(Improve order flow) Rework the process_lims method

cg/server/endpoints/samples.py

@@ -2,9 +2,7 @@
 
 from flask import Blueprint, abort, g, jsonify, request
 
-from cg.server.dto.samples.collaborator_samples_request import (
-    CollaboratorSamplesRequest,
-)
+from cg.server.dto.samples.collaborator_samples_request import CollaboratorSamplesRequest
 from cg.server.dto.samples.samples_response import SamplesResponse
 from cg.server.endpoints.utils import before_request
 from cg.server.ext import db, sample_service

cg/services/order_validation_service/constants.py

@@ -1,4 +1,4 @@
-from enum import Enum, StrEnum, auto
+from enum import StrEnum, auto
 
 
 class TissueBlockEnum(StrEnum):
@@ -18,7 +18,7 @@ class ElutionBuffer(StrEnum):
 MINIMUM_VOLUME, MAXIMUM_VOLUME = 20, 130
 
 
-class ExtractionMethod(Enum):
+class ExtractionMethod(StrEnum):
     EZ1 = "EZ1"
     MAELSTROM = "Maelstrom"
     MAGNAPURE_96 = "MagNaPure 96 (contact Clinical Genomics before submission)"

cg/services/order_validation_service/workflows/balsamic/constants.py

@@ -1,9 +1,13 @@
-from enum import Enum
+from enum import StrEnum
 
 from cg.constants import DataDelivery
 
 
-class BalsamicDeliveryType(Enum):
+class BalsamicDeliveryType(StrEnum):
     ANALYSIS = DataDelivery.ANALYSIS_FILES
+    ANALYSIS_SCOUT = DataDelivery.ANALYSIS_SCOUT
     FASTQ_ANALYSIS = DataDelivery.FASTQ_ANALYSIS
+    FASTQ_SCOUT = DataDelivery.FASTQ_SCOUT
+    FASTQ_ANALYSIS_SCOUT = DataDelivery.FASTQ_ANALYSIS_SCOUT
+    SCOUT = DataDelivery.SCOUT
     NO_DELIVERY = DataDelivery.NO_DELIVERY

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

@@ -1,11 +1,7 @@
 from pydantic import Field
 
-from cg.constants.constants import GenomeVersion
 from cg.models.orders.sample_base import NAME_PATTERN, ControlEnum, SexEnum, StatusEnum
-from cg.services.order_validation_service.constants import (
-    ElutionBuffer,
-    TissueBlockEnum,
-)
+from cg.services.order_validation_service.constants import ElutionBuffer, TissueBlockEnum
 from cg.services.order_validation_service.models.sample import Sample
 
 
@@ -17,15 +13,14 @@ class BalsamicSample(Sample):
     control: ControlEnum | None = None
     elution_buffer: ElutionBuffer | None = None
     formalin_fixation_time: int | None = None
-    is_tumour: bool
     phenotype_groups: list[str] | None = None
     phenotype_terms: list[str] | None = None
     post_formalin_fixation_time: int | None = None
-    reference_genome: GenomeVersion
     require_qc_ok: bool
     sex: SexEnum
     source: str
     status: StatusEnum | None = None
     subject_id: str = Field(pattern=NAME_PATTERN, max_length=128)
     tissue_block_size: TissueBlockEnum | None = None
+    tumour: bool
     tumour_purity: int | None = None

cg/services/order_validation_service/workflows/fastq/constants.py

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

cg/services/order_validation_service/workflows/microsalt/constants.py

@@ -1,9 +1,9 @@
-from enum import Enum
+from enum import StrEnum
 
 from cg.constants import DataDelivery
 
 
-class MicrosaltDeliveryType(Enum):
+class MicrosaltDeliveryType(StrEnum):
     FASTQ_QC = DataDelivery.FASTQ_QC
     FASTQ_QC_ANALYSIS = DataDelivery.FASTQ_QC_ANALYSIS
     NO_DELIVERY = DataDelivery.NO_DELIVERY

cg/services/order_validation_service/workflows/mip_dna/models/order.py

@@ -4,9 +4,7 @@
 from cg.services.order_validation_service.models.discriminators import has_internal_id
 from cg.services.order_validation_service.models.existing_case import ExistingCase
 from cg.services.order_validation_service.models.order_with_cases import OrderWithCases
-from cg.services.order_validation_service.workflows.mip_dna.models.case import (
-    MipDnaCase,
-)
+from cg.services.order_validation_service.workflows.mip_dna.models.case import MipDnaCase
 
 NewCase = Annotated[MipDnaCase, Tag("new")]
 OldCase = Annotated[ExistingCase, Tag("existing")]

cg/services/order_validation_service/workflows/mutant/constants.py

@@ -4,7 +4,7 @@
 
 
 class MutantDeliveryType(Enum):
-    ANALYSIS_FILES = DataDelivery.FASTQ_ANALYSIS
+    ANALYSIS_FILES = DataDelivery.FASTQ
     NO_DELIVERY = DataDelivery.NO_DELIVERY
 
