cb2613feee
Fixes all the paths and routing errors
2020-05-24 23:09:12 -04:00
b1718078ff
Refactors Dockerfile again. Installs gunicorn. Don't run gunicorn until the container starts up.
2020-05-24 20:53:25 -04:00
baaf73b5d9
Bumps Python version to 3.7
2020-05-24 13:43:12 -04:00
be1d54bbc5
Builds Docker image as WSGI + gunicorn
2020-05-24 12:37:11 -04:00
4627318818
Dropping flask_sso library in favor of reading from the headers directly. Updating login to read from ldap once it has the user_id. Adding more information to the sso endpoint.
2020-05-22 07:55:58 -04:00
8647ebee42
Moving spiff back to master branch, with fixes for parallel, and performance improvements.
2020-05-20 10:57:20 -04:00
481a9ed04c
Gets image ids from task data and Injects images into jinja docx
2020-05-19 21:51:54 -04:00
30bd6bef08
Another nav fix from spiff.
2020-05-18 18:27:30 -04:00
ecaac76fa5
More nav fixes via spiffworkflow.
2020-05-18 15:44:28 -04:00
5f2331f081
Bumping w/ fixes in spiffworkflow for reset token.
2020-05-18 06:56:29 -04:00
7ce460fffc
using a branch of spiffworkflow that fixes a deep recursion issue - this isn't perfect, but it's miles better than it was.
2020-05-17 17:06:00 -04:00
d62c173494
Updating with new changes to the spiffworkflow navigation.
2020-05-17 11:57:04 -04:00
43bf8f5337
Fixing a bug with navigation where elements went missing past exclusive gateways on subsequent forks.
2020-05-16 15:33:06 -04:00
53255ef35e
massive overhaul of the Workflow API endpoint.
...
No Previous Task, No Last Task, No Task List. Just the current task, and the Navigation.
Use the token endpoint to set the current task, even if it is a "READY" task in the api.
Previous Task can be set by identifying the prior task in the Navigation (I'm hoping)
Prefering camel case to snake case on all new apis. Maybe clean the rest up later.
2020-05-15 15:54:53 -04:00
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
e723992fde
Found a number of bugs with the parallel multi-instance - pulling in some recent changes from Spiffworkflow to open things up a bit more to allow functional jumping between tasks.
2020-05-12 12:23:43 -04:00
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
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
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
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
5e30e20b67
Updates pipenv lock file
2020-04-28 15:13:39 -04:00
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
e08f6c55d4
Bumping spiffworkflow version to fix a bug.
2020-04-22 10:45:24 -04:00
ec112f52be
Make use of cleaner data provided by Spiffworkflow about multi-instance settings.
2020-04-21 11:43:43 -04:00
8c834302a2
Forgot to upgrade.
2020-04-20 20:10:51 -04:00
2d3402a719
Ldap Service with Test and mocks.
...
LDAP_URL can be set in an environment variable.
2020-04-20 15:16:33 -04:00
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
d7bd2383a1
Fixing tests.
2020-04-17 15:12:48 -04:00
6b71bfaa9f
Updating spiffworkflow.
2020-04-16 11:22:02 -04:00
8f0de37011
Updates Pipenv hashes.
2020-04-15 12:12:51 -04:00
2a6f7d4916
Updating to the latest spiffworkflow so that dot-notation in DMN models works as expected.
2020-04-08 15:25:37 -04:00
bf3066a8b1
Upgrading Spiff to throw better error messages.
2020-04-07 17:15:05 -04:00
c7d2c28178
Vastly more informative ApiError model that provides details on the underlying task where the error occured.
...
Added a validate_workflow_specification endpoint that allows you to check if the workflow will execute from beginning to end using random data.
Minor fixes to existing bpmns to allow them to pass.
All scripts must include a "do_task_validate_only" that restricts external calls and database modifications, but performs as much logic as possible.
2020-03-27 08:29:31 -04:00
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
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
3eb1167b8e
Found a few errors in the sqlalchemy file definition that was causing failures, and had some consistency problems with the IRB Categories file name. The API was bailing out because we had restricted file types to bpmn,svg,or dmn in the connexion config file, I don't restrict this anymore we have plenty of checks elsewhere. Adding xlrd as a dependency - this didn't fail till a push to production.
2020-03-20 08:21:21 -04:00
83d859fd3a
Just merging stuff real quick.
2020-03-18 17:03:36 -04:00
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
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
3ef4860391
Adds user_uid and investigator_ids fields to Study. Gets studies from protocol builder and adds them if they aren't already in the database
2020-02-26 18:06:51 -05:00
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
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
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
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
37df0bf8f4
Converting this over to using Postgres. See the new postgres directory for a docker container to spin this up. Tests and development databases are the same, will try and get this corrected at some point.
2020-02-04 14:25:17 -05:00
93a97e8835
Updates packages
2020-01-31 11:32:46 -05:00
95b75f864d
You can now add multiple files to a workflow spec, and if properly linked, you can associate a DMN file with a BPMN to process decision tables.
2020-01-23 15:32:53 -05:00
532c00fde5
Upgrade to latest spiffworkflow
2020-01-23 11:38:26 -05:00
b63f27f1f0
Updates packages.
2020-01-22 16:50:54 -05:00
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
6361e94af5
Allow submitting data and progressing to the next task in a workflow.
2020-01-14 11:02:44 -05:00
27c3b66a21
ReadTheDocs initial setup and configuration.
2020-01-07 13:40:31 -05:00
e75da611ca
Adds endpoints for creating and updating a Study.
2020-01-03 11:44:24 -05:00
0b71833946
Adding file management. Files are stored in the database along with basic meta data.
2019-12-27 13:50:03 -05:00
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
e8ac73888b
Creating a dependency on the SpiffWorkflow fork we created. and placing the command line script into this code base and demonstrating that our workflow processor works at least on that level. Removing all kinds of garbage that had piled up before to keep this thing clean.
2019-12-11 11:45:44 -05:00
b279246e80
Setting up tests to work correctly when verifying endpoints.
2019-11-21 11:36:32 -05:00
358860918f
Updates to the README and removing a problematic dependency
2019-11-20 17:00:02 -05:00
4fdc2a05c8
Fixes broken pipenv files
2019-11-19 16:53:46 -05:00
983ffb4309
Adds basic Flask, Connexion, and SpiffWorkflow structure
2019-11-19 15:57:46 -05:00
Aaron Louie
Dan Funk
Aaron Louie