Merge de65b3d into 2b47b4d

.travis.yml

@@ -24,6 +24,7 @@ before_install:
   - pip install -r requirements-dev.txt
   - travis_retry pip install --upgrade pip setuptools py
   - travis_retry pip install twine wheel coveralls
+  - travis_retry pip install "mock>=3"
 
 install:
   - travis_retry pip install -e .[all]

reana_workflow_controller/rest.py

@@ -1829,9 +1829,8 @@ def _stop_workflow(workflow):
     """Stop a given workflow."""
     if workflow.status == WorkflowStatus.running:
         kwrm = KubernetesWorkflowRunManager(workflow)
-        job_list = workflow.job_progress.get('running', {}).get('job_ids', [])
         workflow.run_stopped_at = datetime.now()
-        kwrm.stop_batch_workflow_run(job_list)
+        kwrm.stop_batch_workflow_run()
         workflow.status = WorkflowStatus.stopped
         current_db_sessions = Session.object_session(workflow)
         current_db_sessions.add(workflow)

reana_workflow_controller/workflow_run_manager.py

@@ -27,6 +27,7 @@
                                  create_cvmfs_storage_class, format_cmd)
 from reana_db.config import SQLALCHEMY_DATABASE_URI
 from reana_db.database import Session
+from reana_db.models import Job
 
 from reana_workflow_controller.errors import (REANAInteractiveSessionError,
                                               REANAWorkflowControllerError)
@@ -181,6 +182,15 @@ def _workflow_engine_env_vars(self):
 
         return (env_vars)
 
+    def get_workflow_running_jobs_as_backend_ids(self):
+        """Get all running jobs of a workflow as backend job IDs."""
+        session = Session.object_session(self.workflow)
+        job_list = self.workflow.job_progress.get(
+            'running', {}).get('job_ids', [])
+        rows = session.query(Job).filter(Job.id_.in_(job_list))
+        backend_ids = [j.backend_job_id for j in rows.all()]
+        return backend_ids
+
 
 class KubernetesWorkflowRunManager(WorkflowRunManager):
     """Implementation of WorkflowRunManager for Kubernetes."""
@@ -293,15 +303,15 @@ def stop_interactive_session(self):
         current_db_sessions.add(self.workflow)
         current_db_sessions.commit()
 
-    def stop_batch_workflow_run(self, workflow_run_jobs=None):
+    def stop_batch_workflow_run(self):
         """Stop a batch workflow run along with all its dependent jobs.
 
         :param workflow_run_jobs: List of active job id's spawned by the
             workflow run.
         """
         workflow_run_name = self._workflow_run_name_generator('batch')
-        workflow_run_jobs = workflow_run_jobs or []
-        to_delete = workflow_run_jobs + [workflow_run_name]
+        to_delete = self.get_workflow_running_jobs_as_backend_ids() + \
+            [workflow_run_name]
         for job in to_delete:
             current_k8s_batchv1_api_client.delete_namespaced_job(
                 job,

tests/conftest.py

@@ -12,9 +12,10 @@
 
 import os
 import shutil
+import uuid
 
 import pytest
-from reana_db.models import Base, User
+from reana_db.models import Base, Job, JobStatus, User
 from sqlalchemy_utils import create_database, database_exists, drop_database
 
