broadinstitute / canine / 48

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master: 60%

Pull #52

travis-pro

Handle jobs that failed to delocalize in orchestrator

Currently, `orchestrator.make_output_DF()` assumes that the keys of
`self.job_spec` are identical to those of the `outputs` parameter. The `outputs`
parameter is almost always generated by running localizer.delocalize(), so
assuming that `self.job_spec.keys() == outputs.keys()` implicitly assumes that
every single job properly delocalized.

This is not necessarily a safe assumption; for example, a long-running task
that runs out of preemption attempts will never get a chance to run
delocalization.py

This commit fills in values for any missing keys in `outputs` to {}

Future commits in this branch will attempt to run delocalization.py on the
controller, so that we can at least recover stdout/stderr

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