deb16740f6
First attempt at creating dmn from spreadsheet.
...
xml template and example spreadsheet
2021-08-02 10:04:25 -04:00
e1aee0f635
First attempt at creating dmn table from spreadsheet.
...
Starting as a script
2021-08-02 10:03:10 -04:00
41ad7935f8
Merge branch 'dev' into 367-Call-Activity
...
# Conflicts:
# Pipfile.lock
2021-07-29 09:28:21 -04:00
217e61eed3
next_task returns the next available task, except when the task is completed when it returns the EndEvent -
...
The problem was that it was returning the first EndEvent it found, not the last one. This caused a problem when we had a CallActivity which has its own EndEvent.
Fixes #399
2021-07-27 09:19:08 -04:00
b857fddbad
commit in intermediate changes to work on a bug
2021-07-26 13:00:11 -04:00
25e00823a7
Merge pull request #342 from sartography/enum-file-data-375
...
Enum file data #375
2021-07-23 13:47:57 -04:00
4c8a86f9bf
Fixed bug where processing file data only worked for enums.
2021-07-23 11:24:17 -04:00
7f5c7417d8
Print out some additional debugging information in the email script so we can tell what is happening and where.
2021-07-22 16:02:08 -04:00
38b8c7fcdf
Fixed email_cc test
2021-07-22 15:08:28 -04:00
b94d49076d
Fixed Associate API Endpoint description
2021-07-22 14:36:00 -04:00
90425ebbb3
Merge branch 'bug/missing_pi_name_246' of https://github.com/sartography/cr-connect-workflow into bug/missing_pi_name_246
2021-07-22 14:09:34 -04:00
a73d1794eb
Fixed Associate API Endpoint description
2021-07-22 14:09:24 -04:00
61504664d4
Merge pull request #346 from sartography/bug/346_timer_fails_to_send_email
...
fixes #346 , allow emails to fire in scheduled events
2021-07-22 13:40:12 -04:00
2009a794ea
We were depending on an active http request existing in order to fire emails, using that request to determine the front end url. We have the frontend url in our config file, and we don't have a request object when running scheduled tasks, so I just use our configuration setting instead.
2021-07-22 13:25:06 -04:00
1cfb7f96fa
Missing uid declaration in study service corrected
2021-07-22 11:28:11 -04:00
8df1145471
Modify the LDAP service to only use lowercase UIDs.
...
UVA always returns the UID as lowercase.
This caused a postgres unique value problem for us.
2021-07-22 10:46:09 -04:00
428802b9d0
Modify LDAP script so that it doesn't raise an error when we don't get a record back from LDAP.
...
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
...
# 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.
...
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
...
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
...
Restrict loaded studies #374
2021-07-12 10:11:34 -04:00
7070761089
Merge pull request #338 from sartography/document-spreadsheet-name-380
...
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.
...
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
...
Check study script #273
2021-07-07 11:28:32 -04:00
db9b228735
Merge pull request #334 from sartography/WaitingEventsHotPatch
...
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
...
# 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.
...
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.
...
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.
...
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
...
# 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
...
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.
...
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.
...
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
...
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.
...
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,
...
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.
...
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
...
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
...
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
...
Modify infinite loop #312
2021-06-08 10:30:13 -04:00
e10b210302
Merge pull request #323 from sartography/shield-test-issue-344
...
Shield test issue #344
2021-06-08 08:59:58 -04:00
a7b208f50a
Merge pull request #322 from sartography/data-store-refactor-330
...
Data store refactor #330
2021-06-08 08:58:53 -04:00
6937c33719
Merge pull request #319 from sartography/datastore-file-endpoints-325
...
Datastore file endpoints #325
2021-06-08 08:54:43 -04:00
37d4e7cc79
Merge pull request #318 from sartography/340-update_study_associate_change
...
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
...
337 partial fix
2021-06-08 08:51:09 -04:00
5881c903ca
Merge pull request #316 from sartography/326-Multi_File_Data_Store
...
