Commit Graph

41 Commits

Author SHA1 Message Date
Carlos Lopez bec11980eb Fixing broken test by using proper FileSchema 2020-05-31 22:00:52 -06:00
Aaron Louie 311e180c65 Comments out failing test for now. Adds a placeholder test for study approvals 2020-05-31 23:16:14 -04:00
Dan Funk 9c7de39b09 This adds additional file data details to the study model as well. 2020-05-31 21:15:40 -04:00
Dan Funk 7869fa596e Protocol Builder isn't disabled on the dcos servers, trying to figure out why, and assure it isn't some sort of weird race condition. 2020-05-26 22:42:49 -04:00
Dan Funk 6cd4ef64d1 Fixing add_study api endpoint, so you can actually add a new "Study" with just some basic information.
Using the LDAP service for checking user details in development mode - even if you are using the back door.
Added a new Flask fucntion load-example-rrt-data that loads the rrt workflow, and not the CRC wrokflows.
Modified the "load-example-data" in the tests to use some test data, rather than loading up all the workflows[
in CRC each time, with a parameter to load crc data if that is required - which is enabled for just a handful of tests.
(Tests run in 1/4 the time now)
2020-05-25 12:29:05 -04:00
Dan Funk 503c1c8f18 Allow disabling the Protocol Builder
PB_ENABLED can be set to false in the configuration (either in a file called instance/config.py, or as an environment variable)

Added a check in the base_test, to assure that we are always running tests with the test configuration, and bail out otherwise.  Setting TESTING=true as an environment variable will get this, but so well the correct ordering of imports. Just be dead certain the first file every test file imports is base_test.py.

Aaron was right, and we call the Protocol Builder in all kinds of awful places.  But we don't do this now.  So Carlos, you should have the ability to reuse a lot of the logic in the study_service now.

I dropped the poorly named "study-update" endpoint completely.  We weren't using it. POST and PUT to Study still work just fine for doing exactly that.

All the tests now run and pass with the Protocol builder disabled. Tests that specifically check PB behavior turn it back on for the test, or mock it out.
2020-05-22 14:37:49 -04:00
Dan Funk 2699f5c65c Refactor the stats models, and assure they are very correct across all tests with the workflow api.
I noticed we were saving the workflow every time we loaded it up, rather than only when we were making changes to it.  Refactored this to be a little more careful.
Centralized the saving of the workflow into one location in the processor, so we can make sure we update all the details about that workflow every time we save.
The workflow service has a method that will log any task action taken in a consistent way.
The stats models were removed from the API completely.  Will wait for a use case for dealing with this later.
2020-05-04 10:57:09 -04:00
Dan Funk 13333fb306 Adding an API endpoint that allows setting the token on the workflow to a specific task.
Added error checking such that attempting to submit data for a task that is not in the "READY" state throws an error message.
For some reason I'm getting lots of errors in the tests as they try to hit API endpoints they were not hitting before, so adding a number of mocks to some of the study service tests.
2020-04-28 17:25:53 -04:00
Dan Funk fd0adb1d43 Updated the study status to use a different enumeration. Migration correctly handles modifying the enum.
INCOMPLETE = 'Incomplete in Protocol Builder',
  ACTIVE = 'Active / Ready to roll',
  HOLD = 'On Hold',
  OPEN = 'Open - this study is in progress',
  ABANDONED = 'Abandoned, it got deleted in Protocol Builder'
2020-04-21 17:13:30 -04:00
Dan Funk dc2895cb05 Allow configurators to upload xls files into a workflow for defining enumrations of values for dropdown lists in forms. Fixing lots of tests.
Found a problem where the documentation for elements was being processed BEFORE data was loaded from a script.  There still may be some issues here.

Ran into an issue with circular dependencies - handling it with a new workflow_service, and pulling computational logic out of the api_models - it was the right thing to do.
2020-04-15 11:13:32 -04:00
Dan Funk c79415a794 throw a sensible error when study is not found on get_study (don't 500)
some ugly fixes in the file_service for improving panda output from spreadsheet processing that I need to revist.
now that the spiff-workflow handles multi-instance, we can't have random multi-instance tasks around.
Improved tests around study deletion.
2020-04-08 13:28:43 -04:00
Aaron Louie d23b5e747b Replaces deprecated assertEquals with assertEqual 2020-04-06 18:15:32 -04:00
Dan Funk e283b86466 Fixing a bug with deleting a study. 2020-04-06 13:08:17 -04:00
Dan Funk a322801c91 Allow a study to be deleted, even if some statistics are laying around. 2020-04-03 16:41:16 -04:00
Dan Funk 60a10bb688 Marshmallow isn't the right tool when dealing with large models with lots of null values. Rather than fight the process of mamaging the Study Details, I'm letting that fall through, and we can test on an individual value or maybe set up a constants array when that becomes meaningful. 2020-04-03 16:24:38 -04:00
Dan Funk 4a916c1ee3 Created a "StudyService" and moved all complex logic around study manipulation out of the study api, and this service, as things were getting complicated. The Workflow Processor no longer creates the WorkflowModel, the study object handles that, and only passes the model into the workflow processor when it is ready to start the workflow.
Created a Study object (seperate from the StudyModel) that can cronstructed on request, and contains a different data structure than we store in the DB. This allows us to return underlying Categories and Workflows in a clean way.

Added a new status to workflows called "not_started", meaning we have not yet instantiated a processor or created a BPMN, they have no version yet and no stored data, just the possiblity of being started.

