Dan Funk
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
Dan Funk
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
Dan Funk
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
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.
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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
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
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
Dan Funk
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
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.
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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
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
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
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
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
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".
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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
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"
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This reverts commit 9a26fc8e80bbe32081c6edfc394aa1876b1e4327.
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
Aaron Louie
853b2b2502
Populates category
2020-03-18 15:16:15 -04:00
Aaron Louie
532d6b5dd6
Adds CRUD endpoints for workflow spec categories
2020-03-16 16:30:56 -04:00
Aaron Louie
4db456dcea
Adds workflow spec category methods
2020-03-16 16:12:39 -04:00
Aaron Louie
cbd8d2f46c
Silences SQLALCHEMY_TRACK_MODIFICATIONS warning
2020-03-16 13:47:17 -04:00
Aaron Louie
40e12f5ab5
Resolves marshmallow_sqlalchemy.ModelSchema deprecation warning
2020-03-16 13:37:31 -04:00
Aaron Louie
7d31bc24eb
Attempting to address "FutureWarning: Implicit (flask) JSON serialization" warning
2020-03-16 13:24:15 -04:00
Aaron Louie
a98251237b
Adds workflow spec category to API
2020-03-16 12:10:32 -04:00
Aaron Louie
6af1693bdc
Fixes SonarCloud issue L23. Verifies that study ids match.
2020-03-16 10:37:06 -04:00
Aaron Louie
0cc98616fd
Merge branch 'master' into feature/workflow_spec_categories
2020-03-16 10:25:03 -04:00
Aaron Louie
3885bc7624
Merge remote-tracking branch 'origin/master' into feature/delete_study
2020-03-16 08:49:44 -04:00
Aaron Louie
cd6a70b747
Fixes code smell issues identified by SonarCloud
2020-03-16 08:31:19 -04:00
Aaron Louie
f9dbbefe89
Adds status spec to study when workflow is added.
2020-03-16 08:05:30 -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
Aaron Louie
e4af6f77d0
Adds is_status flag to workflow_spec, status_spec_id & version to study, and is_active flag to WorkflowApi
2020-03-15 15:52:59 -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
902dba7191
Adds is_status flag to workflow specs
2020-03-13 14:56:46 -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
Aaron Louie
f177e33ad6
Tiny tweak
2020-03-11 15:31:23 -04:00
Aaron Louie
3262833102
Requires login
2020-03-11 15:27:22 -04:00
