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
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
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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
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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
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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.
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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
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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
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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.
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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.
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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.
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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.
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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.
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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
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Bug/243 complete all
2021-03-14 12:34:55 -04:00
0da07675b7
Merge pull request #258 from sartography/study-associated-email-207-223
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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.
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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,
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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.
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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.
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Mails was removed in previous commit.
2021-03-11 11:34:24 -05:00
67697b5076
Lots of changes!
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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
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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.
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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
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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.
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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
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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)
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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
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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.
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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
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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.
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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.
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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.
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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
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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
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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.
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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.
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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
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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.
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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
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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
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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
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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
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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
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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.
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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
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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.
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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.
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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.
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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.
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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
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Boolean default values 175
2021-02-03 16:34:54 -05:00
effd11f947
Merge pull request #231 from sartography/cancellations-137
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Cancellations 137
2021-02-03 16:31:18 -05:00
2d01b92a50
Merge pull request #230 from sartography/pretty-emails-160
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Pretty emails 160
2021-02-03 16:20:38 -05:00
1eba20f420
Merge pull request #229 from sartography/workflow-spec-order-74
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Workflow spec order 74
2021-02-03 16:18:34 -05:00
b090e31e00
This fixes 2 issues with setting boolean defaults
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- If the default was False, we failed an early test and returned None. We now only return None if default is None
- We have a better test for deciding if the default value we return should be True or False. We used to return True if the value was the string 'false'.
2021-02-03 09:50:16 -05:00
c5cf3ea7ff
Changed call to WorkflowProcessor.reset to reflect change from class method to instance method.
2021-01-29 14:34:09 -05:00
7e76639cf3
When a study is put on hold, we now reset workflows and call any pending cancel_notify events.
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In api.study.update_study we test the study status and call the new WorkflowService method process_workflows_for_cancels.
In services.workflow_service we added the new method process_workflows_for_cancels. It loops through workflows for a study, and resets them if they are in progress.
In services.workflow_processor, we changed the reset method to be an instance method so we can call self.cancel_notify.
In tests.test_lookup_service we changed the call to WorkflowProcessor.reset to reflect the change from class method to instance method
2021-01-29 14:05:07 -05:00
958d5a6281
Possible solution for W3C issues raised by Sonarcloud
2021-01-28 09:45:53 -05:00
d7a3afe8f4
changed the template to use the responsive html email template at https://github.com/leemunroe/responsive-html-email-template
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added method get_cr_connect_wrapper to render our new html email template. This takes the email text generated from the task element documentation as the email_body.
2021-01-27 17:12:03 -05:00
cccb722e07
Merge pull request #226 from sartography/enum_default_value_expression_162
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Enum default value expression 162
2021-01-27 10:43:46 -05:00
81e55b6055
Cleaning up my smell. A task should only have default_value *or* value_expresion, not both.
2021-01-27 10:21:13 -05:00
c99a388405
We now set the display_order automatically. Users can modify order using the arrows.
2021-01-27 09:50:29 -05:00
98f946c119
Merge pull request #227 from sartography/missing_form_key_163
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Missing form key 163
2021-01-27 09:42:46 -05:00
ecc553c4ea
Jinja templates and svg file for pretty emails
2021-01-26 09:20:16 -05:00
909af9b8d6
Change HTML emails so they look like the CR-Connect website. Add logo, color, style, etc.
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Cleaned up email script a little.
Also, email script no longer uses services.mails. It uses email_service directly now.
2021-01-26 09:19:28 -05:00
b71fd93dd4
We now make sure that forms have a form key. Ticket 163
2021-01-22 12:14:17 -05:00
00d9276483
In spiff_task_to_api_task, when looping through fields, if the field doesn't have a value, we now try to set it with the default value
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In test_spec, we now check for FIELD_PROP_VALUE_EXPRESSION when setting default values
2021-01-22 10:00:28 -05:00
5921ce9f10
Merge branch 'dev' into 152-workflow-spec-pull
2021-01-21 12:30:43 -05:00
5b13195182
Merge pull request #224 from sartography/restart-with-no-data-99
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Restart with no data 99
2021-01-20 17:22:18 -05:00
41dac33039
Removed two tests around soft_reset that are no longer required.
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Reset should construct the workflow_processor, thus completing the reset process.
Removed the spec argument from init, as it is never used anywhere.
2021-01-20 13:24:53 -05:00
039a1dcd79
WorkflowProcessor code for new restart_workflow api endpoint. WorkflowProcessor.reset will clear workflow_model.bpmn_workflow_json, and if clear_data is True will clear form data.
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WorkflowProcessor.__init__ is mostly unchanged.
2021-01-19 15:14:36 -05:00
9c71a503ca
Python code for new restart_workflow api endpoint. Cleaned up code and docstring in get_workflow to match.
2021-01-19 15:09:20 -05:00
e1532a90c9
New api endpoint for restarting a workflow. Unsure if I needed the responses section. **Dan, can you check this?**
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Also, removed clear_data and reload_spec as parameters for standard get workflow endpoint.
2021-01-19 15:00:39 -05:00
6a9e6d3570
Restart workflow without form data. Committing so Dan can check it out
2021-01-14 15:32:14 -05:00
cf7990ce85
Refactor for better readability due to code smell test
2021-01-12 08:54:32 -05:00
e14b896225
Add documentation
2021-01-11 09:31:08 -05:00
f282a9ef73
Make sure that top_level_workflow is transferred over, also include reference files in the list of files to sync
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We may want to revisit this because I used a 'Magic' workflow_ref_id of 'REFERENCE_FILES' as a special case so I could re-use most of what I already had. This works well, but we may want to structure it different.
