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
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
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
83d859fd3a
Just merging stuff real quick.
2020-03-18 17:03:36 -04:00
02be8ede75
Merge remote-tracking branch 'origin/master' into feature/reference_files
2020-03-18 15:16:34 -04:00
40e12f5ab5
Resolves marshmallow_sqlalchemy.ModelSchema deprecation warning
2020-03-16 13:37:31 -04:00
f742be3264
Replaces deprecated assertEquals with assertEqual
2020-03-16 13:05:15 -04:00
a0c35fe8cf
Adds test for updating workflow spec
2020-03-16 12:32:39 -04:00
a98251237b
Adds workflow spec category to API
2020-03-16 12:10:32 -04:00
0cc98616fd
Merge branch 'master' into feature/workflow_spec_categories
2020-03-16 10:25:03 -04:00
358a485372
Fixes broken test
2020-03-16 09:07:39 -04:00
3885bc7624
Merge remote-tracking branch 'origin/master' into feature/delete_study
2020-03-16 08:49:44 -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
b1a6c9b6c7
Adds basic status-setting workflow spec and minimal test
2020-03-13 14:58:07 -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
3262833102
Requires login
2020-03-11 15:27:22 -04:00
bbfe9291e0
Adds endpoint to get workflow stats. Adds a test for the endpoint.
2020-03-11 14:28:53 -04:00
1119bb2b6c
Tests that task counts and events are logged.
2020-03-11 12:35:37 -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
c928a6472c
Edits typo
2020-03-06 10:57:24 -05:00
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
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
c0a3bac4f4
missed some test errors in the last push. Just fixing the tests.
2020-03-05 11:23:22 -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
d184ccc8de
Merge pull request #16 from sartography/feature/pb_services
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Feature/pb services
2020-03-03 15:38:38 -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
b965276310
Adds a mock study with same ID a one from data loader.
2020-03-02 15:01:41 -05:00
305118e90e
Adds a test for get_studies endpoint
2020-03-02 14:42:30 -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
5f3ffc9b49
Cleans up imports
2020-02-28 11:37:42 -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
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
1ac9180304
Updates tests to match changing sso_backdoor to query string params
2020-02-21 12:03:14 -05:00
e4efc5e4e2
Fixes broken test
2020-02-21 12:02:35 -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
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
16db1e3504
Adds default_value to Task schema
2020-02-18 10:14:03 -05:00
5f461d9e87
Fixes FactService
2020-02-11 22:13:46 -05:00
0a3a932c50
Comments out study workflow for now. Fixes failing unit tests.
2020-02-11 13:40:14 -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
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
f142d02a30
Adds workflow_spec_id back in to WorkflowApi
2020-02-07 12:36:08 -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
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
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
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
ba9330bc21
Fixes broken tests
2020-01-31 11:33:43 -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
0a44ef04d7
Slight refactoring - makes BaseTest inherit from TestCase. Checks that data loader works properly
2020-01-24 09:35:14 -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
5c5f38e4ee
Adds test for deleting a workflow spec
2020-01-23 16:14:05 -05:00
45f2e52c86
Merge branch 'feature/update-task-data' of github.com:sartography/cr-connect-workflow into feature/update-task-data
2020-01-23 15:35:51 -05:00
95b75f864d
You can now add multiple files to a workflow spec, and if properly linked, you can associate a DMN file with a BPMN to process decision tables.
2020-01-23 15:32:53 -05:00
6158243053
Fixes modify workflow method
2020-01-21 15:24:17 -05:00
790b0dfc3a
Adds endpoint for modifying existing workflow spec
2020-01-14 14:10:53 -05:00
50ee50e3c2
Fixes broken unit test
2020-01-14 11:47:36 -05:00
fe15799ee1
Adds type hinting to db and session to fix Pycharm autocomplete. Replaces db.session with session.
2020-01-14 11:45:12 -05:00
6361e94af5
Allow submitting data and progressing to the next task in a workflow.
2020-01-14 11:02:44 -05:00
75881bf1d3
Adds endpoint for adding a workflow specification
2020-01-13 21:43:09 -05:00
a3d7ba8114
WIP
2020-01-07 13:23:46 -05:00
872f3fca1b
Returns workflow spec id with Workflow schema
2020-01-06 09:18:13 -05:00
e75da611ca
Adds endpoints for creating and updating a Study.
2020-01-03 11:44:24 -05:00
c4cbaeb64e
Refactor models into seperate directories
2019-12-31 16:32:47 -05:00
9a195bedad
Fixing some caching issues and places where the updates were not being processed completed. And updates to the docker file.
2019-12-31 11:31:30 -05:00
0685b282e8
Don't put foreign key constraints on primary keys.
2019-12-30 16:00:33 -05:00
fb465531ca
Add the ability to delete a workflow.
2019-12-30 13:15:39 -05:00
b54bd49cf4
Allow for clearing out the database.
2019-12-30 13:03:57 -05:00
91a91e9677
Read workflow configuration from the database, and not from a file.
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And dropping the API call in the Fact Service so we aren't hitting external apis for the time being.
2019-12-30 11:07:26 -05:00
0b71833946
Adding file management. Files are stored in the database along with basic meta data.
2019-12-27 13:50:03 -05:00
bb6ab4b8e8
Tasks can have forms and they are returned correctly.
2019-12-19 11:58:51 -05:00
0dc422c7f6
we need a commit at the end, but I don't really believe that.
2019-12-18 15:32:06 -05:00
53a8811769
Add workflow to study
2019-12-18 15:22:46 -05:00
fbbd6c6659
Adding a workflow from a spec
2019-12-18 14:42:40 -05:00
9861f6baf3
Lots and lots of random stuff as I organize code and get things to make sense.
2019-12-18 14:02:17 -05:00
e8ac73888b
Creating a dependency on the SpiffWorkflow fork we created. and placing the command line script into this code base and demonstrating that our workflow processor works at least on that level. Removing all kinds of garbage that had piled up before to keep this thing clean.
2019-12-11 11:45:44 -05:00
630ee90b6b
Adding a camunda parser, so we can use this free and beautiful editor to build diagrams.
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Adding a command line implemenation so I can get a grip on what is happening in real time more quickly.
Started working on some custom tasks, but need to put a little more effort into this area.
Minor updates to the readme
Adding a joke BPMN that I can test with.
2019-11-25 16:04:09 -05:00
3bdfba6db0
Still learning - writing tests around the demo. Getting the file structure cleaned up.
2019-11-22 10:50:30 -05:00
9280aab0b6
name tests so they get picked up and run.
2019-11-21 12:01:51 -05:00
b279246e80
Setting up tests to work correctly when verifying endpoints.
2019-11-21 11:36:32 -05:00
92ce0d048a
Creating an "app" base directory - this allows us to organize the source files and keep them separate from tests, configuration, and pipenv stuffs. Adding basic config and test directories and getting that set up and ready to roll.
2019-11-21 09:22:42 -05:00
Dan Funk
Aaron Louie
Aaron Louie