 

cg/services/order_validation_service/workflows/rml/models/order.py

@@ -1,9 +1,9 @@
-from cg.services.order_validation_service.models.order_with_samples import OrderWithNonHumanSamples
+from cg.services.order_validation_service.models.order_with_samples import OrderWithSamples
 from cg.services.order_validation_service.workflows.rml.constants import RmlDeliveryType
 from cg.services.order_validation_service.workflows.rml.models.sample import RmlSample
 
 
-class RmlOrder(OrderWithNonHumanSamples):
+class RmlOrder(OrderWithSamples):
     delivery_type: RmlDeliveryType
     samples: list[RmlSample]
 

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

@@ -9,5 +9,7 @@ class RmlSample(Sample):
     pool: str
     pool_concentration: float
     priority: PriorityEnum
+    rml_plate_name: str | None = None
     sample_concentration: float | None = None
     volume: int
+    well_position_rml: str | None = None

cg/services/orders/order_lims_service/order_lims_service.py

@@ -1,9 +1,9 @@
 import logging
 
 from cg.apps.lims import LimsAPI
+from cg.constants import DataDelivery, Workflow
 from cg.models.lims.sample import LimsSample
-from cg.models.orders.order import OrderIn
-from cg.models.orders.samples import OrderInSample
+from cg.services.order_validation_service.models.sample import Sample
 
 LOG = logging.getLogger(__name__)
 
@@ -14,23 +14,35 @@ 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."""
+    def _build_lims_sample(
+        customer: str, samples: list[Sample], workflow: Workflow, delivery_type: DataDelivery
+    ) -> list[LimsSample]:
+        """Convert order input to LIMS interface input."""
         samples_lims = []
         for sample in samples:
-            dict_sample = sample.__dict__
+            dict_sample = sample.model_dump()
             LOG.debug(f"{sample.name}: prepare LIMS input")
             dict_sample["customer"] = customer
+            dict_sample["data_analysis"] = workflow
+            dict_sample["data_delivery"] = delivery_type
             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]):
+    def process_lims(
+        self,
+        samples: list[Sample],
+        customer: str,
+        ticket: int | None,
+        order_name: str,
+        workflow: Workflow,
+        delivery_type: DataDelivery,
+    ):
         """Process samples to add them to LIMS."""
         samples_lims: list[LimsSample] = self._build_lims_sample(
-            lims_order.customer, samples=new_samples
+            customer=customer, samples=samples, workflow=workflow, delivery_type=delivery_type
         )
-        project_name: str = lims_order.ticket or lims_order.name
+        project_name: str = str(ticket) or order_name
         # Create new lims project
         project_data = self.lims_api.submit_project(
             project_name, [lims_sample.dict() for lims_sample in samples_lims]

cg/services/orders/store_order_services/store_case_order.py

@@ -8,14 +8,7 @@
 from cg.models.orders.samples import Of1508Sample
 from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
 from cg.services.orders.submitters.order_submitter import StoreOrderService
-from cg.store.models import (
-    ApplicationVersion,
-    Case,
-    CaseSample,
-    Customer,
-    Order,
-    Sample,
-)
+from cg.store.models import ApplicationVersion, Case, CaseSample, Customer, Order, Sample
 from cg.store.store import Store
 
 LOG = logging.getLogger(__name__)
@@ -52,9 +45,7 @@ def _process_case_samples(self, order: OrderIn) -> dict:
         # submit new samples to lims
         new_samples = [sample for sample in order.samples if sample.internal_id is None]
         if new_samples:
-            project_data, lims_map = self.lims.process_lims(
-                lims_order=order, new_samples=new_samples
-            )
+            project_data, lims_map = self.lims.process_lims(order=order, new_samples=new_samples)
 
         status_data = self.order_to_status(order=order)
         samples = [sample for family in status_data["families"] for sample in family["samples"]]

cg/services/orders/store_order_services/store_fastq_order_service.py

@@ -8,14 +8,7 @@
 from cg.models.orders.sample_base import StatusEnum
 from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
 from cg.services.orders.submitters.order_submitter import StoreOrderService
-from cg.store.models import (
-    ApplicationVersion,
-    Case,
-    CaseSample,
-    Customer,
-    Order,
-    Sample,
-)
+from cg.store.models import ApplicationVersion, Case, CaseSample, Customer, Order, Sample
 from cg.store.store import Store
 
 LOG = logging.getLogger(__name__)
@@ -31,7 +24,7 @@ def __init__(self, status_db: Store, lims_service: OrderLimsService):
     def store_order(self, order: OrderIn) -> dict:
         """Submit a batch of samples for FASTQ delivery."""
 
