fix(assignment maf cases to special order)

cg/services/orders/store_order_services/constants.py

@@ -0,0 +1,2 @@
+# Hardcoded constant for special order to assign MAF cases to
+MAF_ORDER_ID: int = 12377

cg/services/orders/store_order_services/store_fastq_order_service.py

@@ -8,6 +8,7 @@
 from cg.models.orders.order import OrderIn
 from cg.models.orders.sample_base import StatusEnum
 from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
+from cg.services.orders.store_order_services.constants import MAF_ORDER_ID
 from cg.services.orders.submitters.order_submitter import StoreOrderService
 from cg.store.models import ApplicationVersion, Case, CaseSample, Customer, Order, Sample
 from cg.store.store import Store
@@ -62,9 +63,11 @@ def order_to_status(order: OrderIn) -> dict:
         }
         return status_data
 
-    def create_maf_case(self, sample_obj: Sample, order: Order) -> None:
+    def create_maf_case(self, sample_obj: Sample, order: Order, case: Case) -> None:
         """Add a MAF case to the Status database."""
+        maf_order = self.status_db.get_order_by_id(MAF_ORDER_ID)
         case: Case = self.status_db.add_case(
+            comment=f"MAF case for {case.internal_id} original order id {order.id}",
             data_analysis=Workflow(Workflow.MIP_DNA),
             data_delivery=DataDelivery(DataDelivery.NO_DELIVERY),
             name="_".join([sample_obj.name, "MAF"]),
@@ -78,7 +81,7 @@ def create_maf_case(self, sample_obj: Sample, order: Order) -> None:
         relationship: CaseSample = self.status_db.relate_sample(
             case=case, sample=sample_obj, status=StatusEnum.unknown
         )
-        order.cases.append(case)
+        maf_order.cases.append(case)
         self.status_db.session.add_all([case, relationship])
 
     def store_items_in_status(
@@ -137,7 +140,7 @@ def store_items_in_status(
                     not new_sample.is_tumour
                     and new_sample.prep_category == SeqLibraryPrepCategory.WHOLE_GENOME_SEQUENCING
                 ):
-                    self.create_maf_case(sample_obj=new_sample, order=status_db_order)
+                    self.create_maf_case(sample_obj=new_sample, order=status_db_order, case=case)
                 case.customer = customer
                 new_relationship = self.status_db.relate_sample(
                     case=case, sample=new_sample, status=StatusEnum.unknown

cg/store/crud/create.py

@@ -246,11 +246,13 @@ def add_case(
         priority: Priority | None = Priority.standard,
         synopsis: str | None = None,
         customer_id: int | None = None,
+        comment: str | None = None,
     ) -> Case:
         """Build a new Case record."""
 
         internal_id: str = self.generate_readable_case_id()
         return Case(
+            comment=comment,
             cohorts=cohorts,
             data_analysis=str(data_analysis),
             data_delivery=str(data_delivery),

tests/conftest.py

@@ -59,6 +59,7 @@
 from cg.services.deliver_files.rsync.service import DeliveryRsyncService
 from cg.services.illumina.backup.encrypt_service import IlluminaRunEncryptionService
 from cg.services.illumina.data_transfer.data_transfer_service import IlluminaDataTransferService
+from cg.services.orders.store_order_services.constants import MAF_ORDER_ID
 from cg.store.database import create_all_tables, drop_all_tables, initialize_database
 from cg.store.models import (
     Application,
@@ -1649,6 +1650,9 @@ def base_store(
     store.session.add(organism)
     store.session.commit()
 
+    order: Order = Order(customer_id=1, id=MAF_ORDER_ID, ticket_id="100000000")
+    store.add_multiple_items_to_store([order])
+
     yield store
 
 

tests/meta/orders/conftest.py

@@ -9,6 +9,7 @@
     OrderSubmitterRegistry,
     setup_order_submitter_registry,
 )
+from cg.store.models import Order
 from cg.store.store import Store
 from tests.mocks.limsmock import MockLimsAPI
 

tests/meta/orders/test_meta_orders_api.py

@@ -14,7 +14,7 @@
 from cg.services.orders.validate_order_services.validate_case_order import (
     ValidateCaseOrderService,
 )
-from cg.store.models import Case, Customer, Pool, Sample
+from cg.store.models import Case, Customer, Pool, Sample, Order
 from cg.store.store import Store
 from tests.store_helpers import StoreHelpers
 

tests/services/orders/order_store_service/test_fastq_order_service.py

@@ -6,8 +6,9 @@
 from cg.constants.sequencing import SeqLibraryPrepCategory
 from cg.exc import OrderError
 from cg.models.orders.order import OrderIn, OrderType
+from cg.services.orders.store_order_services.constants import MAF_ORDER_ID
 from cg.services.orders.store_order_services.store_fastq_order_service import StoreFastqOrderService
-from cg.store.models import Application, Case, Sample
+from cg.store.models import Application, Case, Sample, Order
 from cg.store.store import Store
 
 
@@ -63,6 +64,10 @@ def test_store_samples(
     assert family_link.case.data_analysis
     assert family_link.case.data_delivery in [DataDelivery.FASTQ, DataDelivery.NO_DELIVERY]
 
+    # THEN a MAF case should be added to the MAF orders
+    maf_order: Order = base_store.get_order_by_id(MAF_ORDER_ID)
+    assert len(maf_order.cases) == 1
+
 
 def test_store_samples_sex_stored(
     base_store: Store,