Merge pull request #144 from mskcc/develop

Version 1.7.0

requirements.txt

@@ -1,5 +1,5 @@
 Django==2.2.13
-psycopg2==2.7.4
+psycopg2==2.8.6
 djangorestframework==3.9.4
 markdown==3.1.1
 django-filter==2.1.0
@@ -12,6 +12,6 @@ celery==4.4.7
 cwltool==2.0.20200122124526
 ruamel.yaml<=0.16.5
 schema-salad==5.0.20200122085940
-psycopg2-binary==2.8.4
+psycopg2-binary==2.8.6
 mock==4.0.2
 dj-static==0.0.6

ridgeback/__init__.py

@@ -1 +1 @@
-__version__="1.5.0"
+__version__="1.7.0"

toil_orchestrator/serializers.py

@@ -90,6 +90,12 @@ class Meta:
         model = CommandLineToolJob
         fields = '__all__'
 
+class JobIdsSerializer(serializers.Serializer):
+    job_ids = serializers.ListField(
+        allow_empty=True,
+        child=serializers.UUIDField(required=True),
+    )
+
 
 class JobSerializer(serializers.ModelSerializer):
     status = serializers.SerializerMethodField()
@@ -105,6 +111,11 @@ class Meta:
     message = MessageField(required=False)
     commandlinetooljob_set = CommandLineToolJobSerializer(many=True, required=False)
 
+
+class JobStatusSerializer(serializers.Serializer):
+    jobs = serializers.DictField()
+
+
 class JobSubmitSerializer(JobSerializer):
 
 

toil_orchestrator/tasks.py

@@ -42,7 +42,7 @@ def get_message(job_obj):
 def set_message(job_obj, message_obj):
     message_str = json.dumps(message_obj, sort_keys=True, indent=1, cls=DjangoJSONEncoder)
     job_obj.message = message_str
-    job_obj.save()
+    job_obj.save(update_fields=['message'])
 
 
 def update_message_by_key(job_obj, key, value):
@@ -98,8 +98,12 @@ def submit_jobs_to_lsf(self, job_id):
     job.output_directory = job_output_dir
     job.status = Status.PENDING
     log_path = os.path.join(job_work_dir, 'lsf.log')
-    update_message_by_key(job,'log',log_path)
-    job.save()
+    update_message_by_key(job, 'log', log_path)
+    job.save(update_fields=['external_id',
+                            'job_store_location',
+                            'working_dir',
+                            'output_directory',
+                            'status'])
 
 
 @shared_task(bind=True, max_retries=10, retry_jitter=True, retry_backoff=60)

toil_orchestrator/views/job_view.py

@@ -1,5 +1,5 @@
 from toil_orchestrator.models import Job, Status
-from toil_orchestrator.serializers import JobSerializer, JobSubmitSerializer, JobResumeSerializer
+from toil_orchestrator.serializers import JobSerializer, JobSubmitSerializer, JobResumeSerializer, JobIdsSerializer, JobStatusSerializer
 from toil_orchestrator.tasks import submit_jobs_to_lsf, abort_job
 from rest_framework import mixins
 from rest_framework import status
@@ -46,6 +46,27 @@ def resume(self, request, pk=None, *args, **kwargs):
         except Job.DoesNotExist:
             return Response("Could not find the indicated job to resume", status=status.HTTP_404_NOT_FOUND)
 
+    @swagger_auto_schema(request_body=JobIdsSerializer(), responses={status.HTTP_200_OK: JobStatusSerializer})
+    @action(detail=False, methods=['post'])
+    def statuses(self, request):
+        serializer = JobIdsSerializer(data=request.data)
+        if not serializer.is_valid():
+            return Response(serializer.errors,
+                            status=status.HTTP_400_BAD_REQUEST)
+        job_ids = serializer.validated_data.get("job_ids")
+        job_status_data = {}
+        for single_job in self.queryset.filter(id__in=job_ids):
+            job_obj = JobSerializer(single_job)
+            job_data = job_obj.data
+            job_id = job_data["id"]
+            job_status_data[job_id] = job_data
+        resp_serializer = JobStatusSerializer(data={'jobs':job_status_data})
+        if resp_serializer.is_valid():
+            return Response(resp_serializer.data)
+        else:
+            return Response(resp_serializer.errors,
+                            status=status.HTTP_500_INTERNAL_SERVER_ERROR)
+
     @swagger_auto_schema(responses={status.HTTP_200_OK: JobSerializer})
     @action(detail=True, methods=['get'])
     def abort(self, request, pk=None, *args, **kwargs):
@@ -56,7 +77,7 @@ def abort(self, request, pk=None, *args, **kwargs):
         abort_job.delay(str(pk))
         return Response("Job aborted", status=status.HTTP_200_OK)
 
-    @swagger_auto_schema(request_body=JobSubmitSerializer, responses={201: JobSerializer})
+    @swagger_auto_schema(request_body=JobSubmitSerializer, responses={status.HTTP_201_CREATED: JobSerializer})
     def create(self, request, *args, **kwargs):
         return self.validate_and_save(request.data)