(Improve order flow) Export skip reception control

cg/services/orders/lims_service/service.py

@@ -15,7 +15,11 @@ def __init__(self, lims_api: LimsAPI):
 
     @staticmethod
     def _build_lims_sample(
-        customer: str, samples: list[Sample], workflow: Workflow, delivery_type: DataDelivery
+        customer: str,
+        samples: list[Sample],
+        workflow: Workflow,
+        delivery_type: DataDelivery,
+        skip_reception_control: bool,
     ) -> list[LimsSample]:
         """Convert order input to LIMS interface input."""
         samples_lims = []
@@ -26,6 +30,8 @@ def _build_lims_sample(
             dict_sample["data_analysis"] = workflow
             dict_sample["data_delivery"] = delivery_type
             dict_sample["family_name"] = sample._case_name
+            if skip_reception_control:
+                dict_sample["skip_reception_control"] = True
             lims_sample: LimsSample = LimsSample.parse_obj(dict_sample)
             samples_lims.append(lims_sample)
         return samples_lims
@@ -38,10 +44,15 @@ def process_lims(
         order_name: str,
         workflow: Workflow,
         delivery_type: DataDelivery,
+        skip_reception_control: bool,
     ) -> tuple[any, dict]:
         """Process samples to add them to LIMS."""
         samples_lims: list[LimsSample] = self._build_lims_sample(
-            customer=customer, samples=samples, workflow=workflow, delivery_type=delivery_type
+            customer=customer,
+            samples=samples,
+            workflow=workflow,
+            delivery_type=delivery_type,
+            skip_reception_control=skip_reception_control,
         )
         project_name: str = str(ticket) or order_name
         # Create new lims project

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

@@ -51,6 +51,7 @@ def store_order(self, order: OrderWithCases) -> dict:
                 order_name=order.name,
                 workflow=ORDER_TYPE_WORKFLOW_MAP[order.order_type],
                 delivery_type=order.delivery_type,
+                skip_reception_control=order.skip_reception_control,
             )
         if lims_map:
             self._fill_in_sample_ids(samples=new_samples, lims_map=lims_map)

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

@@ -33,6 +33,7 @@ def store_order(self, order: FastqOrder) -> dict:
             workflow=Workflow.RAW_DATA,
             customer=order.customer,
             delivery_type=DataDelivery(order.delivery_type),
+            skip_reception_control=order.skip_reception_control,
         )
         self._fill_in_sample_ids(samples=order.samples, lims_map=lims_map)
         new_samples: list[Sample] = self.store_order_data_in_status_db(order=order)

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

@@ -39,6 +39,7 @@ def store_order(self, order: OrderMetagenome) -> dict:
             order_name=order.name,
             workflow=ORDER_TYPE_WORKFLOW_MAP[order.order_type],
             delivery_type=DataDelivery(order.delivery_type),
+            skip_reception_control=order.skip_reception_control,
         )
         self._fill_in_sample_ids(samples=order.samples, lims_map=lims_map)
         new_samples = self.store_order_data_in_status_db(order)

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

@@ -28,6 +28,7 @@ def store_order(self, order: MicrobialFastqOrder) -> dict:
             workflow=Workflow.RAW_DATA,
             customer=order.customer,
             delivery_type=DataDelivery(order.delivery_type),
+            skip_reception_control=order.skip_reception_control,
         )
         self._fill_in_sample_ids(samples=order.samples, lims_map=lims_map)
         new_samples: list[Sample] = self.store_order_data_in_status_db(order=order)

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

@@ -44,6 +44,7 @@ def store_order(self, order: MicrobialOrder) -> dict:
             order_name=order.name,
             workflow=ORDER_TYPE_WORKFLOW_MAP[order.order_type],
             delivery_type=DataDelivery(order.delivery_type),
+            skip_reception_control=order.skip_reception_control,
         )
         self._fill_in_sample_ids(samples=order.samples, lims_map=lims_map)
 

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

@@ -30,6 +30,7 @@ def store_order(self, order: PacbioOrder) -> dict:
             workflow=Workflow.RAW_DATA,
             customer=order.customer,
             delivery_type=DataDelivery(order.delivery_type),
+            skip_reception_control=order.skip_reception_control,
         )
         self._fill_in_sample_ids(samples=order.samples, lims_map=lims_map)
         new_samples = self.store_order_data_in_status_db(order=order)

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

@@ -33,6 +33,7 @@ def store_order(self, order: OrderWithIndexedSamples) -> dict:
             order_name=order.name,
             workflow=ORDER_TYPE_WORKFLOW_MAP[order.order_type],
             delivery_type=order.delivery_type,
+            skip_reception_control=order.skip_reception_control,
         )
         self._fill_in_sample_ids(samples=order.samples, lims_map=lims_map)
         new_records: list[Pool] = self.store_order_data_in_status_db(order=order)

cg/services/orders/validation/rules/utils.py

@@ -45,8 +45,8 @@ def is_volume_missing(sample: Sample) -> bool:
 def has_sample_invalid_concentration(
     sample: SampleWithSkipRC, allowed_interval: tuple[float, float]
 ) -> bool:
-    concentration: float = sample.concentration_ng_ul
-    return not is_sample_concentration_within_interval(
+    concentration: float | None = sample.concentration_ng_ul
+    return concentration and not is_sample_concentration_within_interval(
         concentration=concentration, interval=allowed_interval
     )