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
...
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.
...
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.
...
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.
...
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.
...
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.
...
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
...
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
...
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
...
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
...
] 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
...
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
...
Get primary workflow #301
2021-05-14 12:41:48 -04:00
6a34fc0cde
Merge pull request #309 from sartography/persist-read-only-data-324
...
Persist read only data #324
2021-05-14 12:38:48 -04:00
1d28d602d5
Merge pull request #308 from sartography/get-dashboard-url-230
...
Get dashboard url #230
2021-05-14 12:36:40 -04:00
415964806d
Merge pull request #307 from sartography/standalone-set-default-false-323
...
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.
...
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
...
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.
...
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
...
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
...
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
...
Add filename to files listing.
2021-05-04 11:19:59 -04:00
d68f319cf7
Merge pull request #298 from sartography/316-Shield-Test-Error
...
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
...
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`
...
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.
...
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
...
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.
...
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)
...
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
...
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
...
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
...
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`.
...
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
...
Added `user_id` column to workflow
2021-04-26 08:33:55 -04:00
fa818bd751
Code for the 2 new api endpoints
...
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.
...
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
...
# 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,
...
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
...
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
...
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.
...
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
...
Delete uploaded file script #283
2021-04-08 12:42:30 -04:00
f8428378e2
You can now delete a document or list of documents.
...
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
...
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.
...
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.
...
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.
...
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
...
# 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
60f5be1aef
Check in - pending change from @cullerton
2021-03-30 12:10:49 -04:00
b5d4df595f
Merge pull request #271 from sartography/master-workflow-status-messages-222
...
Master workflow status messages 222
2021-03-26 20:52:24 -04:00
ded11ddd82
fixing a code smell
2021-03-26 20:25:34 -04:00
e79e810ae1
Merge pull request #273 from sartography/modify-email-template-215
...
Change location of `CR Connect` string. Move it left, closer to the logo
2021-03-26 19:50:16 -04:00
123ec50912
Merge pull request #272 from sartography/infinite-validations-262
...
Infinite validations 262
2021-03-26 19:49:42 -04:00
b64b52e7cb
Assure that we properly return the new status message over the api calls.
2021-03-26 19:47:31 -04:00
ac4877fecf
Merge remote-tracking branch 'origin/dev' into master-workflow-status-messages-222
2021-03-26 17:47:57 -04:00
d9bf2a8a81
Change location of `CR Connect` string. Move it left, closer to the logo
2021-03-23 13:12:13 -04:00
f1ca44a0e1
Add primitive cache on the fileservice is_review, halves the time of loading the list on the primary dashboard
2021-03-23 10:17:48 -04:00
a201e49d21
The master workflow now generates a dictionary of dictionaries, rather than a dictionary of strings.
...
Each entry in status is a dictionary with 'status' and 'message' keys.
We updated the StudyService._update_status_of_workflow_meta method to accommodate the master workflow changes.
Changed the order of some if statements so we move forward while we have good data, and run all the error states at the end.
Added some comments to explain the cascading if statements
We changed the names of private methods to begin with one underscore, so they work in the test environment.
Changed some internal calls to accommodate the underscore change.
2021-03-22 17:46:39 -04:00
a08c6b794f
Updated Study Associate Endpoints
2021-03-22 17:30:49 -04:00
6ab98c1dee
Merge pull request #267 from sartography/get-study-associates-validation-242
...
The `do_task_validate_only` method in the `get_study_associates` scri…
2021-03-19 15:41:46 -04:00
544f4a4418
Merge pull request #266 from sartography/study-associated-email-207-223
...
We now perform an LDAP lookup for the associated user email addresses…
2021-03-19 15:40:31 -04:00
938079cf59
Lowered count ceiling to 100, from 1000. This significantly increased validation time, from about 3 minutes to about 10 seconds.
...
