Feat(wfr) api add "DEPRECATED" state (#770)

* add deprecated state for state api

* add deprecated in stats api

* add api for rerun/deprecated vlidation

* add allowed_dataset_choice in rerun valid api

* bring the emit events back

lib/workload/stateless/stacks/workflow-manager/workflow_manager/serializers/workflow_run.py

@@ -19,7 +19,7 @@ def get_current_state(self, obj) -> dict:
 class WorkflowRunListParamSerializer(OptionalFieldsMixin, WorkflowRunBaseSerializer):
     class Meta:
         model = WorkflowRun
-        fields = "__all__"
+        fields = ["orcabus_id", "workflow", "analysis_run", "workflow_run_name", "portal_run_id", "execution_id", "comment",]
 
 class WorkflowRunSerializer(WorkflowRunBaseSerializer):
     from .workflow import WorkflowMinSerializer
@@ -59,6 +59,7 @@ class WorkflowRunCountByStatusSerializer(serializers.Serializer):
     failed = serializers.IntegerField()
     resolved = serializers.IntegerField()
     ongoing = serializers.IntegerField()
+    deprecated = serializers.IntegerField()
 
     def update(self, instance, validated_data):
         pass

lib/workload/stateless/stacks/workflow-manager/workflow_manager/serializers/workflow_run_action.py

@@ -6,7 +6,11 @@
 
 class AllowedRerunWorkflow(StrEnum):
     RNASUM = "rnasum"
-
+
+class AllowedRerunWorkflowSerializer(serializers.Serializer):
+    is_valid = serializers.BooleanField()
+    allowed_dataset_choice = serializers.ListField(child=serializers.CharField())
+    valid_workflows = serializers.ListField(child=serializers.CharField())
 
 class BaseRerunInputSerializer(serializers.Serializer):
 

lib/workload/stateless/stacks/workflow-manager/workflow_manager/urls/base.py

@@ -20,7 +20,7 @@
 
 router = OptionalSlashDefaultRouter()
 
-router.register("workflowrun/stats", WorkflowRunStatsViewSet, basename="workflowrun_list_all") # put it before workflowrun, as it will match the workflowrun/list_all/ url
+router.register(r"workflowrun/stats", WorkflowRunStatsViewSet, basename="workflowrun_list_all") # put it before workflowrun, as it will match the workflowrun/list_all/ url
 router.register(r"analysis", AnalysisViewSet, basename="analysis")
 router.register(r"analysisrun", AnalysisRunViewSet, basename="analysisrun")
 router.register(r"analysiscontext", AnalysisContextViewSet, basename="analysiscontext")
@@ -29,7 +29,6 @@
 router.register(r"workflowrun", WorkflowRunActionViewSet, basename="workflowrun-action")
 router.register(r"payload", PayloadViewSet, basename="payload")
 
-# may no longer need this as it's currently included in the detail response for an individual WorkflowRun record
 router.register(
     "workflowrun/(?P<orcabus_id>[^/.]+)/state",
     StateViewSet,

lib/workload/stateless/stacks/workflow-manager/workflow_manager/viewsets/state.py

@@ -1,4 +1,6 @@
-
+from drf_spectacular.types import OpenApiTypes
+from drf_spectacular.utils import extend_schema, PolymorphicProxySerializer
+from rest_framework.decorators import action
 from rest_framework import mixins, status
 from rest_framework.response import Response
 from rest_framework.viewsets import GenericViewSet
@@ -14,52 +16,70 @@ class StateViewSet(mixins.CreateModelMixin, mixins.UpdateModelMixin, mixins.List
     orcabus_id_prefix = State.orcabus_id_prefix
     http_method_names = ['get', 'post', 'patch']
     pagination_class = None
+
+    """
+    valid_states_map for state creation, update
+    refer: 
+        "Resolved" -- https://github.com/umccr/orcabus/issues/593
+        "Deprecated" -- https://github.com/umccr/orcabus/issues/695
+    """
+    valid_states_map = {
+        'RESOLVED': ['FAILED'],
+        'DEPRECATED': ['SUCCEEDED']
+    }
 
     def get_queryset(self):
         return State.objects.filter(workflow_run=self.kwargs["orcabus_id"])
 
+    @extend_schema(responses=OpenApiTypes.OBJECT, description="Valid states map for new state creation, update")
+    @action(detail=False, methods=['get'], url_name='valid_states_map', url_path='valid_states_map')
+    def get_valid_states_map(self, request, **kwargs):
+        return Response(self.valid_states_map)
+
     def create(self, request, *args, **kwargs):
+        """
+        Create a customed new state for a workflow run.
+        Currently we support "Resolved", "Deprecated"
+        """
         wfr_orcabus_id = self.kwargs.get("orcabus_id")
         workflow_run = WorkflowRun.objects.get(orcabus_id=wfr_orcabus_id)
 
-        # Check if the workflow run has a "Failed" or "Aborted" state
         latest_state = workflow_run.get_latest_state()
-        if latest_state.status not in ["FAILED"]:
-            return Response({"detail": "Can only create 'Resolved' state for workflow runs with 'Failed' states."},
+        if not latest_state:
+            return Response({"detail": "No state found for workflow run '{}'".format(wfr_orcabus_id)},
                             status=status.HTTP_400_BAD_REQUEST)
-
-        # Check if the new state is "Resolved"
-        if request.data.get('status', '').upper() != "RESOLVED":
-            return Response({"detail": "Can only create 'Resolved' state."},
+        latest_status = latest_state.status
+        request_status = request.data.get('status', '').upper()
+
+        # check if the state status is valid
+        if not self.check_state_status(latest_status, request_status):
+            return Response({"detail": "Invalid state request. Can't add state '{}' to '{}'".format(request_status, latest_status)},
                             status=status.HTTP_400_BAD_REQUEST)
 
