Preserve attributes of published files (take 2)

[bentsherman]

Continuation of #4522

Allow COPY_ATTRIBUTES on S3 copy as a no-op, so that this attribute can be set generically when publishing files.

For some reason this issue did not surface in the previous PR but only once the PR was merged

[netlify]

✅ Deploy Preview for nextflow-docs-staging canceled.

Name	Link
🔨 Latest commit	5ffbcdb
🔍 Latest deploy log	https://app.netlify.com/sites/nextflow-docs-staging/deploys/6793614dd2267900081eacb7

[pditommaso]

Tagging @jordeu for visibility? Does Fusion honour the copy of file timestamps?

[pditommaso]

If the copy attributes is only honoured by local and shared file system, we should consider making this an opt-in feature, because it's not a portable behaviour.

In alternative, instead of copying the file stamps, it could be tried to copy the files ordering them by timestamp. Even if the timestamp would be different it may guarantee they are consistent with expectation of the tool reported in the issue (tho is should be verified the the timestamp is set when stating the upload or when it completes).

[bentsherman]

I don't think re-ordering the publish operations will matter because they are published concurrently

[pditommaso]

Yeah, ordering was more a random thought

[pditommaso]

To recap here, since this rule cannot be generalised StandardCopyOption.COPY_ATTRIBUTES should be added only when enable a specific config (output?) option

[pditommaso]

@bentsherman Am I wrong or there has been a regression after last changes?

[bentsherman]

The last two commits with CI failures report errors with the bitbucket integration:

BitbucketRepositoryProviderTest > testReadContent FAILED
    org.spockframework.runtime.SpockTimeoutError at BitbucketRepositoryProviderTest.groovy:58

BitbucketRepositoryProviderTest > should return content URL FAILED
    org.spockframework.runtime.SpockTimeoutError at BitbucketRepositoryProviderTest.groovy:108

BitbucketRepositoryProviderTest > should read content on main and on separate branch FAILED
    org.spockframework.runtime.SpockTimeoutError at BitbucketRepositoryProviderTest.groovy:137

I don't see how it could be related to this PR, seems like something wrong with bitbucket creds or some networking issue

[bentsherman]

Tests are passing now

[pditommaso]

Nice