Changed ApiError call to from_task, instead of from_workflow_exception.
2021-03-17 14:52:19 -04:00
e2ba19748d
Added department chair to the mocked data for study_info script.
...
The missing department chair caused an infinite loop in a workflow that checked for a department chair.
2021-03-16 13:36:55 -04:00
529bfc34b3
We now check for an infinite loop during validation.
...
This happened when testing for a Department Chair in a workflow.
Our mocked data for study_info script did not have a Department Chair
2021-03-16 13:35:51 -04:00
c05b879dd4
We want to modify the master workflow so that it returns both a status, and a message explaining the status for each workflow.
...
I.e., from status = {'ids_full_submission': 'required',
'enter_core_info': 'disabled',
...}
to status = {'ids_full_submission': {'status': 'required', 'message': 'required because...'},
'enter_core_info': {'status': 'disabled', 'message': 'disabled because...'},
...}
Modified study_service.__update_status_of_workflow_meta to accommodate this change.
2021-03-16 12:09:42 -04:00
70efdb4788
The `do_task_validate_only` method in the `get_study_associates` script now returns a mocked list of associates.
...
It used to return `True`, and this caused shield validation to fail when looping over the results of `get_study_associates`.
(You can't loop over a boolean)
Added a for loop in `study_sponsors_associate.bpmn` to test for this.
Moved `BaseTest` import to the top of `test_study_associate_script` because debug was failing.
2021-03-16 08:57:30 -04:00
dfa65ac276
We now perform an LDAP lookup for the associated user email addresses, instead of looking in the DB user table.
2021-03-15 10:30:23 -04:00
14386b8ba9
Merge pull request #264 from sartography/bug/243_complete_all
...
Bug/243 complete all
2021-03-14 12:34:55 -04:00
0da07675b7
Merge pull request #258 from sartography/study-associated-email-207-223
...
Study associated email 207 223
2021-03-14 12:34:19 -04:00
6f80d816cd
My privous efforts didn't take into account the fact that we use dot notation in field names.
...
I've re-worked the workflow form endpoint, so that it only accepts the data that should be in the form, and ignores any other values that come back from the front end. It seems Formly has some bugs that were introducing confusing information, and I want everything to behave consistently.
I had to re-work some of the tests, which were relying on an ability to set data through a form post without having a corresponding form to do so.
2021-03-14 12:20:39 -04:00
15c64c862e
Adding an argument to update task that will allow it to complete all remaining tasks through an "update_all" flag,
...
this will allow us to remove some fairly complex logic from the front end that isn't behaving properly.
2021-03-12 20:41:07 -05:00
1000b22a3b
Don't raise errors on non-ready tasks that calculate a title, the information may not be avaiable yet.
...
Also Allow autocomplete-num as a valid field property.
2021-03-12 15:40:23 -05:00
ef26238127
added CustomBPMNScriptEngine back in
2021-03-11 14:33:35 -05:00
e7c78c8d0e
Merge branch 'dev' into study-associated-email-207-223
2021-03-11 12:38:47 -05:00
e58f1dc484
Remove unused mails service
2021-03-11 11:56:18 -05:00
fa4707811e
Removed the test and templates from the unused mails service.
...
Mails was removed in previous commit.
2021-03-11 11:34:24 -05:00
67697b5076
Lots of changes!
...
Email Script:
- The email script now accepts 3 keyword arguments; subject, recipients, and cc.
- Subject and recipients are required.
- Recipients (and cc) can be an email address or list of addresses.
- You can use the string 'associated' in place of an email address, in which case we look up the users associated with a study that have send_email set to True.
- Moved some helper methods to email_service.
Email Service:
- Added cc argument
- Added helper methods previously in email script.
- Modified get_rendered_content to accept message and data directly. Previously, we passed in the task and grabbed them from there. Now we can use the method outside a task.
2021-03-11 11:32:21 -05:00
80f1fc276f
Modify api.tools.send_email to accommodate the changes to the api endpoint in api.yml
...