-        # comment is required when status is "Resolved"
+        # comment is required when request change state
         if not request.data.get('comment'):
-            return Response({"detail": "Comment is required when status is 'Resolved'."},
+            return Response({"detail": "Comment is required when request status is '{}'".format(request_status)},
                             status=status.HTTP_400_BAD_REQUEST)
 
-
         # Prepare data for serializer
         data = request.data.copy()
         data['timestamp'] = timezone.now()
         data['workflow_run'] = wfr_orcabus_id
-
+        data['status'] = request_status
+
         serializer = self.get_serializer(data=data)
         serializer.is_valid(raise_exception=True)
-        self.perform_create(serializer)
+        serializer.save()
         headers = self.get_success_headers(serializer.data)
         return Response(serializer.data, status=status.HTTP_201_CREATED, headers=headers)
 
-    def perform_create(self, serializer):
-        serializer.save(workflow_run_id=self.kwargs["orcabus_id"], status="RESOLVED")
-
     def update(self, request, *args, **kwargs):
         partial = kwargs.pop('partial', False)
         instance = self.get_object()
 
         # Check if the state being updated is "Resolved"
-        if instance.status != "RESOLVED":
-            return Response({"detail": "Can only update 'Resolved' state records."},
+        if instance.status not in self.valid_states_map:
+            return Response({"detail": "Invalid state status."},
                             status=status.HTTP_400_BAD_REQUEST)
 
         # Check if only the comment field is being updated
@@ -69,7 +89,7 @@ def update(self, request, *args, **kwargs):
 
         serializer = self.get_serializer(instance, data=request.data, partial=partial)
         serializer.is_valid(raise_exception=True)
-        self.perform_update(serializer)
+        serializer.save()
 
         if getattr(instance, '_prefetched_objects_cache', None):
             # If 'prefetch_related' has been applied to a queryset, we need to
@@ -78,5 +98,14 @@ def update(self, request, *args, **kwargs):
 
         return Response(serializer.data)
 
-    def perform_update(self, serializer):
-        serializer.save(status="RESOLVED")
+
+    def check_state_status(self, current_status, request_status):
+        """
+        check if the state status is valid: 
+        valid_states_map[request_state] == current_state.status
+        """
+        if request_status not in self.valid_states_map:
+            return False
+        if current_status not in self.valid_states_map[request_status]:
+            return False
+        return True

lib/workload/stateless/stacks/workflow-manager/workflow_manager/viewsets/workflow_run_action.py

@@ -15,7 +15,7 @@
 from workflow_manager.models.utils import create_portal_run_id
 from workflow_manager.serializers.library import LibrarySerializer
 from workflow_manager.serializers.payload import PayloadSerializer
-from workflow_manager.serializers.workflow_run_action import AllowedRerunWorkflow, RERUN_INPUT_SERIALIZERS
+from workflow_manager.serializers.workflow_run_action import AllowedRerunWorkflow, RERUN_INPUT_SERIALIZERS, AllowedRerunWorkflowSerializer
 from workflow_manager.models import (
     WorkflowRun,
     State,
@@ -27,6 +27,25 @@ class WorkflowRunActionViewSet(ViewSet):
     queryset = WorkflowRun.objects.prefetch_related('states').all()
     orcabus_id_prefix = WorkflowRun.orcabus_id_prefix
 
+    @extend_schema(responses=AllowedRerunWorkflowSerializer, description="Allowed rerun workflows")
+    @action(detail=True, methods=['get'], url_name='validate_rerun_workflows', url_path='validate_rerun_workflows')
+    def validate_rerun_workflows(self, request, *args, **kwargs):
+        wfl_run = get_object_or_404(self.queryset, pk=kwargs.get('pk'))
+        is_valid = wfl_run.workflow.workflow_name in AllowedRerunWorkflow
+
+        # Get allowed dataset choice for the workflow
+        wfl_name = wfl_run.workflow.workflow_name
+        allowed_dataset_choice = []
+        if wfl_name == AllowedRerunWorkflow.RNASUM.value:
+            allowed_dataset_choice = RERUN_INPUT_SERIALIZERS[wfl_name].allowed_dataset_choice
+
+        reponse = {
+            'is_valid': is_valid,
+            'allowed_dataset_choice': allowed_dataset_choice,
+            'valid_workflows': AllowedRerunWorkflow,
+        }
+        return Response(reponse, status=status.HTTP_200_OK)
+
     @extend_schema(
         request=PolymorphicProxySerializer(
             component_name='WorkflowRunRerun',

lib/workload/stateless/stacks/workflow-manager/workflow_manager/viewsets/workflow_run_stats.py

@@ -69,7 +69,8 @@ def exclude_params(params):
                 ~Q(states__status="FAILED") &
                 ~Q(states__status="ABORTED") &
                 ~Q(states__status="SUCCEEDED") &
-                ~Q(states__status="RESOLVED")
+                ~Q(states__status="RESOLVED") &
+                ~Q(states__status="DEPRECATED")
             )
 
         if status:
@@ -131,6 +132,11 @@ def count_by_status(self, request):
             states__status="RESOLVED"
         ).count()
 
+        deprecated_count = annotate_queryset.filter(
+            states__timestamp=F('latest_state_time'),
+            states__status="DEPRECATED"
+        ).count()
+
         ongoing_count = base_queryset.filter(
             ~Q(states__status="FAILED") &
             ~Q(states__status="ABORTED") &
@@ -143,6 +149,7 @@ def count_by_status(self, request):
             'aborted': aborted_count,
             'failed': failed_count,
             'resolved': resolved_count,
+            'deprecated': deprecated_count,
             'ongoing': ongoing_count
         }, status=200)