Start Galaxy Library timeout when running

[apetkau]

Description of changes

Currently, when transferring files to a Galaxy Data Library, the timeout starts when the task is added to a thread pool queue. This means the timeout before file transfer fails in IRIDA includes the time spent in the queue.

This PR changes the Galaxy Data Library transfer code to only start the timeout of data transfers when the status checking code has begun running. This makes use of a CountDownLatch.

Testing

I'm not sure if you wanted to go through testing this, but what I did is upload 59 samples and set the Galaxy upload timeout limit to 15 seconds and run two scenarios:

• Running all 59 genomes with RefSeq Masher under the old IRIDA - got a bunch of jobs erroring due to upload timeouts
• Running all 59 genomes with RefSeq Masher with IRIDA including these changes - everything works. No errors.

Related issue

Fixes #1338

Checklist

Things for the developer to confirm they've done before the PR should be accepted:

• CHANGELOG.md (and UPGRADING.md if necessary) updated with information for new change.
• Tests added (or description of how to test) for any new features.
• [ ] User documentation updated for UI or technical changes.

[ericenns]

👍 Thanks for adding this