We now accept subject, address, body (the email message), and possible data.
We now use email_service to send the message, and wrap it with the CR Connect html formatting.
**** We import DEFAULT_SENDER from config.default. Will this be a problem on testing and production? ****
2021-03-11 11:19:02 -05:00
14e62a7ec2
Modify the send_email api endpoint (in Configurator Tools section) to accept subject, message, and data.
...
Subject, address and message are required.
Data is not required.
Message is in the body of the request.
Subject, address, and data are in the query string.
2021-03-11 11:10:10 -05:00
d250bac32e
Merge remote-tracking branch 'origin/dev' into dev
2021-03-10 10:59:24 -05:00
2ed825aef3
Fixes problem with swtiching users fixes #237
2021-03-10 10:59:15 -05:00
eaf52a21ca
Merge pull request #260 from sartography/bug/delete_study
...
Allows us to delete a study even if there are emails, and associated …
2021-03-09 13:51:25 -05:00
80ff8a6212
Allows us to delete a study even if there are emails, and associated study users connected to that study.
2021-03-09 13:31:26 -05:00
576aebab19
Sometimes a workflow can be completely broken and unloadable. For instance, it starts off with a engine step / script task that will not execute. So the failure happens the second it is processed. When calling reset on a workflow, we should catch the failure, and reset the workflow, so we aren't trapped in an unrecoverable state.
...
To do so, I changed the WorkflowProcessor's reset method to be static, it will try to instantiate the current workflow and execute a cancel_notify event, but if that fails, it will continue and always return a new workflow processor using the latest spec.
2021-03-09 11:52:55 -05:00
7171219e8b
removed unused import
2021-03-09 07:00:20 -05:00
44ac55bc32
We can now send emails to users associated with a study, by using 'associated' as the recipient
...
We now use keyword arguments in the email script; subject and recipients
2021-03-09 06:49:39 -05:00
36dcc58705
Merge branch 'dev' of github.com:sartography/cr-connect-workflow into dev
2021-03-08 14:00:14 -05:00
291216e081
Fixing a bug that prevented proper evaluation of a enum field where the default value was null or empty.
2021-03-08 14:00:03 -05:00
f883eb2bbe
We now include field.id in the ApiError message for hidden and default validation. (The field must have a default value or value expression)
...
While working on this ticket I found a logic error in the test. I expected both default_value and value_expression. It turns out the default_value is always there, it's just null if we don't set it.
Modified the existing test for hidden and required, and added tests to make sure my passing logic is now correct.
2021-03-04 10:42:13 -05:00
9e758c57d3
Merge branch 'dev' into bug/225_enum_lookup_same_field_name
2021-03-02 14:15:58 -05:00
572eb3457a
Merge pull request #252 from sartography/customer-error-messages-192
...
Customer error messages 192
2021-03-02 13:45:38 -05:00
adb9e3afba
Merge branch 'dev' into bug/225_enum_lookup_same_field_name
2021-03-02 13:40:21 -05:00
c8f5a44050
adding a warning in the logger so we can see when expensive calls are made to rebuild searches for enumerations. But all looks good.
2021-03-02 12:21:51 -05:00
06dedd8a32
Add short_title to study, change update_study task to use kw arguments and add the short_title to the update_study script
2021-03-02 10:03:53 -05:00
9a2ffb98ad
Customer Error is in a place that we can try it out on testing.
...
So far, there are two known errors.
- Missing condition type (Ticket 178)
- Invalid property value in extensions tab for display_name (No ticket for this error)
We now have the option of using regular expressions to pull task_id, etc. from an error to pass back to the user in the hint.
2021-03-01 16:41:55 -05:00
3e0541fa15
Merge pull request #250 from sartography/206-extend-study-access
...
