refactor(submitters) (#3574) (patch)

# Description

refactoring of order submitters.

cg/meta/orders/api.py

@@ -11,66 +11,36 @@
 
 from cg.apps.lims import LimsAPI
 from cg.apps.osticket import OsTicket
-from cg.meta.orders.balsamic_qc_submitter import BalsamicQCSubmitter
-from cg.meta.orders.balsamic_submitter import BalsamicSubmitter
-from cg.meta.orders.balsamic_umi_submitter import BalsamicUmiSubmitter
-from cg.meta.orders.fastq_submitter import FastqSubmitter
-from cg.meta.orders.fluffy_submitter import FluffySubmitter
-from cg.meta.orders.metagenome_submitter import MetagenomeSubmitter
-from cg.meta.orders.microsalt_submitter import MicrosaltSubmitter
-from cg.meta.orders.mip_dna_submitter import MipDnaSubmitter
-from cg.meta.orders.mip_rna_submitter import MipRnaSubmitter
-from cg.meta.orders.rml_submitter import RmlSubmitter
-from cg.meta.orders.rnafusion_submitter import RnafusionSubmitter
-from cg.meta.orders.sars_cov_2_submitter import SarsCov2Submitter
-from cg.meta.orders.submitter import Submitter
 from cg.meta.orders.ticket_handler import TicketHandler
-from cg.meta.orders.tomte_submitter import TomteSubmitter
 from cg.models.orders.order import OrderIn, OrderType
+from cg.services.orders.submitters.order_submitter_registry import OrderSubmitterRegistry
 from cg.store.store import Store
 
 LOG = logging.getLogger(__name__)
 
 
-def _get_submit_handler(project: OrderType, lims: LimsAPI, status: Store) -> Submitter:
-    """Factory Method"""
-
-    submitters = {
-        OrderType.BALSAMIC: BalsamicSubmitter,
-        OrderType.BALSAMIC_QC: BalsamicQCSubmitter,
-        OrderType.BALSAMIC_UMI: BalsamicUmiSubmitter,
-        OrderType.FASTQ: FastqSubmitter,
-        OrderType.FLUFFY: FluffySubmitter,
-        OrderType.METAGENOME: MetagenomeSubmitter,
-        OrderType.MICROSALT: MicrosaltSubmitter,
-        OrderType.MIP_DNA: MipDnaSubmitter,
-        OrderType.MIP_RNA: MipRnaSubmitter,
-        OrderType.RML: RmlSubmitter,
-        OrderType.RNAFUSION: RnafusionSubmitter,
-        OrderType.SARS_COV_2: SarsCov2Submitter,
-        OrderType.TOMTE: TomteSubmitter,
-    }
-    if project in submitters:
-        return submitters[project](lims=lims, status=status)
-
-
 class OrdersAPI:
     """Orders API for accepting new samples into the system."""
 
-    def __init__(self, lims: LimsAPI, status: Store, osticket: OsTicket):
+    def __init__(
+        self,
+        lims: LimsAPI,
+        status: Store,
+        osticket: OsTicket,
+        submitter_registry: OrderSubmitterRegistry,
+    ):
         super().__init__()
         self.lims = lims
         self.status = status
         self.ticket_handler: TicketHandler = TicketHandler(osticket_api=osticket, status_db=status)
+        self.submitter_registry = submitter_registry
 
     def submit(self, project: OrderType, order_in: OrderIn, user_name: str, user_mail: str) -> dict:
         """Submit a batch of samples.
 
         Main entry point for the class towards interfaces that implements it.
         """
-        submit_handler: Submitter = _get_submit_handler(project, lims=self.lims, status=self.status)
-        submit_handler.validate_order(order=order_in)
-
+        submit_handler = self.submitter_registry.get_order_submitter(project)
         # detect manual ticket assignment
         ticket_number: str | None = TicketHandler.parse_ticket_number(order_in.name)
         if not ticket_number:
@@ -86,4 +56,4 @@ def submit(self, project: OrderType, order_in: OrderIn, user_name: str, user_mai
                 ticket_number=ticket_number,
             )
         order_in.ticket = ticket_number
-        return submit_handler.submit_order(order=order_in)
+        return submit_handler.submit_order(order_in=order_in)

cg/server/endpoints/orders.py

@@ -40,6 +40,7 @@
     lims,
     order_service,
     osticket,
+    order_submitter_registry,
 )
 from cg.store.models import (
     Application,
@@ -155,7 +156,9 @@ def create_order_from_form():
 @ORDERS_BLUEPRINT.route("/submit_order/<order_type>", methods=["POST"])
 def submit_order(order_type):
     """Submit an order for samples."""
-    api = OrdersAPI(lims=lims, status=db, osticket=osticket)
+    api = OrdersAPI(
+        lims=lims, status=db, osticket=osticket, submitter_registry=order_submitter_registry
+    )
     error_message: str
     try:
         request_json = request.get_json()

cg/server/ext.py

@@ -13,6 +13,10 @@
 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.sample_service.sample_service import SampleService
 from cg.store.database import initialize_database
 from cg.store.store import Store
@@ -83,3 +87,6 @@ def init_app(self, app):
 summary_service = OrderSummaryService(store=db, analysis_client=analysis_client)
 order_service = OrderService(store=db, status_service=summary_service)
 sample_service = SampleService(db)
+order_submitter_registry: OrderSubmitterRegistry = setup_order_submitter_registry(
+    lims=lims, status_db=db
+)

cg/services/orders/order_lims_service/order_lims_service.py

@@ -0,0 +1,39 @@
+import logging
+
+from cg.apps.lims import LimsAPI
+from cg.models.lims.sample import LimsSample
+from cg.models.orders.order import OrderIn
+from cg.models.orders.samples import OrderInSample
+
+LOG = logging.getLogger(__name__)
+
+
+class OrderLimsService:
+
+    def __init__(self, lims_api: LimsAPI):
+        self.lims_api = lims_api
+
+    @staticmethod
+    def _build_lims_sample(customer: str, samples: list[OrderInSample]) -> list[LimsSample]:
+        """Convert order input to lims interface input."""
+        samples_lims = []
+        for sample in samples:
+            dict_sample = sample.__dict__
+            LOG.debug(f"{sample.name}: prepare LIMS input")
+            dict_sample["customer"] = customer
+            lims_sample: LimsSample = LimsSample.parse_obj(dict_sample)
+            samples_lims.append(lims_sample)
+        return samples_lims
+
+    def process_lims(self, lims_order: OrderIn, new_samples: list[OrderInSample]):
+        """Process samples to add them to LIMS."""
+        samples_lims: list[LimsSample] = self._build_lims_sample(
+            lims_order.customer, samples=new_samples
+        )
+        project_name = lims_order.ticket or lims_order.name
+        # Create new lims project
+        project_data = self.lims_api.submit_project(
+            project_name, [lims_sample.dict() for lims_sample in samples_lims]
+        )
+        lims_map = self.lims_api.get_samples(projectlimsid=project_data["id"], map_ids=True)
+        return project_data, lims_map