consumer: saves workflow engine container logs

* Saves workflow engine container logs and updates WF status if it
  is only needed.

.travis.yml

@@ -24,7 +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"
+  - travis_retry pip install "mock>=3,<4"
 
 install:
   - travis_retry pip install -e .[all]

reana_workflow_controller/consumer.py

@@ -11,13 +11,15 @@
 from __future__ import absolute_import
 
 import json
+import logging
 import uuid
 from datetime import datetime
 
 import requests
 from kubernetes.client.rest import ApiException
 from reana_commons.consumer import BaseConsumer
-from reana_commons.k8s.api_client import current_k8s_batchv1_api_client
+from reana_commons.k8s.api_client import (current_k8s_batchv1_api_client,
+                                          current_k8s_corev1_api_client)
 from reana_commons.k8s.secrets import REANAUserSecretsStore
 from reana_commons.utils import (calculate_file_access_time,
                                  calculate_hash_of_dir,
@@ -74,17 +76,19 @@ def on_message(self, body, message):
 
 def _update_workflow_status(workflow_uuid, status, logs):
     """Update workflow status in DB."""
-    Workflow.update_workflow_status(Session, workflow_uuid,
-                                    status, logs, None)
     workflow = Session.query(Workflow).filter_by(id_=workflow_uuid)\
         .one_or_none()
-    if workflow.git_ref:
-        _update_commit_status(workflow, status)
-    alive_statuses = \
-        [WorkflowStatus.created, WorkflowStatus.running, WorkflowStatus.queued]
-    if status not in alive_statuses:
-        workflow.run_finished_at = datetime.now()
-        _delete_workflow_engine_pod(workflow_uuid)
+    if workflow.status != status:
+        Workflow.update_workflow_status(Session, workflow_uuid,
+                                        status, logs, None)
+        if workflow.git_ref:
+            _update_commit_status(workflow, status)
+        alive_statuses = \
+            [WorkflowStatus.created, WorkflowStatus.running,
+             WorkflowStatus.queued]
+        if status not in alive_statuses:
+            workflow.run_finished_at = datetime.now()
+            _delete_workflow_engine_pod(workflow)
 
 
 def _update_commit_status(workflow, status):
@@ -191,19 +195,27 @@ def _update_job_cache(msg):
     Session.add(cached_job)
 
 
-def _delete_workflow_engine_pod(workflow_uuid):
+def _delete_workflow_engine_pod(workflow):
     """Delete workflow engine pod."""
     try:
-        jobs = current_k8s_batchv1_api_client.list_namespaced_job(
+        jobs = current_k8s_corev1_api_client.list_namespaced_pod(
             namespace='default',
         )
         for job in jobs.items:
-            if workflow_uuid in job.metadata.name:
+            if str(workflow.id_) in job.metadata.name:
+                workflow.logs = \
+                    current_k8s_corev1_api_client.read_namespaced_pod_log(
+                        namespace=job.metadata.namespace,
+                        name=job.metadata.name,
+                        container='workflow-engine')
                 current_k8s_batchv1_api_client.delete_namespaced_job(
                     namespace='default',
                     propagation_policy="Background",
-                    name=job.metadata.name)
+                    name=job.metadata.labels['job-name'])
                 break
     except ApiException as e:
         raise REANAWorkflowControllerError(
             "Workflow engine pod cound not be deleted {}.".format(e))
+    except Exception as e:
+        logging.error(traceback.format_exc())
+        logging.error("Unexpected error: {}".format(e))

setup.py

@@ -52,7 +52,7 @@
     'marshmallow>2.13.0,<=2.20.1',
     'packaging>=18.0',
     'reana-commons[kubernetes]>=0.7.0.dev20200203,<0.8.0',
-    'reana-db>=0.7.0.dev20200129,<0.8.0',
+    'reana-db>=0.7.0.dev20200206,<0.8.0',
     'requests==2.20.0',
     'sqlalchemy-utils>=0.31.0',
     'uwsgi-tools>=1.1.1',