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
Aaron Louie
Dan Funk