Support different authentication methods

[nsoranzo]

This is a revised version of BitBucket PR #555.

Initial modules:

• ActiveDirectory (LDAP)
• LocalDB (fall back to Galaxy user database)
• AlwaysReject (blacklist)

Sysadmin documentation at: https://docs.google.com/document/d/1CJp_m3vW7QKtAyBTMbE1MLgV6FAMuG3VO4HR-wHPkGk

Problems:

• still needs a yapsy egg (@jmchilton volunteered to port the code to the Galaxy plugin system)

Tested and approved by original author @andrewjrobinson .

[natefoo]

A bit more previous discussion on this PR can be found at galaxyproject/galaxy-beta1#4

[jmchilton]

Here is how I would rip out yapsy -

• Make AuthProvider and abstract interface instead (methods seem right though). https://github.com/galaxyproject/galaxy/blob/d1cd4ab4d28c72f365852b75e2f2026c6b76ebbd/lib/galaxy/workflow/schedulers/__init__.py
• Delete all -yapsy files and just give auth implementation classes a short identifier as a class attribute (e.g. plugin_type).
• End implementation files with __all__ = [ ImplementationClassName ]. This is kind of messy, not the way __all__ should be used - feel free to fix.
  

  galaxy/lib/galaxy/workflow/schedulers/core.py

  Line 46 in d1cd4ab

  __all__ = [ CoreWorkflowSchedulingPlugin ]

• Refactor galaxy/auth/__init__.py to basically produce some authentication manager object or something that could be stuck onto Galaxy app. (May be optional - the module-centric stuff instead of object-centric stuff is interesting and we could argue about - but Galaxy mostly configures stuff into objects attached to app for better or worse).
• Add helper to load plugins to the auth manager

from galaxy.util import plugin_config

   def __plugins_dict( self ):
         return plugin_config.plugins_dict( galaxy.auth.providers, 'plugin_type' )

(E.g. https://github.com/galaxyproject/galaxy/blob/d1cd4ab4d28c72f365852b75e2f2026c6b76ebbd/lib/galaxy/workflow/scheduling_manager.py
or
https://github.com/galaxyproject/galaxy/blob/d1cd4ab4d28c72f365852b75e2f2026c6b76ebbd/lib/galaxy/tools/deps/__init__.py)

• Eliminate Yapsy plugin manager - but above dict should be pretty equivalent to getPluginByName.

[nsoranzo]

@jmchilton This WIP commit nsoranzo@b55edfe should address your first 3 points.

[dannon]

This is an automated message. Thanks for your contribution, a Trello card to track this issue has been created. Apply this patch for testing.

[jmchilton]

Picked up where @nsoranzo left off and merged directly - let me know if I broke anything. I made a lot of cosmetic changes to the code to make it mesh with Galaxy standards but the end-user usage should remain largely unchanged - no difference for deployers and plugin developers need to stick a plugin_type class attribute on their plugins instead of writing out a yapsy configuration file.

Many thanks to @nsoranzo and @andrewjrobinson and the people who reviewed the pull request in its various forms!

[martenson]

Thank you @jmchilton for driving this and @nsoranzo for the contributions. 👍 👍

[andrewjrobinson]

Thanks @nsoranzo and @jmchilton for your help here and others for your reviews.

I have tested the changes against the tests I used during development and found one bug with the auto-registration. I have fixed this issue and retested. The fix is currently sitting in my fork of this repo (https://github.com/andrewjrobinson/galaxy dev branch). Should I submit another pull request or do something else to get it merged?

[nsoranzo]

Thanks @jmchilton for finishing and polishing it! I posted a comment on commit 9fd6685 for you.

@andrewjrobinson I think a PR would be ideal!

[dannon]

@andrewjrobinson Yep, sending another PR is the best way to incorporate a bugfix.

[jmchilton]

Some possible follow up tasks here - https://trello.com/c/sxz9SM2R if anyone is bored.