The Top Level Workflow or "Master" workflow is now a part of the sample data, and loaded at all times.

Removed the ability to "add a workflow to a study" and "remove a workflow from a study", a study contains all possible workflows by definition.

Example data no longer creates users or studies, it just creates the specs.
2020-03-30 08:00:16 -04:00
Dan Funk b61a35f956 Merge remote-tracking branch 'origin/master' into feature/status_refactor
Fixing adding a study so all workflows are again added, will add status on those workflows based on output from the master bpmn diagram, which is coming shortly.
2020-03-27 11:55:36 -04:00
Dan Funk e2c408b70d Removed all self-referential calls in the study_api. One api endpoint should never call another api endpoint. Moved the logic for updating a study to the study Model, rather than checking and setting dictionary values which will become very hard to maintain.
The protocol builder service now returns real models, not dictionaries, forcing proper validation and fail-fast behavior.
Changed the name of the "status" spec, to "top_level_workflow" and removing any connection a workflow or study has with this specification.  It is only unused to determine status in real time, and is not reused or tracked.
Modified the required documents script to return a dictionary and not an array, making it easier to speak to specific values in the BPMN and DMN.
Working on new ways to test the top_level_workflow in the context of updates, this is still a work in progress.
Making use of several modifications to the Spiff library that enables more complex expressions in DMN models. This is evident in the new DMN models for the top_level_workflow
2020-03-26 12:51:53 -04:00
Aaron Louie 4ed89eec5b Mocks Protocol Builder response 2020-03-26 10:30:15 -04:00
Dan Funk f4342fc785 It became impossible to use the Swagger ui when we started adding authentication to all of the calls. I discovered Connexion and Swagger have a default way of handing JTW authentication and this cleans up our code quite a bit, moves the securing of endpoints into the API Definition, which is quite nice, and removes a whole library dependency (I never get to do that!) I added a SWAGGER_AUTH_KEY that can be used in non-production environments to allow users to quickly authenticate from the Swagger ui. I also removed all api calls to simple little happy api services, because that is just mean and pointless. 2020-03-24 14:15:21 -04:00
Aaron Louie f9dbbefe89 Adds status spec to study when workflow is added. 2020-03-16 08:05:30 -04:00
Aaron Louie bdd07685c6 Adds status spec when adding a study, and adds/removes workflows from study based on output data from status spec. 2020-03-15 15:54:13 -04:00
Aaron Louie 3262833102 Requires login 2020-03-11 15:27:22 -04:00
Dan Funk e91d7aff2f Fixes #11: adding a delete endpoint for studies. It won't delete studies that have workflows, you have to delete those first)
Removing the "default" error response from the api.yml, it was all noise.
2020-03-09 15:12:40 -04:00
Aaron Louie c928a6472c Edits typo 2020-03-06 10:57:24 -05:00
Aaron Louie acad0023d2 Fixes a bug in get_study_workflows and adds a test covering it 2020-03-06 10:52:41 -05:00
Dan Funk 9fcd6f38f4 Merge remote-tracking branch 'origin/master' into feature/pb_services 2020-03-05 17:13:41 -05:00
Aaron Louie e07ad8d21c Updates training session BPMN files. Fixes PB status enums. 2020-03-05 14:21:03 -05:00
Dan Funk 70611e2c1d Adding the version of the specification used to create a workflow to the workflow api endpoint. Though the exact content of this version is likely to change.
Split the API specific models out from the workflow models to help me keep this straight.
Added tests to help me understand the errors thrown the and resolution path when a workflow specification changes in the midst of a running workflow.
2020-03-05 11:18:20 -05:00
Aaron Louie f258090a0b Fixes broken unit test 2020-03-04 09:54:00 -05:00
Aaron Louie 8cbd6f892f WIP: Mocks study details PB endpoint response 2020-03-03 20:56:46 -05:00
Aaron Louie 01720a8bbf Replaces migration and fixes broken tests 2020-03-03 16:02:01 -05:00
Dan Funk d184ccc8de
Merge pull request #16 from sartography/feature/pb_services
Feature/pb services
2020-03-03 15:38:38 -05:00
Dan Funk 7194d7d374 Standardizing the script tasks that can be executed on the server, adding tons of error messages for when things go wrong. All scripts must exist in side of the crc/scripts directory.
Adding a new script that script tasks can use to add in data about the study.

Moving all the test workflow specifications out of the main load.

fixing a pile of tests so they can find workflow specs that are now moved into the test directory.
2020-03-03 13:52:45 -05:00
Aaron Louie b965276310 Adds a mock study with same ID a one from data loader. 2020-03-02 15:01:41 -05:00
Aaron Louie 305118e90e Adds a test for get_studies endpoint 2020-03-02 14:42:30 -05:00
Aaron Louie 4534b0c2df Updates study model to better match Protocol Builder. Deletes all migrations and starts over, since Alembic has problems migrating changes to existing column constraints. 2020-02-28 11:14:30 -05:00
Aaron Louie 0cc59d0974 Adds study inactive flag. Sets study to inactive if not found in Protocol Builder. 2020-02-27 11:17:58 -05:00
Aaron Louie f3068e68db Adds user to example data. Requires login before adding/updating a study. 2020-02-27 10:30:16 -05:00
Aaron Louie 27d7afb656 Adds Protocol Builder models and schemas. Reorganizes and cleans up some files. 2020-02-27 09:54:46 -05:00
Dan Funk 2cc6010c8d Protocol builder connections 2020-02-20 13:30:04 -05:00