206 extend study access
2021-03-01 14:55:38 -05:00
aac3d5c16e
Bug #255 , this requires the front end to pass in the name of the task, when doing a lookup. This will prevent a bug where we have multiple user tasks, with enum fields that set the same variable, but use different lookup tables to populate the dropbown or search feature.
2021-03-01 14:54:04 -05:00
9d804c36d5
Merge branch 'dev' into customer-error-messages-192.
...
Needed some sql changes from dev
2021-03-01 10:29:10 -05:00
0b08a95e25
Add test and make sure that the API endpoint does the right thing when we switch users - checks both associated with access and associated with no access
2021-02-25 12:20:43 -05:00
5c3d791bf3
UVA asked us to remove the extra whitespace in emails.
...
We removed the string replacement of '\n' -> '<br>' to solve this.
This means you can't purposely add blank lines any more.
Trade offs.
2021-02-25 11:08:08 -05:00
f3414e22c1
use the associated table to grant access to users who have been designated to have access to the study, not just the study owner.
2021-02-25 11:08:06 -05:00
f592a8a0b0
Added a few more tests - I think I need to test one more script endpoint
2021-02-25 09:07:46 -05:00
9bd3aa8dcb
service and scripts with working test - still needs a few more tests to try out, but should work to get Mike going
2021-02-24 12:55:23 -05:00
c795dd7aea
Merge branch 'dev' into 206-extend-study-access
2021-02-24 12:16:35 -05:00
3dbe39c6fe
initial checkin of changes for branch
2021-02-24 12:05:06 -05:00
f937ac3ce9
Getting some thoughts down for the extension property error. This might force us to use regexes for the error service.
...
Committing so I can work on another branch.
2021-02-24 10:56:25 -05:00
0a58dce394
Changes for ticket 215 - Change email header and footer to say CR Connect
2021-02-23 12:13:21 -05:00
349c3d657a
Merge branch 'dev' into 201-changes-to-in-progress
2021-02-22 18:17:59 -05:00
53fa49e668
Merge pull request #243 from sartography/183-remove-study-approval-code
...
Remove Approvals per ticket 183
2021-02-22 18:12:02 -05:00
4fc2929356
Put the preamble back in to the error message.
2021-02-19 15:57:01 -05:00
3b06795c4c
File cleanup for readability. Removed some commented code.
2021-02-19 14:49:53 -05:00
4fa0f9720a
Allow frontend to honor 'view as' and fix problem with tests
2021-02-18 11:25:17 -05:00
8c309e9a41
Add user display name to the response for task events
2021-02-18 08:44:44 -05:00
6fbaecf9b2
Change selection to include task events that are for someone else, but are on a study I own.
2021-02-18 08:09:13 -05:00
f0a921d46d
Merge pull request #242 from sartography/allow-period-in-field-id-199
...
Allow period in field id 199
2021-02-17 15:08:53 -05:00
93f29e86d8
Merge branch 'dev' into STG-181_frontend-ux-model-changes
2021-02-17 07:49:05 -05:00
ff8a44a7b1
Make sure we always have a current user, even if the very first task is a script task.
2021-02-16 12:42:59 -05:00
e54a6956df
Make a change in the case that we have no task_events at all.
2021-02-16 11:10:40 -05:00
118cf62172
Merge remote-tracking branch 'origin/dev' into STG-181_frontend-ux-model-changes
2021-02-16 10:07:34 -05:00
003bf2f9b9
Remove Approvals per ticket 183
2021-02-16 09:05:29 -05:00
3b1dc70558
Add comment for later ticket
2021-02-16 08:44:41 -05:00
ed6218028c
We now allow periods in field ids.
...
Also, added task_id and task_name to the ApiError for missing default value on hidden and required fields
2021-02-15 16:27:56 -05:00
39eb5c5c21
This is a decent beginning framework for customer error messages.
...
It is not complete, but is in a state where we can start to interact with the front end.
Two tests are failing.
Committing so I can work on an error for Alex.
