7f0d8a131d
Import DataStoreBase from service now
2021-06-02 10:00:55 -04:00
506b84a49a
Import DataStoreBase from service now
2021-06-02 10:00:18 -04:00
e2e35b673d
Moved data store code from script to service
2021-06-02 09:59:41 -04:00
162dee45d3
Unused import
2021-06-01 16:34:21 -04:00
2e3d8c7343
Fix for DataStoreSchema missing the file_id column.
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The file_id column is a foreign key.
2021-06-01 13:51:10 -04:00
1ed144536f
New method for file datastore api endpoint
2021-06-01 13:50:04 -04:00
e9fe555e05
New `/datastore/file/{file_id}` endpoint definition
2021-06-01 13:49:21 -04:00
8c04e228e9
Add test and fix to make sure that an empty study associates list (or a blank list) will effectively clear the extra study associates
2021-06-01 11:46:43 -04:00
a5d67bb245
337 partial fix
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if the user calls the file_data_set function for a valid file with the key 'irb_code' and a value of a valid IRB document code, then we should set the irb code on the file.
2021-05-27 12:24:30 -04:00
acccf3b704
Make sure we are using the correct script engine
2021-05-26 10:50:20 -04:00
384da075ef
Removed references to `protocol` from the description
2021-05-20 11:54:12 -04:00
ef7ee284b2
Prefer tasks that share a parent over just the the next available task when returning the next_task in the workflow processor.
2021-05-19 16:26:16 -04:00
77f7fec5d4
Merge pull request #312 from sartography/study-is-none-329
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Study is none #329
2021-05-14 16:33:04 -04:00
668e2f4e3c
Merge pull request #313 from sartography/feature/add_file_data_store_properties_to_file
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Assure that any data store values associated with a file come back as…
2021-05-14 16:30:35 -04:00
ce7c07679b
SonarCloud
2021-05-14 15:52:30 -04:00
8e37f27399
Assure that any data store values associated with a file come back as a part of the get_study_data[documents
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] endooint.
2021-05-14 15:52:25 -04:00
a9e3f7c861
Standalone workflows do not have a study_id, and we do not record task events for them.
2021-05-14 15:34:29 -04:00
4d7ce5eda9
Merge pull request #311 from sartography/deprecate-study-info-protocol-261
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Deprecate study info protocol #261
2021-05-14 14:14:18 -04:00
7e6645db89
Merge branch 'dev' of github.com:sartography/cr-connect-workflow into dev
2021-05-14 14:10:19 -04:00
427875b8dd
upgrading Sartography libraries, and fixing a potential error where a file can't be located in the documents.xslt
2021-05-14 14:10:14 -04:00
ade7812540
Merge pull request #310 from sartography/get-primary-workflow-301
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Get primary workflow #301
2021-05-14 12:41:48 -04:00
6a34fc0cde
Merge pull request #309 from sartography/persist-read-only-data-324
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Persist read only data #324
2021-05-14 12:38:48 -04:00
1d28d602d5
Merge pull request #308 from sartography/get-dashboard-url-230
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Get dashboard url #230
2021-05-14 12:36:40 -04:00
415964806d
Merge pull request #307 from sartography/standalone-set-default-false-323
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Set the default for the `standalone` parameter to `false`. #323
2021-05-14 12:33:33 -04:00
99da502912
Merge branch 'dev' into 321-Markdown-Macro
2021-05-14 12:32:41 -04:00
a1bb30e689
Switching from using "default" to "server_default" for all default time settings, and running migrations so that this is set at the database level rather than in python, to hopefully correct some issues with dates being 4 hours in the future. Having a very hard time replicating this issue locally.
2021-05-14 12:28:50 -04:00
9b24ad319b
Removed the `get_protocol` method from study_service.
2021-05-13 16:29:34 -04:00
d189b84ba1
Removed `protocol` as an option in the study_info script
2021-05-13 16:22:42 -04:00
8a6bef5af4
New service to get the `primary workflow` for a workflow_spec, using a workflow_spec_id.
