Commit Graph

94 Commits

Author SHA1 Message Date
Dan Funk 55a1850e7c adding a navigation component to the Workflow Model.
running all extension/properties through the Jinja template processor so you can have custom display names using data, very helpful for building multi-instance displays.
Properties was returned as an array of key/value pairs, which is just mean.  Switched this to a dictionary.
2020-05-14 13:43:23 -04:00
Dan Funk b7c11fd893 Merge branch 'master' into feature/investigators_reference_file 2020-05-11 17:36:37 -04:00
Dan Funk 02f8764056 Updated to use the latest script engine / evaluation engine that creates a single location where all values used in BPMN/DMN are processed. Right now this is a python based interpreter, but we will eventually base this on FEEL expressions.
The validation process needs to take the api model into account so we catch errors with bad file names.
2020-05-11 17:04:05 -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 1571986c0e I had to give up and live with the idea that we can only render documentation on the current task, not on the previous or next tasks. I think this is ok. If you want to view a task, you need to make it the active task to assure all the parts and pieces are in place. 2020-05-06 13:01:38 -04:00
Dan Funk 9629b36e92 Setting JSON_SORT_KEYS to false, assuring that Flask does not resort all data returned to the front end.
Updating Spiff Workflow which has some critical behavioral changes around MultiInstance.
2020-05-06 10:59:49 -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 bec59a71d7 Deleteing stuff is a damn mess, but this is a little cleaner. 2020-04-29 16:07:39 -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 3e3a249e3c Verifying Sub-Process works, and adding a field to expose a hint as to the sub-process in which the task occurs.
Because the name field is now used to expose workflow/sub-process information on tasks, we can't use it to store the workflow_version, so that is now just stored on the database model.  Which is much cleaner and removes a duplication.
2020-04-28 13:48:44 -04:00
Dan Funk 447f4013f8 Assure that a hard-reset sticks, and the system is properly updated. 2020-04-27 16:08:23 -04:00
Dan Funk 7b085c9c9d Adding an API Endpoint that will return a list of LookupValues that match a given query - can be used to populate an auto-complete table. 2020-04-22 19:40:40 -04:00
Dan Funk 0a74bf8c44 We can now collect, and provide "extension properties" on a task as set in the camunda modeler.
These are provided as "properties" on a task, and are identical in structure to properties on a form field.
2020-04-21 12:07:59 -04:00
Dan Funk ec112f52be Make use of cleaner data provided by Spiffworkflow about multi-instance settings. 2020-04-21 11:43:43 -04:00
Dan Funk d3dd9dcc25 Functional multi-instance - works with no changes to the front end - though I've added some attributes to task so we could give people a sense of how many iterations they will go through. 2020-04-19 15:14:10 -04:00
Dan Funk 241980f98f If you name add a file to a workflow that has the exact same name as a Task Spec's ID, and an extension of "md", it wll use that file as the markdown content, and ignore the markdown in the documentation on the task spec.
Moving the primary process id from the workflow model to the file model, and assuring it is updated properly.  This was causing a bug that would "lose" the workflow.
2020-04-17 13:30:32 -04:00
Dan Funk 3d820fcb21 Inital work on manual instance. 2020-04-16 11:07:29 -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 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
Aaron Louie 40e12f5ab5 Resolves marshmallow_sqlalchemy.ModelSchema deprecation warning 2020-03-16 13:37:31 -04:00
Aaron Louie 358a485372 Fixes broken test 2020-03-16 09:07:39 -04:00
Aaron Louie 3885bc7624 Merge remote-tracking branch 'origin/master' into feature/delete_study 2020-03-16 08:49:44 -04:00
Dan Funk 05b39df745 Fixes #12: Catching some specific common errors and re-raising as APIErrors with detailed codes and descriptions to improve debugging. In doing so, improving the error handling in the event a soft-reset causes an immediate error - and resetting to the original version of the specification in these events, to allow users the chance to try a hard reset instead. 2020-03-11 16:33:18 -04:00
Aaron Louie 3262833102 Requires login 2020-03-11 15:27:22 -04:00
Aaron Louie bbfe9291e0 Adds endpoint to get workflow stats. Adds a test for the endpoint. 2020-03-11 14:28:53 -04:00
Aaron Louie 1119bb2b6c Tests that task counts and events are logged. 2020-03-11 12:35:37 -04:00
Dan Funk 906bacff6a Expose a flag on the workflow model in the api to shown if it is using the latest spec. Added a soft_reset and hard_reset onto the workflow endpoint that will allow you to cause a hard or soft reset. 2020-03-05 16:45:44 -05:00
Dan Funk 7b21b78987 Workflow Processor will deserialize workflows using the version of the BPMN files used during creation, but allows for both a soft and hard reset - soft resets will use the new workflow without a restart and will retain full history. A hard-reset will restart the workflow from scratch, but will retain the data from the last completed task. Workflows have a complex version number associated with them that is used during the deserialization to find the correct files. 2020-03-05 15:38:30 -05:00
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 c0a3bac4f4 missed some test errors in the last push. Just fixing the tests. 2020-03-05 11:23:22 -05:00
Dan Funk 78b6f040eb Add the ability to forcibly restart a workflow, while retaining that workflows data.
A workflow specification knows it's version number, which is generated by the version of the files that make it up.
A workflow specification version number is the primary file (the lead BPMN) followed by a consistency ordered version each extra file associated with the workflow.  A change in any file modifies the specifications version.
2020-03-04 17:08:45 -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
Dan Funk 5e3fdaaa94 New set of "Tools" api endpoints, that provides a way to quickly render markdown or word documents by uploading json data and a template to populate.
Improved Error messages / Error processing.  You can now just throw an APIError anywhere, and it will be properly serialized and returned.
2020-02-29 17:22:38 -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
Dan Funk 1e8a095760 Fixing a rogue comma that made something a tuple and not a string, which drives me CRAZY. 2020-02-25 12:01:25 -05:00
Aaron Louie e4efc5e4e2 Fixes broken test 2020-02-21 12:02:35 -05:00
Dan Funk a94596112d Fixing a rogue comma that made something a tuple and not a string, which drives me CRAZY. 2020-02-20 14:35:21 -05:00
Aaron Louie 16db1e3504 Adds default_value to Task schema 2020-02-18 10:14:03 -05:00
Dan Funk 879a248002 Adding a test to assure the file creation occurs as expected via the API. 2020-02-10 20:54:22 -05:00
Dan Funk 1d24ebe382 Provide a script for generating word documents from template files. Refractored file managment into a service to make it easier to programatically add files. Modified the workflow_processor to inject the study_id and workflow_id into the running workflow so that this meta-information is avialable at the task level. 2020-02-10 16:19:23 -05:00
Aaron Louie f142d02a30 Adds workflow_spec_id back in to WorkflowApi 2020-02-07 12:36:08 -05:00
Dan Funk 9bd93748be Returning better cleaner information about workflow with the workflow endpoint. Removes the get_all_tasks and get_user_tasks endpoints as tasks are returned with the workflow. Workflow endpoint also includes the last task and next_task, which may or may not be user tasks. The task "type" returned is now the class name of the task_spec, rather than just the word "task". 2020-02-07 11:34:44 -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
Dan Funk 9e6fbfee79 Followup on Postgres - had some failing tests that needed cleaning up now that we are using a real database. 2020-02-04 15:44:06 -05:00