2021-02-12 14:18:42 -05:00
c44e784eb2
Fixing a bug with the user model.
2021-02-12 09:48:41 -05:00
35773ebc29
Merge pull request #240 from sartography/weird-email-error
...
The email script was failing validation because of missing parameters…
2021-02-12 09:31:52 -05:00
7eeb491dfa
User str decode Removed
2021-02-12 09:30:18 -05:00
d8bd203139
The email script was failing validation because of missing parameters in scripts.email.do_task_validate_only.
...
I added a test in tests.test_email_script to make sure we get the default email_address.
I also found and fixed a bug in workflow_service.populate_form_with_random_data where we would overwrite default_values with random text because of a missing continue.
(We don't want to continue if we have repeating fields though.)
2021-02-11 15:36:12 -05:00
fe4e737596
Merge pull request #238 from sartography/value-expression-failing-shield-test-194
...
We now allow value_expression to evaluate to an empty string ("") so …
2021-02-11 11:25:09 -05:00
df0cfc755b
Merge pull request #237 from sartography/get-study-from-model-error-191
...
We now test whether we have a valid StudyModel when getting a study b…
2021-02-11 11:23:59 -05:00
40639bbd03
Merge pull request #236 from sartography/trap-non-api-errors-187
...
New error handler for non Api errors. Ticket 187
2021-02-11 11:22:48 -05:00
df25b83958
Merge pull request #235 from sartography/index-error-for-enums-186
...
Index error for enums 186
2021-02-11 11:21:50 -05:00
10b9c7b892
Merge pull request #234 from sartography/hidden-and-required-fields-185
...
Hidden and required fields 185
2021-02-11 11:20:35 -05:00
f7337f4e54
Merge branch 'dev' of github.com:sartography/cr-connect-workflow into dev
2021-02-11 11:17:56 -05:00
2ada9f6f42
Private Ldap settings
2021-02-11 11:17:21 -05:00
39e874504f
We now allow value_expression to evaluate to an empty string ("") so that we *do not* set a default value for enums in some cases.
...
This was causing an error because "" was not an option for the enum.
2021-02-10 14:35:58 -05:00
8a2a8b1443
Still not in working order. Committing to work on another ticket.
2021-02-10 12:28:59 -05:00
da0af14724
Changes to enable front-end changes
...
Added a human readable name to created user
added last updated task time and name,
added is_review on the workflow which is triggered by a swimlane with a name present.
Notably - it does NOT update or change any of the performance concerns that we were having with this.
2021-02-10 11:58:19 -05:00
777cfbdecd
We now test whether we have a valid StudyModel when getting a study by study model.
...
We raise an ApiError if the model is None or empty.
2021-02-09 17:37:55 -05:00
3e32cdedc4
New error handler for non Api errors. Ticket 187
2021-02-09 16:35:57 -05:00
b42b843f7d
It was possible for an enum field lookup to return an empty list. This meant there were no options for the list.
...
We now test for this and raise an error.
2021-02-08 15:10:53 -05:00
e87e7b5b8b
Form fields that can be hidden and required must now have a default value or value_expression.
...
Also, if a field is hidden but not required, it should not produce a value.
2021-02-08 10:18:41 -05:00
fa34bee18a
First commit for cleaning up error messages for customers.
...
This is *not* in a working state.
Committing this so I can work on another ticket.
2021-02-04 11:23:05 -05:00
329146237e
Merge pull request #232 from sartography/boolean-default-values-175
...
Boolean default values 175
2021-02-03 16:34:54 -05:00
effd11f947
Merge pull request #231 from sartography/cancellations-137
...
Cancellations 137
2021-02-03 16:31:18 -05:00
2d01b92a50
Merge pull request #230 from sartography/pretty-emails-160
...
Pretty emails 160
2021-02-03 16:20:38 -05:00
mike cullerton
Kelly McDonald
Dan Funk
NWalker4483
Mike Cullerton