(Improve order flow) Remove submitters (#4062) (minor)

### Changed

- The OrderSubmitterRegistry is a StoringServiceRegistry
- The OrderSubmitters are removed
- The OrdersAPI needs no Store in its init
- The OrdersAPI needs a StoringServiceRegistry instead of a SubmitterRegistry
- The OrdersAPI needs an OrderValidationService

cg/meta/orders/api.py

@@ -13,10 +13,10 @@
 from cg.meta.orders.ticket_handler import TicketHandler
 from cg.models.orders.order import OrderType
 from cg.services.order_validation_service.models.order import Order
-from cg.services.orders.submitters.order_submitter import OrderSubmitter
-from cg.services.orders.submitters.order_submitter_registry import OrderSubmitterRegistry
+from cg.services.order_validation_service.order_validation_service import OrderValidationService
+from cg.services.orders.store_order_services.store_order_service import StoreOrderService
+from cg.services.orders.store_order_services.storing_service_registry import StoringServiceRegistry
 from cg.store.models import User
-from cg.store.store import Store
 
 LOG = logging.getLogger(__name__)
 
@@ -27,27 +27,27 @@ class OrdersAPI:
     def __init__(
         self,
         lims: LimsAPI,
-        status: Store,
         ticket_handler: TicketHandler,
-        submitter_registry: OrderSubmitterRegistry,
+        storing_registry: StoringServiceRegistry,
+        validation_service: OrderValidationService,
     ):
         super().__init__()
         self.lims = lims
-        self.status = status
         self.ticket_handler = ticket_handler
-        self.submitter_registry = submitter_registry
+        self.storing_registry = storing_registry
+        self.validation_service = validation_service
 
     def submit(self, order_type: OrderType, raw_order: dict, user: User) -> dict:
         """Submit a batch of samples.
 
         Main entry point for the class towards interfaces that implements it.
         """
-        submit_handler: OrderSubmitter = self.submitter_registry.get_order_submitter(order_type)
-        order: Order = submit_handler.order_validation_service.parse_and_validate(
+        storing_service: StoreOrderService = self.storing_registry.get_storing_service(order_type)
+        order: Order = self.validation_service.parse_and_validate(
             raw_order=raw_order, order_type=order_type
         )
         ticket_number: int = self.ticket_handler.create_ticket(
             order=order, user_name=user.name, user_mail=user.email, order_type=order_type
         )
         order._generated_ticket_id = ticket_number
-        return submit_handler.submit_order(order)
+        return storing_service.store_order(order)

cg/server/endpoints/orders.py

@@ -37,8 +37,8 @@
     delivery_message_service,
     lims,
     order_service,
-    order_submitter_registry,
     order_validation_service,
+    storing_service_registry,
     ticket_handler,
 )
 from cg.store.models import Application, Customer
@@ -153,9 +153,9 @@ def submit_order(order_type: OrderType):
     """Submit an order for samples."""
     api = OrdersAPI(
         lims=lims,
-        status=db,
         ticket_handler=ticket_handler,
-        submitter_registry=order_submitter_registry,
+        storing_registry=storing_service_registry,
+        validation_service=order_validation_service,
     )
     error_message: str
     try:

cg/server/ext.py

@@ -15,9 +15,9 @@
 from cg.services.order_validation_service.order_validation_service import OrderValidationService
 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.submitters.order_submitter_registry import (
-    OrderSubmitterRegistry,
-    setup_order_submitter_registry,
+from cg.services.orders.store_order_services.storing_service_registry import (
+    StoringServiceRegistry,
+    setup_storing_service_registry,
 )
 from cg.services.sample_run_metrics_service.sample_run_metrics_service import (
     SampleRunMetricsService,
@@ -95,7 +95,7 @@ def init_app(self, app):
 order_service = OrderService(store=db, status_service=summary_service)
 sample_service = SampleService(db)
 flow_cell_service = SampleRunMetricsService(db)
-order_submitter_registry: OrderSubmitterRegistry = setup_order_submitter_registry(
+storing_service_registry: StoringServiceRegistry = setup_storing_service_registry(
     lims=lims,
     status_db=db,
 )

