ENH: Allow cromwell url to be saved in secrets file, harmonize naming…

broadinstitute / cromwell-tools

A collection of Python clients and accessory scripts for interacting with the Cromwell

https://cromwell-tools.readthedocs.io

BSD 3-Clause "New" or "Revised" License

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Closed ambrosejcarr closed 6 years ago

ambrosejcarr commented 6 years ago

Cromwell URL is inextricably linked to password and username, so it makes sense to store all of these data in a secrets file.

Allow url in secrets
harmonize naming of cromwell_url, cromwell_user, cromwell_password and secrets_file across cromwell_tools functions
improve testing to test both input streams (url, user, password vs secrets_file)

ambrosejcarr commented 6 years ago

I ended up having a lot of trouble testing this because:

different auths (user/password, caas, secrets file) all produce different entities
command line tools contains significant code that is not mirrored in the library

I ended up refactoring to fix these problems. Closing this.