Commit Graph

55 Commits

Author SHA1 Message Date
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 8611a23ad3 Renaming to snake case for consistency 2020-02-28 11:54:11 -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
Aaron Louie 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
Aaron Louie 002207cbca Adds redirect URL to login handler 2020-02-24 16:59:16 -05:00
Aaron Louie 443d38a9a1 Prevents duplication of study on update. 2020-02-21 11:24:51 -05:00
Aaron Louie eb6354db6e Moves sso_backdoor parameters to query string. Prevents duplication of user on update. 2020-02-21 11:24:39 -05:00
Aaron Louie a6e0809183 Adds SSO attributes. Prevents uid duplication errors. 2020-02-20 17:23:10 -05:00
Aaron Louie 0cda7c66e5 Merge remote-tracking branch 'origin/master' 2020-02-20 15:43:34 -05:00
Aaron Louie 581434b453 Adds SSO header attributes 2020-02-20 15:43:29 -05:00
Dan Funk 2cc6010c8d Protocol builder connections 2020-02-20 13:30:04 -05:00
Dan Funk 1a9b5b50e5 Merge branch 'master' of github.com:sartography/cr-connect-workflow 2020-02-18 16:39:11 -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
Aaron Louie b0b1a6e5e8 Saves form field key 2020-02-11 15:03:25 -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 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
Aaron Louie 5a6d589e6d Adds form_field_key to API 2020-02-05 15:06:19 -05:00
Aaron Louie e1e866a2b3 Gets docker-compose working.
You'll need to add a .env file to the same directory as the docker-compose.yml file that sets the values for DB_USER and DB_PASS.
2020-02-04 21:42:09 -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 b1a81957ef Merge branch 'feature/update-task-data' of github.com:sartography/cr-connect-workflow into feature/update-task-data 2020-02-04 15:45:05 -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
Aaron Louie 3ee0426ba9 Adds workflow_id to file endpoints. 2020-02-04 14:26:53 -05:00
Aaron Louie 098ecb3e87 Wipes out old migrations, since changing foreign key constraints in SQLite requires a full database reset anyways. 2020-02-04 09:57:02 -05:00
Aaron Louie 0368657549 Adds ability to get FileModel records by study and task 2020-02-03 21:56:18 -05:00
Dan Funk 8fbbed4feb You must all "do engine steps" when completing a task so that it will kick off any automatic tasks/decisions/etc... this will update remaining tasks. Added some tests for parallel, since I wrote them trying to debug this. 2020-02-03 15:15:36 -05:00
Aaron Louie e4b2a7a641 Adds endpoint to retrieve all user tasks for a workflow, regardless of state 2020-01-31 12:40:08 -05:00
Aaron Louie a0e60ddd77 Renames endpoint methods for clarity. Adds endpoint for just updating file info. 2020-01-31 10:39:19 -05:00
Dan Funk 3fb831bae4 When you create a study, all possible workflows are then associated with that study. 2020-01-30 09:11:17 -05:00
Dan Funk acca1523b7 adding an api call for getting a single workflow spec. 2020-01-28 10:14:06 -05:00
Aaron Louie a3b6e4fc7f Fixes import paths 2020-01-24 11:52:52 -05:00
Aaron Louie 50dfa561a9 Fixes import paths, which were screwing up stuff. 2020-01-24 09:29:50 -05:00
Aaron Louie 6faabea8a4 Deletes related files and workflows when a workflow spec is deleted. 2020-01-24 09:26:17 -05:00
Aaron Louie 6aa3d711ce Adds endpoint to delete workflow spec 2020-01-23 16:05:09 -05:00
Aaron Louie 91e33a1768 Deletes associated file_data records when deleting a file. 2020-01-23 12:17:58 -05:00
Aaron Louie 6158243053 Fixes modify workflow method 2020-01-21 15:24:17 -05:00
Dan Funk 900819e647 fixing failed run 2020-01-14 15:39:54 -05:00
Aaron Louie 054bd88760 Fixes path to api methods 2020-01-14 14:55:10 -05:00
Aaron Louie 790b0dfc3a Adds endpoint for modifying existing workflow spec 2020-01-14 14:10:53 -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 6361e94af5 Allow submitting data and progressing to the next task in a workflow. 2020-01-14 11:02:44 -05:00
Aaron Louie 75881bf1d3 Adds endpoint for adding a workflow specification 2020-01-13 21:43:09 -05:00
Dan Funk a3d7ba8114 WIP 2020-01-07 13:23:46 -05:00
Aaron Louie 872f3fca1b Returns workflow spec id with Workflow schema 2020-01-06 09:18:13 -05:00
Aaron Louie e75da611ca Adds endpoints for creating and updating a Study. 2020-01-03 11:44:24 -05:00