Fix references to config.ucsc_display_sites that I missed.
ToolForm: Implements error handling, applies fixes to styles and structure, UI: Fixes code style for frames
History panels: allow foldout display of collections in display_by_slug, pages, and /view
Fix to 618b02d13329: remove console, add documentation
Initial work on a tags manager.
Rest of UsesTagsMixin needs to be copied over similarly and deprecated, following that I guess all references need to be updated and then the mixin eliminated all together I guess (exhausting :)).
Refactor generic controller mixin code for security out for reuse in managers.
Refactor generic controller mixin code for loading objects into managers.
Introduce LDDA manager stub.
Use it to eliminate awful controller dependencies (and associated circular dependency errors when controllers are not loaded before everything else) in galaxy.dataset_collections.
Make dataset collections service a manager.
It would hve been arcitected this way from the beginning but my initial work on it predated Carl's managers work and it had those pesky controller dependencies.
Work on workflow module testing.
Allow uuid values in to_dict.
More workflow module documentation improvements.
I nearly understand workflow modules...
Rework workflow modules to reduce duplication and add more consistency..
Adding a recover_state method that to both implementations (though meant to be part of the module interface) that recovers the configuration state (module.state) from a dictionary. This turns out to reduce a lot of duplication between data and data collection input modules.
Better OOP design for separation between input and input collection modules.
(Lot easier now that I understand what all of the module methods are doing and have an example of a 4th module downstream.) Now with even more unit tests.
Implement workflow requests (API only) and a scheduling 'plugin' framework to evaluate them.

The model changes and WorkQueue class are based on modifications to Kyle Ellrott's Galaxy farm work (https://bitbucket.org/kellrott/galaxy-farm/branch/workflow_migrate). I made heavy modifications to the model to enforce referential integrity on parameter to workflow step mappings and made some cosmetic changes various other details. I further filled out WorkQueue (adding ability to 'complete' requests, implementing tests, etc...). The work context (allowing tool's to be executed outside the context of a web thread), workflow module and API modifications, and the workflow scheduling framework are my own contributions.

I like some of this - I remain skeptical about much of it though. I think maintaining queues of generic requests and distributing them across multiple processes, machines, etc... is both a hard problem and one for which many adequete solutions already exist - some of which we are already using (if only optionally) in other parts of Galaxy - so I don't understand why we need/want to so explicitly replicate this in Galaxy and not just defer to an external message queue.

In internal discussions it has been argued that message queues are appropriate for short requests but long term requests are better tracked in the database. I know that intuitively these operations may feel different - but I am unconvienced they are from a technical standpoint. Delaying an action that would have happened in milliseconds to hours later is many order of magnitude larger than the additional delay when going from the hours to days or weeks.

My own preference would be that both this work and Galaxy farm further investigate using message queues before making such substantial changes to the data model. It certainly may prove that this approach is needed - but I personally would like to understand why maintain the work queue in a message queue would not work first.

However, if the Galaxy project is going to add a WorkRequest object to the database and something that looks like the WorkQueue class in the new galaxy.work module and store and distribute workflows that way for the farm project, then I believe that typical workflow requesting and scheduling should make use of it also instead of developing a competing implementation. (Because my interaction pattern with Galaxy has always been if you cannot beat them join them.)

Testing

One can issue a workflow request to the WorkQueue and scheduled via the scheduling framework by running the following test.

./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_request

Final Note: The workflow scheduling stuff is a bit rough right now - it is just enough to prove to myself that this approach can be taken and the farm-stuff and workflow scheduling stuff can utilize the same models. I wanted to try to spark a broader conversation on this (re-encounrage use of message queues) before putting more effort into this approach.
Implement pause module for workflows.

Extracts base class ouptut of InputModule for modules that are "simple" - i.e. their configuration state is represented as a dictionary and configuration form is rendered via the generic template.