cg/services/orders/order_service/order_service.py

@@ -1,22 +1,19 @@
 from cg.server.dto.orders.orders_request import OrdersRequest
-from cg.server.dto.orders.orders_response import Order as OrderResponse, Order
-from cg.server.dto.orders.orders_response import OrdersResponse
+from cg.server.dto.orders.orders_response import Order, OrdersResponse
 from cg.services.orders.order_service.models import OrderQueryParams
 from cg.services.orders.order_summary_service.dto.order_summary import OrderSummary
-from cg.services.orders.order_summary_service.order_summary_service import (
-    OrderSummaryService,
-)
-from cg.store.store import Store
+from cg.services.orders.order_summary_service.order_summary_service import OrderSummaryService
 from cg.store.models import Order as DatabaseOrder
+from cg.store.store import Store
 
 
 class OrderService:
     def __init__(self, store: Store, status_service: OrderSummaryService) -> None:
         self.store = store
         self.summary_service = status_service
 
-    def get_order(self, order_id: int) -> OrderResponse:
-        order: Order = self.store.get_order_by_id(order_id)
+    def get_order(self, order_id: int) -> Order:
+        order: DatabaseOrder = self.store.get_order_by_id(order_id)
         summary: OrderSummary = self.summary_service.get_summary(order_id)
         return self._create_order_response(order=order, summary=summary)
 
@@ -29,13 +26,13 @@ def get_orders(self, orders_request: OrdersRequest) -> OrdersResponse:
         summaries: list[OrderSummary] = self.summary_service.get_summaries(order_ids)
         return self._create_orders_response(orders=orders, summaries=summaries, total=total_count)
 
-    def set_open(self, order_id: int, open: bool) -> OrderResponse:
-        order: Order = self.store.update_order_status(order_id=order_id, open=open)
+    def set_open(self, order_id: int, open: bool) -> Order:
+        order: DatabaseOrder = self.store.update_order_status(order_id=order_id, open=open)
         return self._create_order_response(order)
 
     def update_is_open(self, order_id: int, delivered_analyses: int) -> None:
         """Update the is_open parameter of an order based on the number of delivered analyses."""
-        order: Order = self.store.get_order_by_id(order_id)
+        order: DatabaseOrder = self.store.get_order_by_id(order_id)
         case_count: int = len(order.cases)
         if self._is_order_closed(case_count=case_count, delivered_analyses=delivered_analyses):
             self.set_open(order_id=order_id, open=False)

cg/services/orders/store_order_services/store_case_order.py → cg/services/orders/store_order_services/implementations/store_case_order.py

@@ -9,7 +9,7 @@
 from cg.services.order_validation_service.models.sample_aliases import SampleInCase
 from cg.services.orders.constants import ORDER_TYPE_WORKFLOW_MAP
 from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
-from cg.services.orders.submitters.order_submitter import StoreOrderService
+from cg.services.orders.store_order_services.store_order_service import StoreOrderService
 from cg.store.models import ApplicationVersion
 from cg.store.models import Case as DbCase
 from cg.store.models import CaseSample, Customer

cg/services/orders/store_order_services/store_fastq_order_service.py → cg/services/orders/store_order_services/implementations/store_fastq_order_service.py

@@ -8,7 +8,7 @@
 from cg.services.order_validation_service.workflows.fastq.models.order import FastqOrder
 from cg.services.order_validation_service.workflows.fastq.models.sample import FastqSample
 from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
-from cg.services.orders.submitters.order_submitter import StoreOrderService
+from cg.services.orders.store_order_services.store_order_service import StoreOrderService
 from cg.store.models import ApplicationVersion, Case, CaseSample, Customer, Order, Sample
 from cg.store.store import Store
 

cg/services/orders/store_order_services/store_metagenome_order.py → cg/services/orders/store_order_services/implementations/store_metagenome_order.py

@@ -11,7 +11,7 @@
 )
 from cg.services.orders.constants import ORDER_TYPE_WORKFLOW_MAP
 from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
-from cg.services.orders.submitters.order_submitter import StoreOrderService
+from cg.services.orders.store_order_services.store_order_service import StoreOrderService
 from cg.store.models import ApplicationVersion
 from cg.store.models import Case as DbCase
 from cg.store.models import CaseSample, Customer

cg/services/orders/store_order_services/store_microbial_fastq_order_service.py → cg/services/orders/store_order_services/implementations/store_microbial_fastq_order_service.py

