Remove debug print statements

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

@@ -19,14 +19,9 @@ def retrieve(self, request, *args, **kwargs):
         Since we have custom orcabus_id prefix for each model, we need to remove the prefix before retrieving it.
         """
         pk = self.kwargs.get('pk')
-        print("DEBUG: pk")
-        print(pk)
         if pk and pk.startswith(self.orcabus_id_prefix):
             pk = pk[len(self.orcabus_id_prefix):]
 
-        print("DEBUG: self.queryset")
-        print(self.queryset)
-        print(self.get_queryset())
         obj = get_object_or_404(self.get_queryset(), pk=pk)
         serializer = self.serializer_class(obj)
         return Response(serializer.data)

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

@@ -18,6 +18,4 @@ def list(self, request, *args, **kwargs):
 
     def get_queryset(self):
         query_params = self.get_query_params()
-        print("DEBUG: query_params")
-        print(query_params)
         return Payload.objects.get_by_keyword(self.queryset, **query_params)

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

@@ -102,12 +102,9 @@ def exclude_params(params):
     def ongoing(self, request):
         self.serializer_class = WorkflowRunSerializer  # use simple view for record listing
         # Get all books marked as favorite
-        print(request)
-        print(self.request.query_params)
         ordering = self.request.query_params.get('ordering', '-orcabus_id')
 
         if "status" in self.request.query_params.keys():
-            print("found status!")
             status = self.request.query_params.get('status')
             result_set = WorkflowRun.objects.get_by_keyword(states__status=status).order_by(ordering)
         else:
@@ -126,8 +123,6 @@ def ongoing(self, request):
     @action(detail=False, methods=['GET'])
     def unresolved(self, request):
         # Get all books marked as favorite
-        print(request)
-        print(self.request.query_params)
         ordering = self.request.query_params.get('ordering', '-id')
 
         result_set = WorkflowRun.objects.get_by_keyword(states__status="FAILED").order_by(ordering)

lib/workload/stateless/stacks/workflow-manager/workflow_manager_proc/lambdas/handle_service_wrsc_event.py

@@ -6,7 +6,10 @@
 import workflow_manager_proc.domain.executionservice.workflowrunstatechange as srv
 import workflow_manager_proc.domain.workflowmanager.workflowrunstatechange as wfm
 from workflow_manager_proc.services import emit_workflow_run_state_change, create_workflow_run_state
+import logging
 
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
 
 def handler(event, context):
     """
@@ -18,7 +21,7 @@ def handler(event, context):
         - create new State for WorkflowRun if required
         - relay the state change as WorkflowManager WRSC event if applicable
     """
-    print(f"Processing {event}, {context}")
+    logger.info(f"Processing {event}, {context}")
 
     # remove the AWSEvent wrapper from our WRSC event
     input_event: srv.AWSEvent = srv.Marshaller.unmarshall(event, srv.AWSEvent)
@@ -28,10 +31,10 @@ def handler(event, context):
     out_wrsc = create_workflow_run_state.handler(srv.Marshaller.marshall(input_wrsc), None)
     if out_wrsc:
         # new state resulted in state transition, we can relay the WRSC
-        print("Emitting WRSC.")
+        logger.info("Emitting WRSC.")
         emit_workflow_run_state_change.handler(wfm.Marshaller.marshall(out_wrsc), None)
     else:
         # ignore - state has not been updated
-        print(f"WorkflowRun state not updated. No event to emit.")
+        logger.info(f"WorkflowRun state not updated. No event to emit.")
 
-    print(f"{__name__} done.")
+    logger.info(f"{__name__} done.")

lib/workload/stateless/stacks/workflow-manager/workflow_manager_proc/lambdas/transition_bcm_fastq_copy.py

@@ -6,11 +6,15 @@
 from workflow_manager.models.workflow_run import WorkflowRun
 import workflow_manager_proc.domain.executionservice.workflowrunstatechange as srv
 import workflow_manager_proc.domain.workflowmanager.workflowrunstatechange as wfm
+import logging
+
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
 
 
 def handler(event, context):
     """event will be a workflowmanager.WorkflowRunStateChange event"""
-    print(f"Processing {event}, {context}")
+    logger.info(f"Processing {event}, {context}")
 
     input_event: wfm.AWSEvent = wfm.Marshaller.unmarshall(event, wfm.AWSEvent)
     input_wrsc: wfm.WorkflowRunStateChange = input_event.detail

lib/workload/stateless/stacks/workflow-manager/workflow_manager_proc/services/create_analysisruns_for_libraries.py

@@ -2,7 +2,10 @@
 from typing import List
 
 from workflow_manager.models import Analysis, AnalysisRun, AnalysisContext, Library
+import logging
 
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
 
 # TODO: get list of libraries (+ required metadata) from list of library IDs
 # TODO: switch pairing based on subject to pairing based on Case (creating a case is someone else's responsibility)
@@ -73,7 +76,7 @@ def create_wgs_analysis(libraries: List[dict]) -> List[AnalysisRun]:
                 normal_lib_record: Library = Library.objects.get(library_id=pairing[sbj]['normal'][0]['library_id'])
 
             if not tumor_lib_record or not normal_lib_record:
-                print("Not a valid pairing.")
+                logger.info("Not a valid pairing.")
                 break
 
             workflow = pairing[sbj]['tumor'][0]['workflow']
@@ -92,7 +95,7 @@ def create_wgs_analysis(libraries: List[dict]) -> List[AnalysisRun]:
             ar_wgs.libraries.add(normal_lib_record)
             analysis_runs.append(ar_wgs)
         else:
-            print(f"No pairing for {sbj}.")
+            logger.info(f"No pairing for {sbj}.")
 
     return analysis_runs
 

lib/workload/stateless/stacks/workflow-manager/workflow_manager_proc/services/emit_workflow_run_state_change.py

@@ -3,6 +3,10 @@
 import json
 import workflow_manager_proc.domain.workflowmanager.workflowrunstatechange as wfm
 from workflow_manager_proc.domain.workflowmanager.workflowrunstatechange import WorkflowRunStateChange
+import logging
+
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
 
 client = boto3.client('events')
 source = "orcabus.workflowmanager"
@@ -13,7 +17,7 @@ def handler(event, context):
     """
     event has to be JSON conform to workflowmanager.WorkflowRunStateChange
     """
-    print(f"Processing {event}, {context}")
+    logger.info(f"Processing {event}, {context}")
 
     response = client.put_events(
         Entries=[
@@ -26,7 +30,7 @@ def handler(event, context):
         ],
     )
 
-    print(f"Sent a WRSC event to event bus {event_bus_name}:")
-    print(event)
-    print(f"{__name__} done.")
+    logger.info(f"Sent a WRSC event to event bus {event_bus_name}:")
+    logger.info(event)
+    logger.info(f"{__name__} done.")
     return response

lib/workload/stateless/stacks/workflow-manager/workflow_manager_proc/tests/test_create_workflow_run_state.py

@@ -242,7 +242,5 @@ def test_get_last_state(self):
         t1 = s1.timestamp
         t2 = s2.timestamp
         delta = t1 - t2  # = 2 days
-        print(f"delta sec: {abs(delta.total_seconds())}")
         window = timedelta(hours=1)
-        print(f"window sec: {window.total_seconds()}")
         self.assertTrue(delta > window, "delta > 1h")