finish_task_attempt fails with SQL error

[nhammond]

Version 0.7.0

Seen in logs:

[2018-08-30 07:19:37,928: ERROR/MainProcess] Task api.async.finish_task_attempt[b50eb5ca-2832-402b-908a-119a048421c9] raised unexpected: ProgrammingError(1064, 'You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near \'id="364" THEN 77 END WHERE id IN (384, 364)\' at line 1')

Attempt and task are in "finished" state, but run remains in "running" state. In SCG workflow, "align_bwamem" is ok, but "sort_by_queryname" and "fastqc_raw_read_metrics" had this error.

[nhammond]

Error comes from wrongly using a comma in CASE statements, e.g.:

UPDATE api_datanode SET data_object_id= CASE WHEN id="342" THEN 69, WHEN id="366" THEN 69 END WHERE id IN (366, 342)

should be

UPDATE api_datanode SET data_object_id= CASE WHEN id="342" THEN 69 WHEN id="366" THEN 69 END WHERE id IN (366, 342)

Confirmed with interactive testing.

[nhammond]

Fixed in #557