New module type that pauses a workflow and gives time for the runner to review it before proceeding with execution.
- Introduce concept of beta workflow modules - I guess we should just keep the pause module as beta until their is a UI to support it.
- 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.
- Test Cases (for this changeset and a bunch of stuff that is now testable with the pause module in place from the scheduling framework commit).
Models:
Workflow invocations have been augmented with significantly more state - inputs, parameters, runtime step state, are all being tracked now. Workflow invocations have a state that can be changed over time, the UUIDs generated for workflow invocations in Pull Request #465 have to be persisted so they can be reused when scheduling new jobs for theworkflow invocation. Workflow invocation steps now have an action parameter for persisting state provided by users during the execution of the workflow (see forthcoming PauseModule for further details).
Some initial elements of these model changes were based on model changes in 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.
Scheduling Plugins:
Used the pattern setup with dependency resolvers and job metrics to build a dynamic plugin infrastructure for defining workflow schedulers. I hesistate calling anything with only one implementation a plugin infrastructure, but I am confident enough that the combination of persisted workflow request combined with scheduler tag could be used to build a galaxy-farm plugin that would wait for another Galaxy instance to become available and it would pull the workflow down and
This work piggy backs on Galaxy job handlers to have workflow scheduled in the background (i.e. during submission each workflow being scheduled in the background is assigned a unique job handler and only that job handler thread will process the workflow). It should be pretty easy to allow the definition of a new kind of handler - that is a workflow handler instead of a job handler if that is of interest.
I will probably move a bunch of stuff that is happening in workflow/scheduling_manager.py more into the scheduler itself so that it can be more configurable and closer to a true plugin.
API:
There are a number of new API points here for flushing out dealing with workflow invocations (called usages in existing parlance).
- POST /api/workflows/{encoded_workflow_id}/usage
Schedule a worklfow to be run in the background and return just the workflow invocation information.
RESTfully speaking this should be plural but the matching GET endpoint is likewise usage and not usages - so I am favoring consistency over RESTful correctness here. Also, likewise creating a 'usage' feel like odd - I would like to make all of the usage endpoints aliases to a more RESTfully correct invocations endpoints.
The existing workflow run API endpoints still work and still work the way they use usually - but the output now includes all of the workflow invocation to_dict stuff as well as the list of outputs it initially used. Once everything is scheduled this way - that list of outputs is going to have to disappear but hopefully people can start using the invocation stuff now to help the transition.
- DELETE /api/workflows/{workflow_id}/usage/{usage_id}
Cancel a scheduled workflow invocation.
- GET /api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id}
Get information about a workflow invocation step.
- PUT /api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id}
Update a workflow invocation step - for ones with modifiable state. Extension point added to workflow modules to support this but it is unused by all existing worklfow modules. A subsequent PauseModule will use this to either continue or cancel a workflow invocation at a particular step.
Modules:
Workflow modules can now define new methods for dealing with recovering state and interacting with user requests.
Testing:
One can issue a workflow request by running the following test.
./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_request
Including same test with workflow parameter substition - gotta admit I thought that workflow test was going to fail - so this week is looking pretty good :).
There may now be multiple WorkflowInvocationSteps for each WorkflowStep for steps that are mapped over collections - so to_dict creating a dictionary of this information indexed on order step is problematic because only one WorkflowInvocationStep will be represented per step. Instead now just returning a big list of all of the invocations - which contains all of the same information. This is a backward incompatible API change for the workflow invocation API.
Also update the input mapping stuff with logic for dealing with data collection inputs.
Sharing a workflow with a user was previously sufficient to grant access to all invocations of that workflow. This isn't a huge problem since the information potentially leaking out was limitted to invocation counts, various encoded ids, and update times. Still I think no information about invocations should be avaialble as a result of sharing a workflow - and upcoming changes to Galaxy will result in much more information being made available via the workflow invocation API.
Convert workflow API to use new-style API decorator throughout.
Improved workflow exception handling - now more explicit status code setting and returning of raw error strings in the API. Most obvious exceptional paths out of the API are now coming through MessageExceptions of things even more specific. Add API tests for many of these exceptional conditions.
Use more helper methods to reduce method length, duplication.
Previous route was "POST /api/workflows/upload", this still works but should be condisdered deprecated in favor
of POSTing to /api/workflows with 'workflow' in the payload.
The old 'ds_map' parameter remains in place for backward compatibility and with the same behavior. A new parameter 'inputs' can now be specified instead however, and its keys corresponding to the steps 'order_index' instead of the raw unencoded database ids 'ds_map' uses. This variant has the nice property that this map can be constructed without prior knowledge of how Galaxy will assign ids during import - hence it is easier to use and more portable.
Additionally, 'inputs' is more flexiable and can revert to the old behavior by specifying a new parameter 'inputs_by' as 'step_id'. 'inputs_by' can also be 'name' - this is even more human friendly because it will assign the ids based on data input names (this is what I intend to use mostly, but I have not made it the default because not all workflows will have data inputs with distinct names).
Finally, the new name 'inputs' will be more appropriate once data collection inputs can be explicitly mapped via the API.
Probably should do something like this server side so workflow API can be used more deterministically (wouldn't need to import a workflow and then hit the API to know how to use it).
With expanded test case that checks such a connection. This takes care of of subsequent connections by iteratively updating hid_to_output_pair correctly (... I think, test works with at least two).
Replace ad-hoc tools API test method for skipping tests with a more general purpose decorator. Use new decorator to specify required tools for workflow tests.
Add functional test to verify the correctness of this tracking.
TODO: refactor __skip_unless_tool from tools test so this new workflow test can be skipped if not run with -with_framework_test_tools.
API now properly expects hids. That was unfortunate - need to figure out why the existing functional test did not break because of this and improve it.
John Chilton