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
0cd584880f
Fixing a bug where the workflow specification can not be deleted.
2020-03-23 12:48:31 -04:00
967ac65d0e
Just raise the ApiError, no need to marshal it.
2020-03-23 12:22:26 -04:00
b35427523d
Merge remote-tracking branch 'origin/master' into feature/reference_files
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# 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
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".
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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
ac7c7b42c4
Revert "Merge remote-tracking branch 'origin/feature/reference_files' into feature/workflow_spec_categories"
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This reverts commit 9a26fc8e80
2020-03-18 17:05:13 -04:00
9a26fc8e80
Merge remote-tracking branch 'origin/feature/reference_files' into feature/workflow_spec_categories
2020-03-18 16:58:57 -04:00
f0678b43d4
Minor fixes
2020-03-18 16:58:50 -04:00
02be8ede75
Merge remote-tracking branch 'origin/master' into feature/reference_files
2020-03-18 15:16:34 -04:00
532d6b5dd6
Adds CRUD endpoints for workflow spec categories
2020-03-16 16:30:56 -04:00
4db456dcea
Adds workflow spec category methods
2020-03-16 16:12:39 -04:00
f9dbbefe89
Adds status spec to study when workflow is added.
2020-03-16 08:05:30 -04:00
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
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
f177e33ad6
Tiny tweak
2020-03-11 15:31:23 -04:00
3262833102
Requires login
2020-03-11 15:27:22 -04:00
e977ee9e0d
Updates task counts when getting workflow
2020-03-11 15:16:42 -04:00
bbfe9291e0
Adds endpoint to get workflow stats. Adds a test for the endpoint.
2020-03-11 14:28:53 -04:00
be17c2159c
Adds workflow stats and task events models and schemas. Updates workflow stats and logs task completion when task data is updated.
2020-03-10 21:29:57 -04:00
f1b6718068
Adds task counts
2020-03-10 15:46:14 -04:00
e91d7aff2f
Fixes #11 : adding a delete endpoint for studies. It won't delete studies that have workflows, you have to delete those first)
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Removing the "default" error response from the api.yml, it was all noise.
2020-03-09 15:12:40 -04:00
acad0023d2
Fixes a bug in get_study_workflows and adds a test covering it
2020-03-06 10:52:41 -05:00
9fcd6f38f4
Merge remote-tracking branch 'origin/master' into feature/pb_services
2020-03-05 17:13:41 -05:00
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
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.
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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
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.
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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
c5cee4761e
Improve version handling of files. Consolidate more of this logic in FileService. Place the version on the actual data model, not the file model, so the file model remains the same, and we just version the data associated with it.
2020-03-04 13:40:25 -05:00
f258090a0b
Fixes broken unit test
2020-03-04 09:54:00 -05:00
8cbd6f892f
WIP: Mocks study details PB endpoint response
2020-03-03 20:56:46 -05:00
01720a8bbf
Replaces migration and fixes broken tests
2020-03-03 16:02:01 -05:00
93168482c2
Merge remote-tracking branch 'origin/master'
2020-03-03 15:46:24 -05:00
668de6c4dc
Edits Protocol Builder statuses
2020-03-03 15:46:20 -05:00
94f828dfd6
Adding a simple endpoint that describes what scripts are currently available, along with a brief description.
2020-03-03 15:30:42 -05:00
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.
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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
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.
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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
8611a23ad3
Renaming to snake case for consistency
2020-02-28 11:54:11 -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
0cc59d0974
Adds study inactive flag. Sets study to inactive if not found in Protocol Builder.
2020-02-27 11:17:58 -05:00
f3068e68db
Adds user to example data. Requires login before adding/updating a study.
2020-02-27 10:30:16 -05:00
27d7afb656
Adds Protocol Builder models and schemas. Reorganizes and cleans up some files.
2020-02-27 09:54:46 -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
002207cbca
Adds redirect URL to login handler
2020-02-24 16:59:16 -05:00
443d38a9a1
Prevents duplication of study on update.
2020-02-21 11:24:51 -05:00
eb6354db6e
Moves sso_backdoor parameters to query string. Prevents duplication of user on update.
2020-02-21 11:24:39 -05:00
a6e0809183
Adds SSO attributes. Prevents uid duplication errors.
2020-02-20 17:23:10 -05:00
0cda7c66e5
Merge remote-tracking branch 'origin/master'
2020-02-20 15:43:34 -05:00
581434b453
Adds SSO header attributes
2020-02-20 15:43:29 -05:00
2cc6010c8d
Protocol builder connections
2020-02-20 13:30:04 -05:00
1a9b5b50e5
Merge branch 'master' of github.com:sartography/cr-connect-workflow
2020-02-18 16:39:11 -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
Dan Funk
Aaron Louie