fix: improve handling of URLs in file functions.

[peterhuene]

• allow glob to operate off of file:// URLs.
• allow size to operate off of file:// URLs.
• allow basename to operate off of any URLs.

This PR also removes custom diagnostics from the stdlib functions so that all of the standard library functions now use function_called_failed diagnostics for errors. It gives a more consistent diagnostic for function calls.

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[a-frantz]

Two questions about using fewer hardcoded strings in the error messages. I'm not sure how feasible either request is, so maybe they can be ignored. Just trying to think of easing future maintenance.

Otherwise, LGTM

[peterhuene]

CI is failing due to docker hub rate limiting.

We need to fix the pull image functionality in Crankshaft to gate to a single request if there are a number of concurrent tasks all requesting to pull the same image; I think that may be contributing to the problem.

[peterhuene]

As a workaround, I think we could do what bollard does in CI and use a local docker hub container that we've pushed any images we need for the tests, which will limit the pull requests to Docker Hub to only the number of images needed to run the tests.

[a-frantz]

all that sounds good, but a perhaps simpler workaround is to pull from quay.io instead of docker hub to avoid rate limits entirely 🤷

[peterhuene]

CI is failing on windows for the join_paths tests as absolute file paths on Windows are being successfully parsed as URLs (sigh).

[peterhuene]

all that sounds good, but a perhaps simpler workaround is to pull from quay.io instead of docker hub to avoid rate limits entirely 🤷

As far as I know, there's no way to tell the local docker daemon to use an alternative default namespace for the image names, so we'd have to run the workflow/task evaluation tests with an engine config that overrides the default container and also update any explicit container names in the test WDLs (some of which are 1:1 with the example WDL in the spec).

Not terribly difficult to do, though. Alternatively, I think if we pulled ubuntu:latest at the start of CI, that'd also do the trick (the daemon would already see it locally and not fetch it from hub).