Mizzou-CBMI / COSMOS2

Python Scientific Pipeline Management System
GNU General Public License v3.0
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Hackathon patches, round 2 #40

Closed mdpearson closed 8 years ago

mdpearson commented 8 years ago

Various changes to help with the output_dir deprecation and make Cosmos more resilient to drmaa errors.

4598a89 adds os.getcwd() to exception text if a log file can't be created (to help pin down remaining output_dir nits in client code. c86deab restores the ability to pass a None argument to a Task's params. d98127c silences secondary exceptions when tearing down running Tasks during a Cosmos crash. 1306369, 7549ef7 defend against degenerate drmaa responses when a Task is submitted to SGE with invalid options. 52c8170 should prevent completed jobs from being flagged as failed if the dreaded commlib monster rears its ugly head again.