@@ -9,7 +9,7 @@
     MicrobialFastqSample,
 )
 from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
-from cg.services.orders.submitters.order_submitter import StoreOrderService
+from cg.services.orders.store_order_services.store_order_service import StoreOrderService
 from cg.store.models import ApplicationVersion, Case, CaseSample, Customer, Order, Sample
 from cg.store.store import Store
 

cg/services/orders/store_order_services/store_microbial_order.py → cg/services/orders/store_order_services/implementations/store_microbial_order.py

@@ -8,7 +8,7 @@
 from cg.services.order_validation_service.workflows.mutant.models.sample import MutantSample
 from cg.services.orders.constants import ORDER_TYPE_WORKFLOW_MAP
 from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
-from cg.services.orders.submitters.order_submitter import StoreOrderService
+from cg.services.orders.store_order_services.store_order_service import StoreOrderService
 from cg.store.models import ApplicationVersion
 from cg.store.models import Case as DbCase
 from cg.store.models import CaseSample, Customer

cg/services/orders/store_order_services/store_pacbio_order_service.py → cg/services/orders/store_order_services/implementations/store_pacbio_order_service.py

@@ -2,14 +2,13 @@
 from datetime import datetime
 
 from cg.constants import DataDelivery, Workflow
-from cg.models.orders.order import OrderIn
 from cg.models.orders.sample_base import StatusEnum
 from cg.services.order_validation_service.workflows.pacbio_long_read.models.order import PacbioOrder
 from cg.services.order_validation_service.workflows.pacbio_long_read.models.sample import (
     PacbioSample,
 )
 from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
-from cg.services.orders.submitters.order_submitter import StoreOrderService
+from cg.services.orders.store_order_services.store_order_service import StoreOrderService
 from cg.store.models import ApplicationVersion, Case, CaseSample, Customer, Order, Sample
 from cg.store.store import Store
 

cg/services/orders/store_order_services/store_pool_order.py → cg/services/orders/store_order_services/implementations/store_pool_order.py

@@ -8,7 +8,7 @@
 )
 from cg.services.orders.constants import ORDER_TYPE_WORKFLOW_MAP
 from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
-from cg.services.orders.submitters.order_submitter import StoreOrderService
+from cg.services.orders.store_order_services.store_order_service import StoreOrderService
 from cg.store.models import ApplicationVersion, Case, CaseSample, Customer, Order, Pool, Sample
 from cg.store.store import Store
 

cg/services/orders/submitters/order_submitter.py → cg/services/orders/store_order_services/store_order_service.py

@@ -4,8 +4,8 @@
 from abc import ABC, abstractmethod
 
 from cg.models.orders.order import OrderIn
+from cg.services.order_validation_service.models.order import Order
 from cg.services.order_validation_service.models.sample import Sample
-from cg.services.order_validation_service.order_validation_service import OrderValidationService
 from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
 from cg.store.store import Store
 
@@ -29,7 +29,7 @@ def __init__(self, status_db: Store, lims_service: OrderLimsService):
         self.lims = lims_service
 
     @abstractmethod
-    def store_order(self, order_in: OrderIn):
+    def store_order(self, order: Order):
         pass
 
     @staticmethod
@@ -40,18 +40,3 @@ def _fill_in_sample_ids(samples: list[Sample], lims_map: dict):
             internal_id = lims_map[sample.name]
             LOG.info(f"{sample.name} -> {internal_id}: connect sample to LIMS")
             sample._generated_lims_id = internal_id
-
-
-class OrderSubmitter(ABC):
-    @abstractmethod
-    def __init__(
-        self,
-        validate_order_service: OrderValidationService,
-        store_order_service: StoreOrderService,
-    ):
-        self.order_validation_service = validate_order_service
-        self.order_store_service = store_order_service
-
-    @abstractmethod
-    def submit_order(self, order_in: OrderIn) -> dict:
-        pass

