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
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
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
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
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
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
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
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
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
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
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
83d859fd3a
Just merging stuff real quick.
2020-03-18 17:03:36 -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
853b2b2502
Populates category
2020-03-18 15:16:15 -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
cbd8d2f46c
Silences SQLALCHEMY_TRACK_MODIFICATIONS warning
2020-03-16 13:47:17 -04:00
40e12f5ab5
Resolves marshmallow_sqlalchemy.ModelSchema deprecation warning
2020-03-16 13:37:31 -04:00
7d31bc24eb
Attempting to address "FutureWarning: Implicit (flask) JSON serialization" warning
2020-03-16 13:24:15 -04:00
a98251237b
Adds workflow spec category to API
2020-03-16 12:10:32 -04:00
6af1693bdc
Fixes SonarCloud issue L23. Verifies that study ids match.
2020-03-16 10:37:06 -04:00
0cc98616fd
Merge branch 'master' into feature/workflow_spec_categories
2020-03-16 10:25:03 -04:00
3885bc7624
Merge remote-tracking branch 'origin/master' into feature/delete_study
2020-03-16 08:49:44 -04:00
cd6a70b747
Fixes code smell issues identified by SonarCloud
2020-03-16 08:31:19 -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
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
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
902dba7191
Adds is_status flag to workflow specs
2020-03-13 14:56:46 -04:00
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
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
95750d4fb0
Merge branch 'feature/pb_services' of github.com:sartography/cr-connect-workflow into feature/pb_services
2020-03-09 12:41:42 -04:00
3b39f3875d
Fix data being over-written in the study_info.
2020-03-09 12:41:35 -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
e501fb31fd
Cleaning up swagger docs.
2020-03-05 17:10:00 -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
7b21b78987
Workflow Processor will deserialize workflows using the version of the BPMN files used during creation, but allows for both a soft and hard reset - soft resets will use the new workflow without a restart and will retain full history. A hard-reset will restart the workflow from scratch, but will retain the data from the last completed task. Workflows have a complex version number associated with them that is used during the deserialization to find the correct files.
2020-03-05 15:38:30 -05:00
e07ad8d21c
Updates training session BPMN files. Fixes PB status enums.
2020-03-05 14:21:03 -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
78b6f040eb
Add the ability to forcibly restart a workflow, while retaining that workflows data.
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A workflow specification knows it's version number, which is generated by the version of the files that make it up.
A workflow specification version number is the primary file (the lead BPMN) followed by a consistency ordered version each extra file associated with the workflow. A change in any file modifies the specifications version.
2020-03-04 17:08:45 -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
f7416065da
Merge remote-tracking branch 'origin/master'
2020-03-02 13:16:43 -05:00
a24b67d5db
Updates DSP BPMN
2020-03-02 13:16:36 -05:00
b0c4996fb3
Populates documentation.
2020-03-02 13:14:03 -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
5f944af0d7
Adds CR Connect training workflow specs
2020-02-28 15:39:44 -05:00
8611a23ad3
Renaming to snake case for consistency
2020-02-28 11:54:11 -05:00
f4a0c32cec
Fixes path to testing config file
2020-02-28 11:33:08 -05:00
dc53939eb1
Merge remote-tracking branch 'origin/master' into feature/protocol-builder
2020-02-28 11:17:17 -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
c6eb2d937d
Enable autoescape security feature for processing markdown data in descriptions from the BPMN Diagrams
2020-02-25 16:21:47 -05:00
1e8a095760
Fixing a rogue comma that made something a tuple and not a string, which drives me CRAZY.
2020-02-25 12:01:25 -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
9f4301712e
Merge remote-tracking branch 'origin/master'
2020-02-20 17:23:17 -05:00
a6e0809183
Adds SSO attributes. Prevents uid duplication errors.
2020-02-20 17:23:10 -05:00
d3c51af1f5
Merge branch 'master' of github.com:sartography/cr-connect-workflow
2020-02-20 16:04:44 -05:00
af35f182f6
Random Fact updated with a markdown set of examples
2020-02-20 16:04:38 -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
a94596112d
Fixing a rogue comma that made something a tuple and not a string, which drives me CRAZY.
2020-02-20 14:35:21 -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
6075a32d07
Edits default value
2020-02-18 10:17:14 -05:00
16db1e3504
Adds default_value to Task schema
2020-02-18 10:14:03 -05:00
5a53ddb88c
Fixes vulnerability identified by SonarCloud
2020-02-12 11:07:01 -05:00
5f461d9e87
Fixes FactService
2020-02-11 22:13:46 -05:00
b0b1a6e5e8
Saves form field key
2020-02-11 15:03:25 -05:00
0a3a932c50
Comments out study workflow for now. Fixes failing unit tests.
