- print("run-command: caught exception: {}".format(e))
-
-finally:
- # restore default signal handlers.
- signal.signal(signal.SIGINT, signal.SIG_DFL)
- signal.signal(signal.SIGTERM, signal.SIG_DFL)
- signal.signal(signal.SIGQUIT, signal.SIG_DFL)
-
- for l in links:
- os.unlink(l)
-
- print("run-command: the follow output files will be saved to keep:")
-
- subprocess.call(["find", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"])
-
- print("run-command: start writing output to keep")
-
- done = False
- resume_cache = put.ResumeCache(os.path.join(arvados.current_task().tmpdir, "upload-output-checkpoint"))
- reporter = put.progress_writer(machine_progress)
- bytes_expected = put.expected_bytes_for(".")
- while not done:
- try:
- out = put.ArvPutCollectionWriter(resume_cache, reporter, bytes_expected)
- out.do_queued_work()
- out.write_directory_tree(".", max_manifest_depth=0)
- outuuid = out.finish()
- api.job_tasks().update(uuid=arvados.current_task()['uuid'],
- body={
- 'output':outuuid,
- 'success': (rcode == 0),
- 'progress':1.0
- }).execute()
- done = True
- except KeyboardInterrupt:
- print("run-command: terminating on signal SIGINT")
- done = True
- except Exception as e:
- print("run-command: caught exception: {}".format(e))
- time.sleep(5)
+ logging.exception("caught exception")
+
+# restore default signal handlers.
+signal.signal(signal.SIGINT, signal.SIG_DFL)
+signal.signal(signal.SIGTERM, signal.SIG_DFL)
+signal.signal(signal.SIGQUIT, signal.SIG_DFL)
+
+for l in links:
+ os.unlink(l)
+
+logging.info("the following output files will be saved to keep:")
+
+subprocess.call(["find", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"], stdout=sys.stderr)
+
+logging.info("start writing output to keep")
+
+done = False
+resume_cache = put.ResumeCache(os.path.join(arvados.current_task().tmpdir, "upload-output-checkpoint"))
+reporter = put.progress_writer(machine_progress)
+bytes_expected = put.expected_bytes_for(".")
+while not done:
+ try:
+ out = put.ArvPutCollectionWriter.from_cache(resume_cache, reporter, bytes_expected)
+ out.do_queued_work()
+ out.write_directory_tree(".", max_manifest_depth=0)
+ outuuid = out.finish()
+ api.job_tasks().update(uuid=arvados.current_task()['uuid'],
+ body={
+ 'output':outuuid,
+ 'success': (rcode == 0),
+ 'progress':1.0
+ }).execute()
+ done = True
+ except KeyboardInterrupt:
+ logging.critical("terminating on signal 2")
+ sys.exit(2)
+ except Exception as e:
+ logging.exception("caught exception:")
+ time.sleep(5)