add(fields to pacbio sample) (#3826) (patch)

# Description add fields to pacbio orderin
Clinical-Genomics · Oct 14, 2024 · 5e2b3ad · 5e2b3ad
1 parent d545379
commit 5e2b3ad
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Showing 4 changed files with 17 additions and 6 deletions.
diff --git a/cg/models/orders/samples.py b/cg/models/orders/samples.py
@@ -195,8 +195,12 @@ def str_to_int(cls, v: str) -> int | None:
 class PacBioSample(OrderInSample):
     _suitable_project = OrderType.PACBIO_LONG_READ
 
-    capture_kit: str | None = None
+    buffer: str
+    container: ContainerEnum
+    container_name: str | None = None
     sex: SexEnum = SexEnum.unknown
+    source: str
+    subject_id: str
     tumour: bool
 
 

diff --git a/cg/services/orders/store_order_services/store_pacbio_order_service.py b/cg/services/orders/store_order_services/store_pacbio_order_service.py
@@ -43,7 +43,6 @@ def order_to_status(order: OrderIn) -> dict:
             "samples": [
                 {
                     "application": sample.application,
-                    "capture_kit": sample.capture_kit,
                     "comment": sample.comment,
                     "data_analysis": sample.data_analysis,
                     "data_delivery": sample.data_delivery,
@@ -52,6 +51,7 @@ def order_to_status(order: OrderIn) -> dict:
                     "sex": sample.sex,
                     "tumour": sample.tumour,
                     "volume": sample.volume,
+                    "subject_id": sample.subject_id,
                 }
                 for sample in order.samples
             ],
@@ -79,7 +79,7 @@ def _store_samples_in_statusdb(
                     original_ticket=ticket_id,
                     priority=sample["priority"],
                     tumour=sample["tumour"],
-                    capture_kit=sample["capture_kit"],
+                    subject_id=sample["subject_id"],
                 )
                 new_sample.customer = customer
                 application_tag: str = sample["application"]

diff --git a/tests/fixtures/cgweb_orders/pacbio.json b/tests/fixtures/cgweb_orders/pacbio.json
@@ -17,7 +17,9 @@
             "source": "blood",
             "tumour": false,
             "volume": "25",
-            "well_position": ""
+            "well_position": "",
+            "buffer": "Nuclease-free water",
+            "subject_id": "subject2"
         },
         {
             "application": "WGSPCFC060",
@@ -33,7 +35,9 @@
             "source": "cell line",
             "tumour": true,
             "volume": "35",
-            "well_position": ""
+            "well_position": "",
+            "buffer": "Nuclease-free water",
+            "subject_id": "subject1"
         }
     ]
 }
diff --git a/tests/services/orders/test_validate_order_service/conftest.py b/tests/services/orders/test_validate_order_service/conftest.py
@@ -14,13 +14,16 @@
 def pacbio_sample() -> PacBioSample:
     return PacBioSample(
         application="WGSPCFC060",
-        capture_kit=None,
         data_analysis=Workflow.RAW_DATA,
         data_delivery=DataDelivery.NO_DELIVERY,
         name="PacbioSample",
         sex=SexEnum.unknown,
         tumour=False,
         volume="50",
+        buffer="buffer",
+        source="source",
+        subject_id="subject_id",
+        container="Tube",
     )