cg/services/orders/store_order_services/storing_service_registry.py

@@ -0,0 +1,134 @@
+from cg.apps.lims import LimsAPI
+from cg.models.orders.constants import OrderType
+from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
+from cg.services.orders.store_order_services.implementations.store_case_order import (
+    StoreCaseOrderService,
+)
+from cg.services.orders.store_order_services.implementations.store_fastq_order_service import (
+    StoreFastqOrderService,
+)
+from cg.services.orders.store_order_services.implementations.store_metagenome_order import (
+    StoreMetagenomeOrderService,
+)
+from cg.services.orders.store_order_services.implementations.store_microbial_fastq_order_service import (
+    StoreMicrobialFastqOrderService,
+)
+from cg.services.orders.store_order_services.implementations.store_microbial_order import (
+    StoreMicrobialOrderService,
+)
+from cg.services.orders.store_order_services.implementations.store_pacbio_order_service import (
+    StorePacBioOrderService,
+)
+from cg.services.orders.store_order_services.implementations.store_pool_order import (
+    StorePoolOrderService,
+)
+from cg.services.orders.store_order_services.store_order_service import StoreOrderService
+from cg.store.store import Store
+
+
+class StoringServiceRegistry:
+    """
+    A registry for StoreOrderService instances, keyed by OrderType.
+    """
+
+    def __init__(self):
+        self._registry = {}
+
+    def register(self, order_type: OrderType, storing_service: StoreOrderService):
+        """Register a StoreOrderService instance for a given OrderType."""
+        self._registry[order_type] = storing_service
+
+    def get_storing_service(self, order_type: OrderType) -> StoreOrderService:
+        """Fetch the registered StoreOrderService for the given OrderType."""
+        if storing_service := self._registry.get(order_type):
+            return storing_service
+        raise ValueError(f"No StoreOrderService registered for order type: {order_type}")
+
+
+order_service_mapping = {
+    OrderType.BALSAMIC: (
+        OrderLimsService,
+        StoreCaseOrderService,
+    ),
+    OrderType.BALSAMIC_QC: (
+        OrderLimsService,
+        StoreCaseOrderService,
+    ),
+    OrderType.BALSAMIC_UMI: (
+        OrderLimsService,
+        StoreCaseOrderService,
+    ),
+    OrderType.FASTQ: (
+        OrderLimsService,
+        StoreFastqOrderService,
+    ),
+    OrderType.FLUFFY: (
+        OrderLimsService,
+        StorePoolOrderService,
+    ),
+    OrderType.METAGENOME: (
+        OrderLimsService,
+        StoreMetagenomeOrderService,
+    ),
+    OrderType.MICROBIAL_FASTQ: (
+        OrderLimsService,
+        StoreMicrobialFastqOrderService,
+    ),
+    OrderType.MICROSALT: (
+        OrderLimsService,
+        StoreMicrobialOrderService,
+    ),
+    OrderType.MIP_DNA: (
+        OrderLimsService,
+        StoreCaseOrderService,
+    ),
+    OrderType.MIP_RNA: (
+        OrderLimsService,
+        StoreCaseOrderService,
+    ),
+    OrderType.PACBIO_LONG_READ: (
+        OrderLimsService,
+        StorePacBioOrderService,
+    ),
+    OrderType.RML: (
+        OrderLimsService,
+        StorePoolOrderService,
+    ),
+    OrderType.RNAFUSION: (
+        OrderLimsService,
+        StoreCaseOrderService,
+    ),
+    OrderType.SARS_COV_2: (
+        OrderLimsService,
+        StoreMicrobialOrderService,
+    ),
+    OrderType.TAXPROFILER: (
+        OrderLimsService,
+        StoreMetagenomeOrderService,
+    ),
+    OrderType.TOMTE: (
+        OrderLimsService,
+        StoreCaseOrderService,
+    ),
+}
+
+
+def build_storing_service(
+    lims: LimsAPI, status_db: Store, order_type: OrderType
+) -> StoreOrderService:
+    """Build a StoreOrderService instance for the given OrderType."""
+    lims_service, store_service = order_service_mapping[order_type]
+    return store_service(status_db, lims_service(lims))
+
+
+def setup_storing_service_registry(lims: LimsAPI, status_db: Store) -> StoringServiceRegistry:
+    """Set up the StoringServiceRegistry with all StoreOrderService instances."""
+    registry = StoringServiceRegistry()
+    for order_type in order_service_mapping.keys():
+        registry.register(
+            order_type=order_type,
+            storing_service=build_storing_service(
+                lims=lims, status_db=status_db, order_type=order_type
+            ),
+        )
+    return registry