428802b9d0
Modify LDAP script so that it doesn't raise an error when we don't get a record back from LDAP.
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We now return an empty dictionary
2021-07-22 10:44:41 -04:00
48516e4009
Parent side working
2021-07-22 10:23:05 -04:00
2455495457
got library side working - still need to have parent working
2021-07-22 10:20:34 -04:00
3906580604
Merges getStudyAssociates() endpoint
2021-07-20 14:25:01 -04:00
a263447806
Merges getStudyAssociates() endpoint
2021-07-20 13:57:32 -04:00
4632c6374f
Merge branch 'dev' into bug/missing_pi_name_246
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# Conflicts:
# crc/api.yml
# crc/services/study_service.py
2021-07-20 11:44:11 -04:00
354e20c34b
Use the data_store_service to set the data_store, rather than access DB directly.
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Pass the label explicitly (as the value)
2021-07-15 13:09:40 -04:00
dd67a5e650
Never set the date to datetime.utcnow() on DateTime fields. We want this to fall back on the func.now() method and allow the database to set the time on insert.
2021-07-12 15:58:32 -04:00
522ca9d164
Merge pull request #340 from sartography/bug/better_errors_on_scheduled_tasks
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Assure we log reasonably clear errors when executing scheduled tasks …
2021-07-12 10:13:02 -04:00
d1bf370a39
Merge pull request #339 from sartography/restrict-loaded-studies-374
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Restrict loaded studies #374
2021-07-12 10:11:34 -04:00
7070761089
Merge pull request #338 from sartography/document-spreadsheet-name-380
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Document spreadsheet name #380
2021-07-12 10:11:16 -04:00
f982745d32
fixing a failing test, don't assume the study and workflow ids will always be 1.
2021-07-12 10:00:39 -04:00
1916c4ff54
Assure we log reasonably clear errors when executing scheduled tasks in the background, so that sentry can pick them up and they can be addressed effectively.
2021-07-12 09:43:12 -04:00
690c059335
get_studies_for_user is no longer a static method
2021-07-09 10:37:57 -04:00
dad2de9f0c
get_user_studies now checks study_details['REVIEW_TYPE'] before displaying a study.
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This corresponds to REVIEWTYPENAME being `Full Committee`, `Expedited`, `Non-UVA IRB Full Board`, or `Non-UVA IRB Expedited`
2021-07-09 10:37:25 -04:00
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
mike cullerton
Kelly McDonald
NWalker4483
Dan
Mike Cullerton