Commit Graph

41 Commits

Author SHA1 Message Date
Kelly McDonald 1844c93919 STG-26 - basic test case for a looping task
Criteria :
task.multi_instance_type == 'looping'

to terminate, use the standard endpoint for submitting form data with a query variable of terminate_loop=true

Will likely need two buttons:
"Submit and quit"
"Submit and add another"
or something similar
2020-06-17 11:35:06 -04:00
Aaron Louie e3126620b3 Eschews obfuscation 2020-06-12 14:09:08 -04:00
Aaron Louie 561e254315 Prevents non-admin users from editing each others' tasks. Fixes bug where test user uid was not being set from token. Moves complete form and get workflow API test utility methods into BaseTest. 2020-06-12 13:46:10 -04:00
Aaron Louie f51e5e4e6b Adds tests for approval counts and all approvals endpoints 2020-06-11 16:39:00 -04:00
Aaron Louie 768f14b3ac Cleans up console logging 2020-06-11 13:42:44 -04:00
Dan Funk 4e006e2653 Clear out the g.user between tests. 2020-06-11 11:49:07 -04:00
Aaron Louie cccff9b856 Fixes broken unit tests. But still broken. 2020-06-11 11:29:58 -04:00
Aaron Louie 87e2379871 Merge branch 'rrt/dev' into feature/swagger_admin_authentication 2020-06-08 10:30:16 -04:00
Carlos Lopez 4727d87adb Hooking up emails into process - start 2020-06-04 20:37:28 -06:00
Aaron Louie c4a84ac509 Work in progress: Trying to get Swagger to use verify_token_admin to protect admin endpoints. Not working for some reason, though. 2020-05-31 18:01:08 -04:00
Aaron Louie be9b613bbb Refactors user authentication endpoints so we can use the Swagger UI in production mode 2020-05-31 16:49:39 -04:00
Dan Funk 98fb305868 Run the validation process twice, each time it is requested, first populating everything, and then a second time
using on the required form fields.
2020-05-30 18:43:20 -04:00
Dan Funk 77f72e408f Lookup Service now raises exact matches to the top. Very hackish, but it works. 2020-05-27 14:36:10 -04:00
Dan Funk e9645fa3fd Renamed redirect_url to just redirect. 2020-05-26 15:47:41 -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 d39ef658a2 Made some modifications to the Approval so that it knows exactly what versions of every file are being sent for approval
Added the following columns:
  * date_created - so we know when the file was created
  * renamed workflow_version to just "version", because everything has a version,  this is the version of the request.
  * workflow_hash - this is just a quick way to see what files and versions are associated with the request, it could be factored out.
  * study - a quick relationship link to the study, so that this model is easier to use.
  * workflow - ditto
  * approval_files - these is a list from a new link table that links an approval to specific files and versions.

The RequestApproval is logically sound, but still needs some additional pieces in place to be callable from a BPMN workflow diagram.

Altered the file service to pick up on changes to files vs adding new files, so that versions are picked up correctly as
users modify their submission - adding new files or replacing existing ones.  Deleting files worries me, and I will need to revisit this.

The damn base test keeps giving me a headache, so I made changes there to see if clearing and dropping the database each time won't allow the tests to pass more consistently.

Lots more tests around the file service to make sure it is versioning user uploaded files correctly.

The "Test Request Approval Script" tries to find to assure the correct behavior as this is likely to be called many times repeatedly and with little knowledge of the internal system.  So it should just "do the right thing".
2020-05-23 15:08:17 -04:00
Dan Funk 148e86bb42 Building out the boilerplate code to make pushing forward on this a little friendlier.
There is an approval api file, and approval model file and an approval test file.
2020-05-22 18:25:00 -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 951710d762 ldap lookup.
Refactored calls into a new lookup_service to keep things tidy.