 from reana_workflow_controller.factory import create_app
@@ -34,3 +35,58 @@ def base_app(tmp_shared_volume_path):
     }
     app_ = create_app(config_mapping)
     return app_
+
+
+@pytest.fixture()
+def add_kubernetes_jobs_to_workflow(session):
+    """Create and add jobs to a workflow.
+
+    This fixture provides a callable which takes the workflow to which the
+    created jobs should belong to. It can be parametrized to customize the
+    backend of the created jobs and the number of jobs to create.
+
+    .. code-block:: python
+
+        def test_stop_workflow(workflow, add_kubernetes_jobs_to_workflow):
+            workflow_jobs = add_kubernetes_jobs_to_workflow(workflow.id_
+                                                            backend='htcondor',
+                                                            num_jobs=4)
+    """
+    def add_kubernetes_jobs_to_workflow_callable(workflow, backend=None,
+                                                 num_jobs=2, status=None):
+        """Add Kubernetes jobs to a given workflow.
+
+        :param workflow_uuid: Workflow which the jobs should belong to.
+        :param backend: Backend of the created jobs.
+        :param num_jobs: Number of jobs to create.
+        :param status: String representing the status of the created jobs,
+            by default ``running``.
+        """
+        jobs = []
+        if status and status not in JobStatus.__members__:
+            raise ValueError('Unknown status {} use one of {}'.format(
+                status, JobStatus.__members__))
+
+        status = status or JobStatus.running.name
+        backend = backend or 'kubernetes'
+        progress_dict = {
+            'total': {'job_ids': [], 'total': 0},
+            JobStatus.running.name: {'job_ids': [], 'total': 0},
+            JobStatus.failed.name: {'job_ids': [], 'total': 0},
+            JobStatus.finished.name: {'job_ids': [], 'total': 0},
+        }
+        for num in range(num_jobs):
+            reana_job_id = uuid.uuid4()
+            backend_job_id = uuid.uuid4()
+            job = Job(id_=reana_job_id,
+                      backend_job_id=str(backend_job_id),
+                      workflow_uuid=workflow.id_)
+            progress_dict[status]['job_ids'].append(str(job.id_))
+            progress_dict[status]['total'] += 1
+            session.add(job)
+            jobs.append(job)
+        workflow.job_progress = progress_dict
+        session.add(workflow)
+        session.commit()
+        return jobs
+    yield add_kubernetes_jobs_to_workflow_callable

tests/test_workflow_run_manager.py

@@ -17,6 +17,7 @@
 from kubernetes.client.rest import ApiException
 from mock import DEFAULT, Mock, patch
 from reana_commons.config import INTERACTIVE_SESSION_TYPES
+from reana_db.models import WorkflowStatus
 
 from reana_workflow_controller.errors import REANAInteractiveSessionError
 from reana_workflow_controller.workflow_run_manager import \
@@ -55,9 +56,11 @@ def test_start_interactive_workflow_k8s_failure(sample_serial_workflow_in_db):
 
 
 def test_atomic_creation_of_interactive_session(sample_serial_workflow_in_db):
-    """Test the correct creation of all objects related to an interactive
-       sesison as well as writing the state to DB, either all should be done
-       or nothing.."""
+    """Test atomic creation of interactive sessions.
+
+    All interactive session should be created as  well as writing the state
+    to DB, either all should be done or nothing.
+    """
     mocked_k8s_client = Mock()
     mocked_k8s_client.create_namespaced_deployment =\
         Mock(side_effect=ApiException(
@@ -79,3 +82,23 @@ def test_atomic_creation_of_interactive_session(sample_serial_workflow_in_db):
             mocked_k8s_client.delete_namespaced_ingress.assert_called_once()
             mocked_k8s_client.delete_namespaced_deployment.assert_called_once()
             assert sample_serial_workflow_in_db.interactive_session is None
+
+
+def test_stop_workflow_backend_only_kubernetes(
+        sample_serial_workflow_in_db,
+        add_kubernetes_jobs_to_workflow):
+    """Test deletion of workflows with only Kubernetes based jobs."""
+    workflow = sample_serial_workflow_in_db
+    workflow.status = WorkflowStatus.running
+    workflow_jobs = add_kubernetes_jobs_to_workflow(workflow)
+    backend_job_ids = [job.backend_job_id for job in workflow_jobs]
+    with patch("reana_workflow_controller.workflow_run_manager."
+               "current_k8s_batchv1_api_client") as api_client:
+        kwrm = KubernetesWorkflowRunManager(workflow)
+        kwrm.stop_batch_workflow_run()
+        for delete_call in api_client.delete_namespaced_job.call_args_list:
+            if delete_call.args[0] in backend_job_ids:
+                del backend_job_ids[backend_job_ids.index(
+                    delete_call.args[0])]
+
+        assert not backend_job_ids