- Separate configs out into example files that we can link to and point at from documentaiton more easily.
- Reduce a bunch of duplication around inject environment variables to streamline the integration-style tests.
I think the result is a lot more clean.
- Fix s3 which broke during the migration because we stopped adding a / I thought was silly.
- Use the test case I wrote that mimics the integration test failure to also fix the boto3 and azure_blob object stores for these failures.
Also make note of a lingering issue that is pretty important
Allow attaching a device ID on object stores that indicates they produce equivalent paths. Implement an API endpoint that allows swapping datsets between equivalent object stores if they have not been copied by new users.
We were updated the configured cache size only if the cache was configured - that is less than ideal. Fixed that and added some abstractions to make things a little cleaner in my eyes.
Per @bgruening's request - s3 -> aws_s3 and swift -> generic_s3.
I think we only construct object stores with the one method - so this should be backward compatible.
There are subtle differences between object stores, user object store instance models, and object store templates in the downstream "bring-your-own-object-store" branch so breaking this stuff out like this should allow for cleaner diffs and reuse.
with manual fixes to 3 files to make them compatible with black 22.12.0 .
We need to keep black pinned at `<23` until we vendorise `packaging`, since
the new version of black depends on `packaging >=22.0` which is the version
where `LegacyVersion` (which we use for tool lineages) was removed.
Apply the following fixes for s3.py to cloud.py
Be more explcit about starting cache monitor thread 494c15cb9d
Disable cleanup thread in set_metadata.py 6a56f3a5de
Fix S3 object store shutdown 7a63fd1db2
Upgrade syntax using `pyupgrade --py36-plus` .
Manually drop several `six` imports.
Also:
- Remove broken pr_cache in scripts/bootstrap_history.py
- Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
John Chilton