-        project_data, lims_map = self.lims.process_lims(lims_order=order, new_samples=order.samples)
+        project_data, lims_map = self.lims.process_lims(order=order, new_samples=order.samples)
         status_data = self.order_to_status(order)
         self._fill_in_sample_ids(samples=status_data["samples"], lims_map=lims_map)
         new_samples = self.store_items_in_status(

cg/services/orders/store_order_services/store_metagenome_order.py

@@ -7,14 +7,7 @@
 from cg.models.orders.sample_base import StatusEnum
 from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
 from cg.services.orders.submitters.order_submitter import StoreOrderService
-from cg.store.models import (
-    ApplicationVersion,
-    Case,
-    CaseSample,
-    Customer,
-    Order,
-    Sample,
-)
+from cg.store.models import ApplicationVersion, Case, CaseSample, Customer, Order, Sample
 from cg.store.store import Store
 
 LOG = logging.getLogger(__name__)
@@ -29,7 +22,7 @@ def __init__(self, status_db: Store, lims_service: OrderLimsService):
 
     def store_order(self, order: OrderIn) -> dict:
         """Submit a batch of metagenome samples."""
-        project_data, lims_map = self.lims.process_lims(lims_order=order, new_samples=order.samples)
+        project_data, lims_map = self.lims.process_lims(order=order, new_samples=order.samples)
         status_data = self.order_to_status(order)
         self._fill_in_sample_ids(samples=status_data["families"][0]["samples"], lims_map=lims_map)
         new_samples = self.store_items_in_status(

cg/services/orders/store_order_services/store_microbial_fastq_order_service.py

@@ -17,7 +17,7 @@ def __init__(self, status_db: Store, lims_service: OrderLimsService):
         self.lims = lims_service
 
     def store_order(self, order: OrderIn) -> dict:
-        project_data, lims_map = self.lims.process_lims(lims_order=order, new_samples=order.samples)
+        project_data, lims_map = self.lims.process_lims(order=order, new_samples=order.samples)
         status_data: dict = self.order_to_status(order)
         self._fill_in_sample_ids(samples=status_data["samples"], lims_map=lims_map)
         new_samples: list[Sample] = self.store_items_in_status(

cg/services/orders/store_order_services/store_microbial_order.py

@@ -28,7 +28,7 @@ def __init__(self, status_db: Store, lims_service: OrderLimsService):
     def store_order(self, order: OrderIn) -> dict:
         self._fill_in_sample_verified_organism(order.samples)
         # submit samples to LIMS
-        project_data, lims_map = self.lims.process_lims(lims_order=order, new_samples=order.samples)
+        project_data, lims_map = self.lims.process_lims(order=order, new_samples=order.samples)
         # prepare order for status database
         status_data = self.order_to_status(order)
         self._fill_in_sample_ids(samples=status_data["samples"], lims_map=lims_map)

cg/services/orders/store_order_services/store_pacbio_order_service.py

@@ -22,7 +22,7 @@ def __init__(self, status_db: Store, lims_service: OrderLimsService):
     def store_order(self, order: OrderIn) -> dict:
         """Submit a batch of samples for PacBio Long Read delivery."""
 
-        project_data, lims_map = self.lims.process_lims(lims_order=order, new_samples=order.samples)
+        project_data, lims_map = self.lims.process_lims(order=order, new_samples=order.samples)
         status_data: dict = self.order_to_status(order)
         self._fill_in_sample_ids(samples=status_data["samples"], lims_map=lims_map)
         new_samples = self._store_samples_in_statusdb(

cg/services/orders/store_order_services/store_pool_order.py

@@ -8,15 +8,7 @@
 from cg.models.orders.samples import RmlSample
 from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
 from cg.services.orders.submitters.order_submitter import StoreOrderService
-from cg.store.models import (
-    ApplicationVersion,
-    Case,
-    CaseSample,
-    Customer,
-    Order,
-    Pool,
-    Sample,
-)
+from cg.store.models import ApplicationVersion, Case, CaseSample, Customer, Order, Pool, Sample
 from cg.store.store import Store
 
 LOG = logging.getLogger(__name__)
@@ -36,7 +28,7 @@ def __init__(self, status_db: Store, lims_service: OrderLimsService):
 
     def store_order(self, order: OrderIn) -> dict:
         status_data = self.order_to_status(order)
-        project_data, lims_map = self.lims.process_lims(lims_order=order, new_samples=order.samples)
+        project_data, lims_map = self.lims.process_lims(order=order, new_samples=order.samples)
         samples = [sample for pool in status_data["pools"] for sample in pool["samples"]]
         self._fill_in_sample_ids(samples=samples, lims_map=lims_map, id_key="internal_id")
         new_records = self.store_items_in_status(