Uses k8s pod log as stdout/stderr.

lib/galaxy/jobs/runners/kubernetes.py

@@ -8,6 +8,7 @@
 from galaxy.jobs import JobDestination
 from galaxy.jobs.runners import AsynchronousJobState, AsynchronousJobRunner
 from .util.cli import CliInterface, split_params
+from os import sep as os_sep
 
 # pykube imports:
 try:
@@ -218,9 +219,13 @@ def check_watched_item(self, job_state):
             if 'failed' in job.obj['status']:
                 failed = job.obj['status']['failed']
 
-            # This assumes jobs dependent on a single pod.
+            # This assumes jobs dependent on a single pod, single container
             if succeeded > 0:
+                logs_file_path = self.__produce_log_file(job_state)
+                job_state.output_file = logs_file_path
+
                 self.mark_as_finished(job_state)
+
             elif active > 0 or succeeded + active + failed == 0:
                 self.mark_as_queued(job_state)
             elif failed > job_state.job_destination.params['max_pod_retrials']:
@@ -235,9 +240,24 @@ def check_watched_item(self, job_state):
             # TODO: possibly some warning or message should be provided here to stderr
             # TODO: of the job
             # there is more than one job associated to the expected unique job id used as selector.
+            job_state.error_file = self.__produce_log_file(job_state)
             self.mark_as_failed(job_state)
             return job_state
 
+    def __produce_log_file(self, job_state):
+        pod_r = Pod.objects(self._pykube_api).filter(selector="app=" + job_state.job_id)
+        logs = ""
+        for pod_obj in pod_r.response['items']:
+            pod = Pod(self._pykube_api, pod_obj)
+            logs += "\n\n==== Pod " + pod.name + " log start ====\n\n"
+            logs += pod.get_logs(timestamps=True)
+            logs += "\n\n==== Pod " + pod.name + " log end   ===="
+        logs_file_path = job_state.files_dir + os_sep + pod.name + '.log'
+        logs_file = open(logs_file_path)
+        logs_file.write(logs)
+        logs_file.close()
+        return logs_file_path
+
     def stop_job( self, job ):
         """Attempts to delete a dispatched job to the k8s cluster"""
         try: