79c69037dd
Filter out Library categories from the list returned
2021-07-08 08:57:40 -04:00
d6f9b013f7
Change `irb_documents` to `documents`
2021-07-07 12:54:03 -04:00
23180908c8
Undo change. Wrong branch
2021-07-07 12:43:51 -04:00
c39e08972d
Change irb_documents to documents
2021-07-07 12:42:01 -04:00
3c52453c26
Merge branch 'dev' into add-name-error-hint-8
2021-07-07 11:35:24 -04:00
2ed436327f
Merge pull request #333 from sartography/check-study-script-273
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Check study script #273
2021-07-07 11:28:32 -04:00
db9b228735
Merge pull request #334 from sartography/WaitingEventsHotPatch
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Make a change so that anything that has a waiting event is labeled in…
2021-07-07 11:27:10 -04:00
2a45f2fcda
Merge branch 'dev' into add-name-error-hint-8
2021-07-07 11:24:00 -04:00
b0cf74fa3d
Merge branch 'dev' into add-by-user-61
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# Conflicts:
# tests/files/test_files_api.py
2021-07-07 10:46:50 -04:00
c11b5cfb29
Add user_uid to api output
2021-07-07 08:18:02 -04:00
fb54edac1c
Adding additional details to error messages, and cleaning up the cruft around these messages to keep them clear and succinct.
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Most noteable is the addition of the line on which the error occurs for script tasks. It will report the line number and pass back the content of
the line that failed.
The validator only returns the first error it encounters, as it's clear that all we ever get right now is two of the same error.
Did a lot of work between this and spiffworkflow to remove all the places where we obfuscate or drop details as we converted between workflowExceptions and APIExceptions.
Dropped the python levenshtein dependency, in favor of just rolling a simple one ourselves in Spiffworkflow.
2021-07-07 00:53:49 -04:00
894377a607
Add user_uid to FileDataModel calls
2021-07-06 17:09:00 -04:00
23be257db0
Add user_uid column to file_data table
2021-07-06 17:07:47 -04:00
a9805ad40c
Adding some documentation for clarity.
2021-07-06 14:40:20 -04:00
cafdc4d100
Removing an unneeded modification to the database structure for lookup tables.
2021-07-06 14:02:07 -04:00
04842aa66b
Undo change to 1 minute.
2021-07-06 13:13:07 -04:00
7aa4b0833c
Merge remote-tracking branch 'origin/dev' into feature/documents_xls_refactor
2021-07-06 13:11:08 -04:00
1b1a994360
Refactoring Reference files to use the lookup table, rather than parsing the results directly out of the spreadsheet, or attempting to cache them.
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Adding a DocumentService to clean up the FileService, and get Documents well seperated, as it seems likely be pulled out or seperated in the future, there is now a Documents api file as well, for the same reason.
Some other minor changes are just fixing white space to assure our code is linting correctly.
I removed _create_study_workflow_approvals from the base test, as we don't use approvals like this anymore.
2021-07-06 13:10:20 -04:00
9803a04d6d
Make a change so that anything that has a waiting event is labeled in the database as waiting, even if it is sitting around waiting on a user input task that is ready
2021-07-06 11:46:47 -04:00
dce1d86e93
commit changes before looking at something else
2021-07-06 10:34:57 -04:00
f647390e1c
Added description and validate_only
2021-07-02 15:51:24 -04:00
9690c69b6c
added check_study method to protocol_builder service for new endpoint
2021-07-02 15:25:33 -04:00
cd26654b3a
Script to call new pb mock api endpoint `check_study`
2021-07-02 15:21:35 -04:00
db44882733
When we encounter a name error running a script, look in the task data and see if there is a variable with a similar name.
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If a variable with a similar name exists, add it to the ApiError as a hint
2021-07-01 15:38:45 -04:00
98d641f54d
Merge branch 'dev' into partial_testing
2021-06-30 16:13:31 -04:00
508ef1ff2b
Readded exit_at to workflow param
2021-06-30 11:15:48 -04:00
9a32fadc2f
Merge branch 'dev' into 346-waiting-task-schedule
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# Conflicts:
# Pipfile.lock
# crc/services/workflow_service.py
2021-06-30 10:14:37 -04:00
a79ba22410
fixes to get the tests passing. We were missing a dependency in the Pipfile and the data_store had some invalid imports.
2021-06-30 10:06:57 -04:00
2ba52a7095
Merge remote-tracking branch 'origin/HEAD' into partial_testing
2021-06-29 11:21:49 -04:00
187221537b
fixing a corner case around file_data attributes.
2021-06-25 16:18:28 -04:00
628a587d97
We weren't committing to the database in the correct spot, so the delete wasn't sticking, and we were ending up with test workflows showing up in the main interface.
2021-06-23 16:39:58 -04:00
48bf721b23
Merge pull request #331 from sartography/bug/356_duplicate_workflow
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Bug/356 duplicate workflow
2021-06-22 17:42:24 -04:00
92ca506c8e
Calls to eval no longer return the data, rather it will accept and return a key, allowing the front end to cache similar queries and not re-execute them.
2021-06-22 17:23:18 -04:00
61ad371680
Clean up the file api so we don't have a bunch of extra stuff in there. Just include the raw data from the document spraedsheet if it is available.
2021-06-22 15:08:08 -04:00
1f3febe2df
Fix the panda warnings, which means we only support xlsx files now.
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Include the document details when reutnring a file from the file model.
Improve the validation of file form elements.
2021-06-22 14:58:52 -04:00
369b518384
Removed WorkflowService.delete_test_data()
2021-06-22 11:29:00 -04:00
07eb3f9ca8
Moving metrics into SpiffWorkflow so we can run the performance metrics deeply across both systems simultaniously.
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Upgrading libraries.
Fixing deprication issue with Pandas and numpy.
We can only process xlsx files now, plain oldschool xls is fully removed.
2021-06-18 16:41:55 -04:00
4ca94b39ce
Merge branch 'dev' of https://github.com/sartography/cr-connect-workflow into partial_testing
2021-06-17 15:12:28 -04:00
19d63e2aa2
Merge pull request #328 from sartography/restart-workflow-programmatically-347
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Restart workflow programmatically #347
2021-06-17 10:36:46 -04:00
a4caae8d64
when validating, we need to take every step to remove the workflows we create during the validation.
2021-06-16 14:40:20 -04:00
acae6030f5
The API for evaluating python expressions should not raise an error, it can simply return a result of false, and provide an error to explain the problem. In this way the front end doesn't error out when it's running the script tasks but doesn't have enough information to get a valid response back.
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The validation should take into account that repeating sections must be evaluated in the context of the data within the repeating section, not outside of it.
2021-06-15 16:17:15 -04:00
02949dc6e2
WorkflowProcessor handles this error
2021-06-15 11:12:50 -04:00
5c5b966bc4
Merge branch 'dev' of https://github.com/sartography/cr-connect-workflow into partial_testing
2021-06-15 09:11:18 -04:00
c8f8888c17
Script to reset workflow. Requires workflow spec name.
2021-06-14 14:51:16 -04:00
738a984dcd
Merge branch 'dev' of github.com:sartography/cr-connect-workflow into dev
2021-06-11 17:21:47 -04:00
879d6e1df3
missed a critical change on the backend with the recent file updates, this assures that we properly handle repeating sections during the post process,
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and we update the file doc code in those repeating sections.
2021-06-11 17:20:25 -04:00
7282419174
modified the tools api to return the expression and data with the result, making it easier to cash results on the front end, This should help drastically reduce the calls to the python_eval from the front end.
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The post processors for form submissions needs to take repeating sections into account, or it won't find the files it is looking for.
