Feature/force import

beagle_etl/jobs/metadb_jobs.py

@@ -180,17 +180,17 @@ def request_update_notification(request_id):
 
 
 @shared_task
-def new_request(message_id):
+def new_request(message_id, force_import=False):
     message = SMILEMessage.objects.get(id=message_id)
 
     try:
-        data = RequestMetadata.from_dict(json.loads(message.message))
+        data = RequestMetadata.from_dict(json.loads(message.message), force_import=force_import)
     except Exception as e:
         message.add_log(str(e))
         message.failed()
         return
 
-    if not data.isCmoRequest:
+    if not data.isCmoRequest and not force_import:
         # Non CmoRequests not supported
         logger.info(f"Request {data.igoRequestId} is not CMO Request")
         message.add_log(f"Request {data.igoRequestId} is not CMO Request")

beagle_etl/smile_message/objects/request_object.py

@@ -41,15 +41,15 @@ class RequestMetadata:
     pooledNormals: Optional[List[str]] = None
 
     @classmethod
-    def from_dict(cls, data: Dict[str, Any]) -> "RequestMetadata":
+    def from_dict(cls, data: Dict[str, Any], force_import: bool = False) -> "RequestMetadata":
         """Deserialize from dictionary."""
         # Handle nested status
         status_data = data.get("status", {})
         status = RequestStatus(**status_data) if status_data else RequestStatus(False, "{}")
 
         # Handle nested samples
         samples_data = data.get("samples", [])
-        samples = [SampleMetadata.from_dict(sample) for sample in samples_data]
+        samples = [SampleMetadata.from_dict(sample, force_import=force_import) for sample in samples_data]
 
         # Handle delivery date conversion
         delivery_date = None

beagle_etl/smile_message/objects/sample_object.py

@@ -1,6 +1,6 @@
 import re
 import logging
-from dataclasses import dataclass
+from dataclasses import dataclass, field
 from typing import List, Optional, Dict, Any
 from django.conf import settings
 from beagle_etl.exceptions import (
@@ -217,9 +217,10 @@ class SampleMetadata:
     tubeId: Optional[str] = None
     cfDNA2dBarcode: Optional[str] = None
     cmoInfoIgoId: Optional[str] = None
+    skip_validation: bool = field(default=False, compare=False, repr=False)
 
     @classmethod
-    def from_dict(cls, data: Dict[str, Any]) -> "SampleMetadata":
+    def from_dict(cls, data: Dict[str, Any], force_import: bool = False) -> "SampleMetadata":
         """Deserialize SampleMetadata from dictionary."""
         # Handle nested status
         status_data = data.get("status", {})
@@ -275,9 +276,12 @@ def from_dict(cls, data: Dict[str, Any]) -> "SampleMetadata":
             sampleAliases=sample_aliases,
             patientAliases=patient_aliases,
             additionalProperties=data.get("additionalProperties", {}),
+            skip_validation=force_import,
         )
 
     def __post_init__(self):
+        if self.skip_validation:
+            return
         self._validate_primary_id()
         required = PANEL_REQUIRED_FIELDS.get(self.genePanel, DEFAULT_REQUIRED_FIELDS)
         self._validate_required_fields(required)

file_system/urls.py

@@ -11,7 +11,7 @@
 from file_system.views.file_type_view import FileTypeView
 from file_system.views.sample_view import SampleViewSet
 from file_system.views.patient_view import PatientViewSet
-from file_system.views.request_view import RequestViewSet
+from file_system.views.request_view import RequestViewSet, ForceImportRequestView
 from file_system.views.distribution_view import DistributionView
 from file_system.views.sample_view import SampleFullViewSet
 
@@ -33,4 +33,5 @@
     path("batch-patch-files", BatchPatchFiles.as_view()),
     path("copy-files", CopyFilesView.as_view()),
     path("manifest/", Manifest.as_view()),
+    path("request/force-import/<str:request_id>/", ForceImportRequestView.as_view()),
 ]

file_system/views/request_view.py

@@ -1,9 +1,14 @@
-from rest_framework import mixins
+from django.conf import settings
+from rest_framework import mixins, status
+from rest_framework.response import Response
+from rest_framework.views import APIView
 from file_system.models import Request
 from file_system.serializers import RequestSerializer
 from rest_framework.viewsets import GenericViewSet
 from rest_framework.permissions import IsAuthenticated
 from rest_framework.filters import SearchFilter
+from beagle_etl.models import SMILEMessage
+from beagle_etl.jobs.metadb_jobs import new_request
 
 
 class RequestViewSet(
@@ -16,3 +21,24 @@ class RequestViewSet(
 
     def get_serializer_class(self):
         return RequestSerializer
+
+
+class ForceImportRequestView(APIView):
+    permission_classes = (IsAuthenticated,)
+
+    def post(self, _request, request_id):
+        message = (
+            SMILEMessage.objects.filter(request_id=request_id, topic=settings.METADB_NATS_NEW_REQUEST)
+            .order_by("-created_date")
+            .first()
+        )
+        if not message:
+            return Response(
+                {"detail": f"No new-request SMILEMessage found for request_id {request_id}."},
+                status=status.HTTP_404_NOT_FOUND,
+            )
+        new_request(str(message.id), force_import=True)
+        return Response(
+            {"detail": f"Force import complete for request {request_id} (message {message.id})."},
+            status=status.HTTP_200_OK,
+        )