2020-02-11 13:40:14 -05:00
0ef1a178ed
Merge branch 'master' into feature/crc_demo_workflows
2020-02-11 13:30:57 -05:00
f58ed5b6ee
Adds another user task at the end
2020-02-11 12:14:10 -05:00
709bae76b2
Removing a rogue comma that was causing havoc. Also, don't fail if a mock already exists in the test database.
2020-02-11 11:11:21 -05:00
879a248002
Adding a test to assure the file creation occurs as expected via the API.
2020-02-10 20:54:22 -05:00
359fb4a2f3
Adds draft demo workflow specs
2020-02-10 17:19:11 -05:00
f128e7206b
Adds placeholder scripts for testing
2020-02-10 17:18:51 -05:00
9f0eb8477a
Fix for a bug in the File service where it was being overly restrictive.
2020-02-10 16:27:57 -05:00
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
fd9c685979
Handles processes with multiple top-level elements
2020-02-10 15:20:45 -05:00
f142d02a30
Adds workflow_spec_id back in to WorkflowApi
2020-02-07 12:36:08 -05:00
eae6c8dd1a
update to last commit, left an extra column on workflow model that does not need to exist.
2020-02-07 11:57:48 -05:00
e1148e1b3d
Merge branch 'master' of github.com:sartography/cr-connect-workflow
2020-02-07 11:34:57 -05:00
9bd93748be
Returning better cleaner information about workflow with the workflow endpoint. Removes the get_all_tasks and get_user_tasks endpoints as tasks are returned with the workflow. Workflow endpoint also includes the last task and next_task, which may or may not be user tasks. The task "type" returned is now the class name of the task_spec, rather than just the word "task".
2020-02-07 11:34:44 -05:00
9fb3a96a50
Fixes instance path
2020-02-06 14:36:02 -05:00
71dac70e1f
Updates list of allowed files. Removes unnecessary migrations. Note this will require a full wipe & reset of the database to work.
2020-02-05 17:23:37 -05:00
5a6d589e6d
Adds form_field_key to API
2020-02-05 15:06:19 -05:00
58982ab306
Merge remote-tracking branch 'origin/feature/update-task-data' into feature/update-task-data
2020-02-05 14:55:59 -05:00
933a235471
Adds multiple and single file upload form controls
2020-02-05 14:55:52 -05:00
654f39e7fd
Adds form field key to file model.
2020-02-05 14:55:31 -05:00
ff63978da0
read the instance/config.py file in IF it exists.
2020-02-05 13:43:59 -05:00
e1e866a2b3
Gets docker-compose working.
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You'll need to add a .env file to the same directory as the docker-compose.yml file that sets the values for DB_USER and DB_PASS.
2020-02-04 21:42:09 -05:00
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
b1a81957ef
Merge branch 'feature/update-task-data' of github.com:sartography/cr-connect-workflow into feature/update-task-data
2020-02-04 15:45:05 -05:00
9e6fbfee79
Followup on Postgres - had some failing tests that needed cleaning up now that we are using a real database.
2020-02-04 15:44:06 -05:00
3ee0426ba9
Adds workflow_id to file endpoints.
2020-02-04 14:26:53 -05:00
098ecb3e87
Wipes out old migrations, since changing foreign key constraints in SQLite requires a full database reset anyways.
2020-02-04 09:57:02 -05:00
e717c25a25
Study ID is an integer. Task ID is a string.
2020-02-03 22:29:41 -05:00
0368657549
Adds ability to get FileModel records by study and task
2020-02-03 21:56:18 -05:00
8fbbed4feb
You must all "do engine steps" when completing a task so that it will kick off any automatic tasks/decisions/etc... this will update remaining tasks. Added some tests for parallel, since I wrote them trying to debug this.
2020-02-03 15:15:36 -05:00
8cc04aaad2
Adds task data to Task schema
2020-02-03 10:49:48 -05:00
e4b2a7a641
Adds endpoint to retrieve all user tasks for a workflow, regardless of state
2020-01-31 12:40:08 -05:00
8d39a96606
Adds workflow spec & BPMN with parallel tasks
2020-01-31 12:01:41 -05:00
918a6d5ab7
Removes unsupported read-only flag on File schema for now
2020-01-31 11:33:31 -05:00
a0e60ddd77
Renames endpoint methods for clarity. Adds endpoint for just updating file info.
2020-01-31 10:39:19 -05:00
3fb831bae4
When you create a study, all possible workflows are then associated with that study.
2020-01-30 09:11:17 -05:00
acca1523b7
adding an api call for getting a single workflow spec.
2020-01-28 10:14:06 -05:00
a3b6e4fc7f
Fixes import paths
2020-01-24 11:52:52 -05:00
50dfa561a9
Fixes import paths, which were screwing up stuff.
2020-01-24 09:29:50 -05:00
6faabea8a4
Deletes related files and workflows when a workflow spec is deleted.
2020-01-24 09:26:17 -05:00
6aa3d711ce
Adds endpoint to delete workflow spec
2020-01-23 16:05:09 -05:00
Dan Funk
Aaron Louie