New keys for all enum/auto-complete fields:
    PROP_OPTIONS_FILE = "spreadsheet.name"
    PROP_OPTIONS_VALUE_COLUMN = "spreadsheet.value.column"
    PROP_OPTIONS_LABEL_COL = "spreadsheet.label.column"
    PROP_LDAP_LOOKUP = "ldap.lookup"
    FIELD_TYPE_AUTO_COMPLETE = "autocomplete"
2020-05-19 16:11:43 -04:00
Dan Funk da7cae51b8 Adding a new reference file that provides greater details about the investigators related to a study.
Improving the study_info script documentation to provide detailed examples of values returned based on arguments.
Making the tests a little more targetted and less subject to breaking through better mocks.
Allow all tests to pass even when ther protocol builder mock isn't running locally.
Removing the duplication of reference files in tests and static, as this seems silly to me at the moment.
2020-05-07 13:57:24 -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 17796193de fixing a bug that was causing failing tests.
Adding id and spec_version to the workflow metadata.
Refactoring the processing of the master_spec so that it doesn't polute the workflow database.
Adding tests to assure that the status and counts are updated on the workflow model as users make progress.
2020-03-30 14:01:57 -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 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
Dan Funk 6e3b6c2635 Assure that files uploaded through web forms and files generated from templates can be cross-referenced to known document requirements from the protocol builder. Configurators can control this by managing an XLS Spreadsheet called "irb_documents.xslx".
Required Documents is becoming complicated, so making this it's own script task, removing it from study_info.py
The file_service is now very aware of this irb_documents file, so it will always need to exist.  We seed this file
during setup, but it can be overwritten by the configurator.
2020-03-19 17:14:20 -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
Dan Funk 697d930eab Modify the workflow processor to accept a workflow model - so it can take on more of the responsibilities of updating this model and managing versions.
Changing the version information so that it includes the numbers of the files used to generate the serialized workflow.
2020-03-05 13:25:28 -05:00
Dan Funk c5cee4761e Improve version handling of files. Consolidate more of this logic in FileService. Place the version on the actual data model, not the file model, so the file model remains the same, and we just version the data associated with it. 2020-03-04 13:40:25 -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
Dan Funk 2cc6010c8d Protocol builder connections 2020-02-20 13:30:04 -05:00
Dan Funk a642593e3d Adding support to handle Single Sign On (Shibboleth) authentication using Flask SSO and an attribute map that has worked in the past with UVA's implementation. Aside from the new user endpoint, nothing requires authentication, but soon everything will expect it. I'm setting up a backdoor we can use for development and staging that will cause a round-robin affair that should make this relatively painless. Dropped "RestException" as we had two ways or raising errors, and that was silly. 2020-02-18 16:38:56 -05:00
Dan Funk 709bae76b2 Removing a rogue comma that was causing havoc. Also, don't fail if a mock already exists in the test database. 2020-02-11 11:11:21 -05:00
Dan Funk ec4df2b3fa Cleaning up the tests and making it easier to test workflows without adding them to the example data structure. 2020-02-04 16:49:28 -05:00
Aaron Louie a3b6e4fc7f Fixes import paths 2020-01-24 11:52:52 -05:00
Aaron Louie 0a44ef04d7 Slight refactoring - makes BaseTest inherit from TestCase. Checks that data loader works properly 2020-01-24 09:35:14 -05:00
Aaron Louie fe15799ee1 Adds type hinting to db and session to fix Pycharm autocomplete. Replaces db.session with session. 2020-01-14 11:45:12 -05:00
Dan Funk fb465531ca Add the ability to delete a workflow. 2019-12-30 13:15:39 -05:00
Dan Funk b54bd49cf4 Allow for clearing out the database. 2019-12-30 13:03:57 -05:00
Dan Funk 0b71833946 Adding file management. Files are stored in the database along with basic meta data. 2019-12-27 13:50:03 -05:00
Dan Funk 9861f6baf3 Lots and lots of random stuff as I organize code and get things to make sense. 2019-12-18 14:02:17 -05:00
Dan Funk 9280aab0b6 name tests so they get picked up and run. 2019-11-21 12:01:51 -05:00