Commit Graph

480 Commits

Author SHA1 Message Date
Aaron Louie b0e49943a0 Sends message to DCOS when Docker Hub image is updated 2020-04-03 09:53:47 -04:00
Dan Funk b39e4b382f Catch more template processing errors. 2020-04-02 15:06:00 -04:00
Dan Funk 785918cb7f Be sure the validation process examines the data located in the documentation and correctly handles boolean fields. 2020-04-02 14:47:20 -04:00
Dan Funk 534e8493a4 Deleting was broken because statistics were causing an integrity constraint.
Updating IDS bpmn to the latest for testing.
Adding a TODO
2020-04-02 12:58:52 -04:00
Dan Funk af5ab6a2c2
Merge pull request #25 from sartography/feature/status_refactor
Feature/status refactor
2020-03-31 09:31:53 -04:00
Dan Funk c86f3321c5 reworking the test_study_service to run from a clean state, this is growing so complex. Tests really need to be isolated better. 2020-03-30 15:39:50 -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 34b6ec92bf updating the API
Removing the call for study/workflows - as workflow information is returned with the study by default.
Fixing a bug in the workflow spec model schema.
2020-03-30 10:12:10 -04:00
Dan Funk 2cd5d70a77 missing another migration. This should fix it. 2020-03-30 09:40:56 -04:00
Dan Funk f8cca274d4 Adding a migration for the last commit. 2020-03-30 08:36:10 -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 c9900d787e Every good deed goes punished. 2020-03-27 15:48:21 -04:00
Aaron Louie 6ebd4dce42 WIP: Adds default workflow spec categories 2020-03-27 15:32:07 -04:00
Dan Funk 57f1fa670e fixing a stupid mistake. 2020-03-27 14:55:53 -04:00
Dan Funk 907e1cbbb3 minor fixes that were breaking when connecting to the front end. 2020-03-27 14:27:50 -04:00
Dan Funk b5fca2f683 Forgot a migration 2020-03-27 12:19:32 -04:00
Dan Funk b61a35f956 Merge remote-tracking branch 'origin/master' into feature/status_refactor
Fixing adding a study so all workflows are again added, will add status on those workflows based on output from the master bpmn diagram, which is coming shortly.
2020-03-27 11:55:36 -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 6c832829b0 Merge remote-tracking branch 'origin' into feature/status_refactor 2020-03-26 20:47:37 -04:00
Aaron Louie f77ebe3177 Adds display order to categories 2020-03-26 15:29:52 -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
Aaron Louie 4ed89eec5b Mocks Protocol Builder response 2020-03-26 10:30:15 -04:00
Aaron Louie 3fb9fb9b22 Simplifies status BPMN & DMN. 2020-03-26 10:06:12 -04:00
Aaron Louie 8752a81042 Disables broken spec 2020-03-26 08:52:53 -04:00
Aaron Louie dd5971bea9 Updates workflow specs for data loader 2020-03-25 11:13:52 -04:00
Dan Funk bd92c230e4 Fix the API so we are clear what is being returned when updating a file. 2020-03-25 08:06:58 -04:00
Dan Funk 37a8b69ffe Cleaning up a failing test, not sure why this isn't failing locally? 2020-03-24 14:40:24 -04:00
Dan Funk 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
Dan Funk 473c81ac8b Allow migration even when data exists. 2020-03-23 13:39:54 -04:00
Dan Funk ef0bb7aaaa Allow migration even when data exists. 2020-03-23 13:22:09 -04:00
Dan Funk f205fffc3c Allow migration even when data exists. 2020-03-23 13:03:31 -04:00
Dan Funk 0cd584880f Fixing a bug where the workflow specification can not be deleted. 2020-03-23 12:48:31 -04:00
Dan Funk 967ac65d0e Just raise the ApiError, no need to marshal it. 2020-03-23 12:22:26 -04:00
Dan Funk e2331330e5
Merge pull request #24 from sartography/feature/reference_files
Feature/reference files
2020-03-23 12:13:39 -04:00
Dan Funk 3ec8196979 Cleaning up migration hell. 2020-03-20 11:19:43 -04:00
Dan Funk b35427523d Merge remote-tracking branch 'origin/master' into feature/reference_files
# Conflicts:
#	crc/models/file.py
#	crc/services/file_service.py
#	tests/data/reference/irb_documents.xlsx
#	tests/test_files_api.py
2020-03-20 11:07:55 -04:00
Dan Funk 62685997c8
Merge pull request #23 from sartography/feature/workflow_spec_categories
Feature/workflow spec categories
2020-03-20 10:27:14 -04:00
Dan Funk 61a46a9c41 Fixing the primary flag on the file table - it should never be null, it shoud just default to false. 2020-03-20 08:36:50 -04:00
Dan Funk 16c6ba9661 Removing unneeded files. 2020-03-20 08:33:37 -04:00
Dan Funk 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
Dan Funk 13a688048c Fixing failed tests, setting unknown=EXCLUDE on the workflow spec model schema so that it can handle getting back the dump-only workflow_spec_category and just ignore it. 2020-03-20 07:54:01 -04:00
Dan Funk e529e149f6 Assure that reference file exists on data-reload. 2020-03-20 07:41:21 -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 dbe6701bb2 Removing the doc_types from the protocol builder, as these will eventually contradict what is coming from IRB and should not be used as an reference. Also fixing a failing test and assuring that only one reference file ever exists with a given name. 2020-03-19 10:40:07 -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
Aaron Louie ac7c7b42c4 Revert "Merge remote-tracking branch 'origin/feature/reference_files' into feature/workflow_spec_categories"
This reverts commit 9a26fc8e80.
2020-03-18 17:05:13 -04:00
Dan Funk 83d859fd3a Just merging stuff real quick. 2020-03-18 17:03:36 -04:00
Aaron Louie 9a26fc8e80 Merge remote-tracking branch 'origin/feature/reference_files' into feature/workflow_spec_categories 2020-03-18 16:58:57 -04:00
Aaron Louie f0678b43d4 Minor fixes 2020-03-18 16:58:50 -04:00
Dan Funk 02be8ede75 Merge remote-tracking branch 'origin/master' into feature/reference_files 2020-03-18 15:16:34 -04:00