Rewrite CLI

[moonso]

Summary

This pull request reworks the CLI completely. The idea is to make it more clear how bundles, versions and files are linked together. Each subcommand will follow the same structure so there will for example housekeeper get

housekeeper get --help
Usage: housekeeper get [OPTIONS] COMMAND [ARGS]...

  Get info from database

Options:
  --help  Show this message and exit.

Commands:
  bundles  Get bundle from database
  files    Get files from database
  tags     Get the tags from database
  version  Get versions from database

and add:

housekeeper add --help
Usage: housekeeper add [OPTIONS] COMMAND [ARGS]...

  Add things to the store.

Options:
  --help  Show this message and exit.

Commands:
  bundle   Add a new bundle.
  file     Add a file to the latest version of a bundle.
  tag      Add tags to housekeeper.
  version  Add a new version to a bundle.

Testing

How to prepare for test

• ssh to hasta
• install on stage:
  bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-housekeeper-stage.sh log-output
• Check that there is a mip cases to store (vitalmouse)

How to test

• Store a case in housekeeper (this is to check that the interaction between CG and hk works as expected)

Expected test outcome

• check that the test succeded
• Take a screenshot and attach or copy/paste the output.

Review

• code approved by @Mropat
• tests executed by @moonso
• "Merge and deploy" approved by @moonso
  Thanks for filling in who performed the code review and the test!

This version is a:

• MAJOR - when you make incompatible API changes

[patrikgrenfeldt]

Suggestion, please change "cannot delete X, X contains Y" to "Cannot delete X, please remove all Ys first" to let the user know what actions are needed

[moonso]

Merged and deployed