2021-06-11 08:27:50 -04:00
394906d840
Add refresh_waiting_tasks to the processor do_engine_steps so that if we have a waiting task that has met its condition prior to the scheduler running, it will go ahead and proceed
2021-06-10 08:33:24 -04:00
e1a4a79b03
Added Partial Workflow spec
2021-06-09 15:21:21 -04:00
2364c240b2
Error Text Changed
2021-06-09 14:54:43 -04:00
338fe30984
Merge branch 'dev' of https://github.com/sartography/cr-connect-workflow into partial_testing
2021-06-09 14:32:01 -04:00
17077be701
exit at task
2021-06-09 12:40:38 -04:00
5f722d675f
Add a function that gets runs via a background scheduler to look for any workflows that are in a 'waiting' state - it runs the update waiting tasks and does do_engine_steps
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We have a test for the function that runs, but an assumption was made that the scheduler module has its own unit tests and we do not need to test that.
fixes #346
2021-06-09 10:42:34 -04:00
fce9166c4a
Do not require users to be admins for viewing the document directory tab.
2021-06-09 09:51:30 -04:00
0d8d251e8e
Temp save to test dev
2021-06-09 09:24:37 -04:00
286803d10b
fixing a big stupid bug I created when merging all the code and making changes to the files.
2021-06-08 14:24:59 -04:00
586a0f2f1a
Merge pull request #325 from sartography/feature/file_refactor
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Prefer tasks that share a parent over just the the next available tas…
2021-06-08 11:28:23 -04:00
8d79fe9d94
Fixing failing tests, and now asserting that we only perform the post_process_form if we actually have a form.
2021-06-08 11:16:10 -04:00
9c4994581d
Merge pull request #324 from sartography/modify-infinite-loop-312
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Modify infinite loop #312
2021-06-08 10:30:13 -04:00
e10b210302
Merge pull request #323 from sartography/shield-test-issue-344
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Shield test issue #344
2021-06-08 08:59:58 -04:00
a7b208f50a
Merge pull request #322 from sartography/data-store-refactor-330
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Data store refactor #330
2021-06-08 08:58:53 -04:00
6937c33719
Merge pull request #319 from sartography/datastore-file-endpoints-325
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Datastore file endpoints #325
2021-06-08 08:54:43 -04:00
37d4e7cc79
Merge pull request #318 from sartography/340-update_study_associate_change
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Add test and fix to make sure that an empty study associates list (or…
2021-06-08 08:52:44 -04:00
c4a6fbb516
Merge pull request #317 from sartography/337-Data-Store-IRB-Code
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337 partial fix
2021-06-08 08:51:09 -04:00
5881c903ca
Merge pull request #316 from sartography/326-Multi_File_Data_Store
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Make sure we are using the correct script engine
2021-06-08 08:49:43 -04:00
710921cfe1
Merge pull request #314 from sartography/deprecate-study-info-protocol-261
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Remove protocol from study_info script #261
2021-06-08 08:47:43 -04:00
59f605c3df
Prefer tasks that share a parent over just the the next available task when returning the next_task in the workflow processor.
2021-06-08 08:03:14 -04:00
a3a485dd34
Changed do_task_validate_only so it returns a mocked value, instead of True/False.
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True/False caused problems for workflow validations
2021-06-04 11:44:55 -04:00
9a63ab9c4f
Change `do_task_validate_only` in study_info script to call the real do_task.
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We do this so we can seed settings into the workflow for testing different scenarios using the study from validate_study_id
2021-06-03 14:28:24 -04:00
c41657301a
Modify `test_spec` and `make_test_workflow` to accept new optional `validate_study_id` parameter.
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Modify `make_test_workflow` to use study_id when creating test workflow for validation.
2021-06-03 14:22:26 -04:00
0dfc96d7f6
Modified `validate_workflow_specification` to accept new optional `validate_study_id` parameter.
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We then pass validate_study_id on to WorkflowService.test_spec
2021-06-03 14:19:41 -04:00
d657744816
Added optional `validate_study_id` parameter to the validation api endpoint.
2021-06-03 14:17:12 -04:00
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
Kelly McDonald
mike cullerton
Dan Funk
Mike Cullerton
NWalker4483