Commit Graph

176 Commits

Author SHA1 Message Date
Dan Funk 697127660f Assure that all script tasks place data in a dictionary that is named exactly the same as the class - which is also the same as the Script tag. 2020-04-07 14:09:21 -04:00
Dan Funk c6b6ee5d70 Renamed the required_docs script to just "documents", and it returns all documented in the irb_documents look up table indexed on the "Code" - so details become available in the task data like "documents.IRB_INFOSEC_DOC.required".
Updated the irb_documents with shorter code names, thanks to Alex. Re-worked the DMN models so they can properly read from this new datastructure.
2020-04-06 16:56:00 -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 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
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 16c6ba9661 Removing unneeded files. 2020-03-20 08:33:37 -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 560b8a8782 Mergers details from the irb_documents.xlsx into the values returned from the Protocol Builder to create a more complete picture of required document details. 2020-03-19 10:23:50 -04:00
Dan Funk 83d859fd3a Just merging stuff real quick. 2020-03-18 17:03:36 -04:00
Dan Funk 02be8ede75 Merge remote-tracking branch 'origin/master' into feature/reference_files 2020-03-18 15:16:34 -04:00
Aaron Louie 0cc98616fd Merge branch 'master' into feature/workflow_spec_categories 2020-03-16 10:25:03 -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
Dan Funk 779674ab60 Add the ability to upload and request general reference files by name. These will be used across workflows and will frequently contain lookup tables that can be referenced by various script tasks. 2020-03-13 15:03:57 -04:00
Aaron Louie b1a6c9b6c7 Adds basic status-setting workflow spec and minimal test 2020-03-13 14:58:07 -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
Dan Funk 9fcd6f38f4 Merge remote-tracking branch 'origin/master' into feature/pb_services 2020-03-05 17:13:41 -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
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
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
Dan Funk 2cc6010c8d Protocol builder connections 2020-02-20 13:30:04 -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
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