
         )
         case.customer = customer
         return case

cg/services/orders/storing/implementations/pacbio_order_service.py

@@ -3,6 +3,7 @@
 
 from cg.constants import DataDelivery, Workflow
 from cg.models.orders.sample_base import StatusEnum
+from cg.services.orders.constants import ORDER_TYPE_WORKFLOW_MAP
 from cg.services.orders.lims_service.service import OrderLimsService
 from cg.services.orders.storing.service import StoreOrderService
 from cg.services.orders.validation.workflows.pacbio_long_read.models.order import PacbioOrder
@@ -28,7 +29,7 @@ def store_order(self, order: PacbioOrder) -> dict:
             order_name=order.name,
             workflow=Workflow.RAW_DATA,
             customer=order.customer,
-            delivery_type=order.delivery_type,
+            delivery_type=DataDelivery(order.delivery_type),
         )
         self._fill_in_sample_ids(samples=order.samples, lims_map=lims_map)
         new_samples = self.store_order_data_in_status_db(order=order)
@@ -50,7 +51,7 @@ def store_order_data_in_status_db(self, order: PacbioOrder) -> list[Sample]:
                 case: Case = self._create_db_case_for_sample(
                     sample=sample,
                     customer=status_db_order.customer,
-                    ticket_id=str(status_db_order.ticket_id),
+                    order=order,
                 )
                 db_sample: Sample = self._create_db_sample(
                     sample=sample,
@@ -77,16 +78,16 @@ def _create_db_order(self, order: PacbioOrder) -> Order:
         return self.status_db.add_order(customer=customer, ticket_id=ticket_id)
 
     def _create_db_case_for_sample(
-        self, sample: PacbioSample, customer: Customer, ticket_id: str
+        self, sample: PacbioSample, customer: Customer, order: PacbioOrder
     ) -> Case:
         """Return a Case database object for a PacbioSample."""
         case_name: str = f"{sample.name}-case"
         case: Case = self.status_db.add_case(
-            data_analysis=Workflow.RAW_DATA,
-            data_delivery=DataDelivery.BAM,
+            data_analysis=ORDER_TYPE_WORKFLOW_MAP[order.order_type],
+            data_delivery=DataDelivery(order.delivery_type),
             name=case_name,
             priority=sample.priority,
-            ticket=ticket_id,
+            ticket=str(order._generated_ticket_id),
         )
         case.customer = customer
         return case

cg/services/orders/validation/workflows/pacbio_long_read/constants.py

@@ -1,8 +1,8 @@
-from enum import Enum
+from enum import StrEnum
 
 from cg.constants import DataDelivery
 
 
-class PacbioDeliveryType(Enum):
+class PacbioDeliveryType(StrEnum):
     BAM = DataDelivery.BAM
     NO_DELIVERY = DataDelivery.NO_DELIVERY