07551ed4a8
Moves AWS CLI install step into deploy script
2020-04-03 15:53:24 -04:00
222e4635c3
Merge remote-tracking branch 'origin/master'
2020-04-03 15:38:32 -04:00
846b64d93a
Skips cleanup in deploy step
2020-04-03 15:38:23 -04:00
5de850cfdb
Merge branch 'master' of github.com:sartography/cr-connect-workflow
2020-04-03 13:52:19 -04:00
fe40be752f
fixing a bug in the Protocol builder schema, more to fix there, and deserves a test, but this corrects the investigators
2020-04-03 13:52:12 -04:00
71d9bbec02
Replaced password with token
2020-04-03 11:29:33 -04:00
13542d78c7
Moves awscli install to after script success
2020-04-03 10:14:28 -04:00
f501fc47fb
Removes duplicate build command
2020-04-03 10:09:06 -04:00
b0e49943a0
Sends message to DCOS when Docker Hub image is updated
2020-04-03 09:53:47 -04:00
b39e4b382f
Catch more template processing errors.
2020-04-02 15:06:00 -04:00
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
534e8493a4
Deleting was broken because statistics were causing an integrity constraint.
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Updating IDS bpmn to the latest for testing.
Adding a TODO
2020-04-02 12:58:52 -04:00
af5ab6a2c2
Merge pull request #25 from sartography/feature/status_refactor
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Feature/status refactor
2020-03-31 09:31:53 -04:00
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
17796193de
fixing a bug that was causing failing tests.
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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
34b6ec92bf
updating the API
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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
2cd5d70a77
missing another migration. This should fix it.
2020-03-30 09:40:56 -04:00
f8cca274d4
Adding a migration for the last commit.
2020-03-30 08:36:10 -04:00
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.
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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
c9900d787e
Every good deed goes punished.
2020-03-27 15:48:21 -04:00
6ebd4dce42
WIP: Adds default workflow spec categories
2020-03-27 15:32:07 -04:00
57f1fa670e
fixing a stupid mistake.
2020-03-27 14:55:53 -04:00
907e1cbbb3
minor fixes that were breaking when connecting to the front end.
2020-03-27 14:27:50 -04:00
b5fca2f683
Forgot a migration
2020-03-27 12:19:32 -04:00
b61a35f956
Merge remote-tracking branch 'origin/master' into feature/status_refactor
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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
c7d2c28178
Vastly more informative ApiError model that provides details on the underlying task where the error occured.
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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
6c832829b0
Merge remote-tracking branch 'origin' into feature/status_refactor
2020-03-26 20:47:37 -04:00
f77ebe3177
Adds display order to categories
2020-03-26 15:29:52 -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.
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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
4ed89eec5b
Mocks Protocol Builder response
2020-03-26 10:30:15 -04:00
3fb9fb9b22
Simplifies status BPMN & DMN.
2020-03-26 10:06:12 -04:00
8752a81042
Disables broken spec
2020-03-26 08:52:53 -04:00
dd5971bea9
Updates workflow specs for data loader
2020-03-25 11:13:52 -04:00
bd92c230e4
Fix the API so we are clear what is being returned when updating a file.
2020-03-25 08:06:58 -04:00
37a8b69ffe
Cleaning up a failing test, not sure why this isn't failing locally?
2020-03-24 14:40:24 -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
473c81ac8b
Allow migration even when data exists.
2020-03-23 13:39:54 -04:00
ef0bb7aaaa
Allow migration even when data exists.
2020-03-23 13:22:09 -04:00
f205fffc3c
Allow migration even when data exists.
2020-03-23 13:03:31 -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
e2331330e5
Merge pull request #24 from sartography/feature/reference_files
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Feature/reference files
2020-03-23 12:13:39 -04:00
3ec8196979
Cleaning up migration hell.
2020-03-20 11:19:43 -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
62685997c8
Merge pull request #23 from sartography/feature/workflow_spec_categories
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Feature/workflow spec categories
2020-03-20 10:27:14 -04:00
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
16c6ba9661
Removing unneeded files.
2020-03-20 08:33:37 -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
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
e529e149f6
Assure that reference file exists on data-reload.
2020-03-20 07:41:21 -04:00
Aaron Louie
Dan Funk