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This is necessary because `primary` is a file parameter, not a workflow_spec parameter.
- you can ask a workflow file whether it is primary, but
- you cannot ask a workflow_spec for its primary workflow file
Now, you can use `workflow_service.get_primary_workflow(workflow_spec_id)`
2021-05-12 13:51:51 -04:00
07f3d2c2ee
Allow data from read-only fields to persist in task_data
2021-05-07 14:06:53 -04:00
5efb1a72ce
Changed URL to use HTTPS instead of HTTP
2021-05-06 15:52:27 -04:00
09a395fa34
Start for ticket 230 - Get Dashboard URL
2021-05-06 14:07:21 -04:00
6b242c07e2
Set the default for the `standalone` parameter to `false`.
2021-05-06 11:54:04 -04:00
620b9a5188
Fixing a regression. It's critical that Spiffworkflow's box implement deepcopy, as this is used by Jinga prior to generating a word document.
2021-05-05 21:36:57 -04:00
5a79b80f32
fixes #322 , do not error out deleting files that have assocaited data stores, just remove the data store.
2021-05-05 20:21:33 -04:00
7831bef050
Don't fail the sync completely when a remote file does not exist.
2021-05-05 15:59:00 -04:00
cbd1d01203
Add URL to the study_info('documents') script
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fixes #321 - I merged in branches that fix #320 and #297
320-add-default-for-file-data-get
297-filename-in-documents
2021-05-05 11:30:08 -04:00
7ed30ef25a
Merge branch '320-add-default-for-file-data-get' into 321-Markdown-Macro
2021-05-05 11:13:01 -04:00
8f28970f92
Resolving an alembic conflict.
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Upgrading libraries, and resolving issues from that upgrade, including changes to how we manage tokens. This seems to be working locally.
2021-05-04 13:39:49 -04:00
8b0afa4437
Merge pull request #304 from sartography/irb-info-script-307
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Irb info script #307
2021-05-04 11:40:52 -04:00
7b3287f67b
Save a sample file while I try to figure out how the JS is going to work
2021-05-04 11:32:34 -04:00
34759a2f3d
Merge branch 'dev' into feature/performance-refactor
2021-05-04 11:30:13 -04:00
4780240103
Merge pull request #302 from sartography/320-add-default-for-file-data-get
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Add default capability to file_data_get script
2021-05-04 11:28:40 -04:00
d6054a9846
Merge branch 'dev' into 310-task-event-timezone
2021-05-04 11:21:36 -04:00
81467d6a8d
Merge pull request #299 from sartography/297-filename-in-documents
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Add filename to files listing.
2021-05-04 11:19:59 -04:00
d68f319cf7
Merge pull request #298 from sartography/316-Shield-Test-Error
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Emulate checks on keyword arguments and then return. Validate only sh…
2021-05-04 11:18:36 -04:00
77d9bfca43
Merge pull request #296 from sartography/launch-workflow-outside-study-204
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Launch workflow outside study 204
2021-05-04 11:16:08 -04:00
7689281d68
Fixed typo. Response should be list, not dict.
2021-05-03 14:52:29 -04:00
804926dbac
Fixed problem where WorkflowService.make_test_workflow did not add a study to the workflow_model
2021-05-01 15:55:20 -04:00
060ee5076d
New script to get IRB Info for a study
2021-05-01 15:52:41 -04:00
22b3230243
Added service `get_irb_info` to `crc.services.protocol_builder.ProtocolBuilderService`
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Added environment variable `PB_IRB_INFO_URL` for new `get_irb_info` service
2021-05-01 15:20:47 -04:00
a719cf4bf9
When retrieving the study, only update the status of underlying workflows if specifically requested.
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Record the size of a file in the database for quick access (this helps with a frontend refactor, so it isn't downloading the file just to see it's size)
Cleaning up the timing/performance metric reporting to make it easier to read.
Fixing a bug that prevented non-admins for getting the document-directory
2021-04-30 11:55:12 -04:00
7608a889fb
Add default capability to file_data_get
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script
2021-04-30 10:11:50 -04:00
24c818bf31
Added study_id to workflow_api
2021-04-29 14:29:21 -04:00
2b9cee6b89
Update database to include timezone and change all points where we set the time on an event to be utc time. If we get something in the database with a timezone, it will display properly on the front end, but by default everything will be put in the database in UTC
2021-04-29 10:25:28 -04:00
cc77a9182c
Add filename to files listing.
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Fixes #297
2021-04-28 10:37:14 -04:00
dc6f1cc80d
Emulate checks on keyword arguments and then return. Validate only should have no side effects so the previous behavior was a bug.
2021-04-28 10:03:52 -04:00
c029dad688
Convert some datetime columns to include timezone
2021-04-28 10:00:22 -04:00
71a63c049d
Merge remote-tracking branch 'origin/dev' into dev
2021-04-27 12:16:36 -04:00
248ca6a33a
Don't require people to be admins just so they can see the list of documents, or we get recursive loads on Kelly's non admin account (and everyone elsees)
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todo: Create a ticket to assure we don't get in an infinite loading loop.
2021-04-27 12:14:37 -04:00
799747d638
Add filter for non-active studies so that the events for them do not get returned to the front end for the 'InProgress' data pane.
2021-04-27 12:13:49 -04:00
21e95b106d
Merge pull request #295 from sartography/299-document-datastore
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Add file_data_get and file_data_set functions that can be accessed in…
2021-04-26 12:49:46 -04:00
047c68b2b5
Just some quick tidying up. Dropping commented out code, and using the SQLAlchemyAutoSchema to handle serializing db models
2021-04-26 12:31:22 -04:00
39fcab3730
Merge branch 'dev' into launch-workflow-outside-study-204
2021-04-26 10:27:32 -04:00
40ee20ecca
Add file_data_get and file_data_set functions that can be accessed in a bpmn script function
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Fixes #299
2021-04-26 09:55:28 -04:00
d3d7eeb309
Add file_data_get and file_data_set functions that can be accessed in a bpmn script function
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Fixes #299
2021-04-26 09:41:14 -04:00
077b68c1e2
When creating a workflow for a study, set the user_id to None
2021-04-26 08:46:19 -04:00
f17a9dc0f4
Modified `get_users_assigned_to_task`.
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If we are running a standalone workflow, only return the current user.
2021-04-26 08:45:08 -04:00
b6f5001687
Added methods for the 2 new api endpoints
2021-04-26 08:43:14 -04:00
22432aaf2c
study_id is no longer required for task events
2021-04-26 08:36:09 -04:00
c0655c9d03
Added `standalone` column to workflow_spec
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Added `user_id` column to workflow
2021-04-26 08:33:55 -04:00
fa818bd751
Code for the 2 new api endpoints
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Also modified `update_task` so that it no longer requires a study_id
2021-04-26 08:31:12 -04:00
5936b2e8ef
Created 2 api endpoints; one to get a workflow from a workflow spec, and one to list all standalone workflow specs.
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Also added `standalone` argument to workflow_spec schema properties
2021-04-26 08:27:24 -04:00
dd7c5fd1c1
Fixes #306 assure that we take the doc_code into account if passed in as an argument to the API for get_files.
2021-04-23 16:16:19 -04:00
cf051a7d4f
Merge branch 'dev' into 277-Document-pane
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# Conflicts:
# crc/api/file.py
2021-04-21 14:09:44 -04:00
ecff7d20d3
Adding a test for the new endpoint and cleaning up the API documenation
2021-04-21 14:00:19 -04:00
19e94da6b6
Fix slight bug in expansion code,
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a non-expanded node was causing all parent levels to not expand.
2021-04-20 11:11:11 -04:00
e2197ddab9
Changes to support the frontend data pane
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fixes #277 and requires frontend branch 277-document-pane
2021-04-20 08:12:27 -04:00
277beb345f
Merge pull request #290 from sartography/auto-set-primary-bpmn-142
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Auto set primary bpmn #142
2021-04-16 13:36:02 -04:00
2374400542
Automatically set the first workflow for a workflow_spec to primary
2021-04-15 12:39:12 -04:00
91e80d01bc
Added delete_files argument to the workflow_processor reset method.
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Added code to delete the files when delete_files is True.
2021-04-15 11:25:58 -04:00
3332b9c7c0
Added delete_files argument to the restart_workflow api method, and pass it along to WorkflowProcessor.reset
2021-04-15 11:23:20 -04:00
4615649938
Added delete_files argument to the workflow restart api endpoint
2021-04-15 11:21:51 -04:00
949f3be403
give an endpoint to return all files associated with a study
2021-04-12 12:23:33 -04:00
6427a54d74
Set the correct default value on enumerations - if it is a multi-select enum (checkbox is set) then it should return a default value of an empty array, and not a dictionary.
2021-04-09 08:40:58 -04:00
41310b6879
Allow both a keyword argument, a single argument when calling delete_file. And call it "delete_file" to be more conssitent with existing scripts.
2021-04-08 13:42:17 -04:00
611c72f431
Merge pull request #284 from sartography/delete-uploaded-file-script-283
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Delete uploaded file script #283
2021-04-08 12:42:30 -04:00
f8428378e2
You can now delete a document or list of documents.
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Also, refactored the fancy bits into `process_document_deletion`
2021-04-05 15:11:06 -04:00
f0f5cff8d7
Added some checks to do_task to look for valid irb_doc_code and whether or not we found a file
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Added code for do_task_validate
2021-04-05 13:15:09 -04:00
4fd8fd13f8
Remove approvals from the study_info script. It was broken, and isn't really possible in this way anymore
2021-04-05 12:52:23 -04:00
501487b31c
Assure we convert to box for validations as well, and test the bloodly snot out of this.
2021-04-05 12:47:50 -04:00
727aa72e18
Fix a bug from recent performance improvments - be sure that our study info script returns dicts that can be referenced immediately with dot notation, as this is a common pattern in our bpmn script tasks.
2021-04-05 11:31:06 -04:00
9317e49e65
Merge branch 'dev' into delete-uploaded-file-script-283
2021-04-05 10:40:33 -04:00
0eb6291740
Script to delete an IRB document. Takes an `irb_document` argument.
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Deletes all files associated with the workflow with that IRB document code
2021-04-05 08:55:02 -04:00
dcb4e7b736
fixing an error by taking a bit of the magic out of one of Mike's regex hinting tools. I figure the hint is still good, and a little less bittle, and all the information is already there if people need to dig.
2021-04-02 17:58:27 -04:00
3ad3a086ba
Merge branch 'dev' into 263-optimize-dashboard
2021-04-02 17:12:02 -04:00
2100f27976
fixing the api.yml file which was starting to throw errors when updating the libraries.
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Seems that sqlalchemy now has a hard time incrementing sequences, so putting in a fix for this.
Upgrading many of our libraries, to avoid any disconnects as we try to handle security patches from these automated bumps.
2021-04-02 17:10:05 -04:00
d7894f43b6
These changes relate to changes in PB Mock ticket 273, where we removed Q_COMPLETE as a column in the PB Mock Study table. It is now a relationship.
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Here, we removed Q_COMPLETE from ProtocolBuilderStudy and ProtocolBuilderStudySchema definitions to accommodate the PB Mock changes.
***This push will need to be coordinated with ticket 273***
2021-04-02 12:01:00 -04:00
116bf5e7aa
Merge branch 'dev' into 263-optimize-dashboard
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# Conflicts:
# crc/services/study_service.py
2021-03-31 10:20:33 -04:00
9084866015
Update error message - it may be that we should spend a bit and see if we can make the Box error
2021-03-31 10:17:08 -04:00
mike cullerton
Kelly McDonald
Dan
Mike Cullerton