2021-01-11 09:21:44 -05:00
336c093bf8
Catch errors when building enumeration lists.
2021-01-08 15:15:24 -05:00
26655b26d3
merging in dev, and fixing a failing test from dev.
2021-01-08 14:42:13 -05:00
9118517995
Merge pull request #220 from sartography/prevent-duplicate-template-upload-111
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Users cannot upload a workflow_spec_file that already exists. We rais…
2021-01-08 13:55:19 -05:00
be288ae048
Merge pull request #219 from sartography/fix-api-call-missing-fieldname-143
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Fixed ApiError call. Now includes task_id and task_name.
2021-01-08 13:46:26 -05:00
81fe3e7957
Merge pull request #218 from sartography/is-file-uploaded-143
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Ticket 143. Test whether file is uploaded.
2021-01-08 13:45:24 -05:00
72a73c1fc4
Allow for synch to work even if the local set of workflow specifications are completely empty.
2021-01-08 13:23:01 -05:00
d274813ae5
We now check form field IDs so they play well with Python and Javascript.
2021-01-07 11:10:31 -05:00
c9a4a9685f
Users cannot upload a workflow_spec_file that already exists. We raise an error that is displayed on the fron end.
2021-01-04 15:47:45 -05:00
0ae4448fbe
Fixed ApiError call. Now includes task_id and task_name.
2021-01-04 13:48:34 -05:00
b0dc834682
Don't error out on autocomplete_num
2021-01-04 13:41:57 -05:00
0c47d09972
Ticket 143. Test whether file is uploaded.
2021-01-04 10:53:21 -05:00
386feddeed
Merge pull request #214 from sartography/validate-hide-expression-103
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Modified study_info do_task_validate_only so that we take the default…
2020-12-31 10:53:27 -05:00
cf106fb9cd
Merge pull request #216 from sartography/place-study-on-hold-20
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Studies can now be put on hold in the dashboard. We were overriding t…
2020-12-31 10:53:03 -05:00
ede5df4df5
Studies can now be put on hold in the dashboard. We were overriding the status in StudyModel.update_from_protocol_builder.
2020-12-30 17:49:59 -05:00
efdbbcbc72
StudyInfo sometimes returns arrays of items, each item in the array should be coverted to a Box dictionary if possible.
2020-12-30 14:51:51 -05:00
f29429f0d0
Modified study_info do_task_validate_only so that we take the default path in ind_update workflow.
2020-12-30 10:04:10 -05:00
e5a38874f6
A hard or soft reset should also cause a 'cancel_notify' which will kick off any CANCEL events. If this happens during
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a hard or soft reset, and an error is thrown trying to fulfil a cancel event, the reset should still fire.
Sending emails still had a number of issues correctly parsing it's arguments. This is corrected.
2020-12-29 18:05:13 -05:00
c288a8a2bc
Merge branch 'dev' into check-field-type#143
2020-12-29 11:11:43 -05:00
7938ac8eed
We now assure each form field has a field type. Modified populate_form_with_random_data, added check at beginning of form field loop.
2020-12-28 18:02:16 -05:00
6cfce839c1
Validation now assures that we won't encounter errors when generating navigation lists.
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Fixing workflow sync paths that were incorrect.
Repairing a suddenly failing test in files, that just don't make no sense.
Bumping spiffworkflow that contains a fix for issue #155
2020-12-28 17:33:38 -05:00
1f9bf72c59
Merge branch 'dev' into bug/navigation
2020-12-14 11:46:44 -05:00
4268d0f482
Merge pull request #208 from sartography/152-workflow-spec-pull
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152 workflow spec pull
2020-12-14 11:35:06 -05:00
bcb78de225
Merge branch 'dev' into bug/navigation
2020-12-14 11:33:51 -05:00
e54404e424
Merge pull request #205 from sartography/test-email-script
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Test email script
2020-12-14 11:28:14 -05:00
6bf24cc438
fixing some failing tests related to changes in the underlying spiffworkflow library.
2020-12-14 11:27:38 -05:00
b62a9c7074
Merge remote-tracking branch 'origin/dev' into bug/navigation
2020-12-14 10:40:21 -05:00
fd4b881416
upgrading the pip libraries.
2020-12-14 10:30:10 -05:00
ee3ee9fd4a
Added tests to cover most of the use cases and code, and a bunch of stuff to make the mocks happy
2020-12-14 10:27:40 -05:00
02ea414b94
Additional fixes to Navigation to allow a nested navigation structure.
2020-12-14 10:07:19 -05:00
7defc2b02f
Tests for uid in logs. Currently we test for uid in a response. This covers ApiError.
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Currently, we don't have a test for Sentry. Unsure how to do this.
Also added a script, service and test workflow to help. (Also to learn about adding a script and service.)
2020-12-11 17:47:53 -05:00
856fe445b0
Added user.uid to ApiError and Sentry logging
2020-12-11 16:26:03 -05:00
adc4dc4453
redid the api a bit so that nothing was using open security - added a new endpoint for getting a workflow spec that uses the alternate API_TOKEN security and leave the original endpoint as it was.
2020-12-11 12:03:41 -05:00
55e6f5b753
refactored calls into a service - forgot to add actual service
2020-12-11 11:42:00 -05:00
3a1160efac
refactored calls into a service
2020-12-11 11:41:32 -05:00
9eea26e019
add workflow_sync test
2020-12-11 08:34:59 -05:00
993c7bc76e
fixed error on api.yml from search / replace
2020-12-11 08:29:37 -05:00
3f56dfe484
Move all workflow sync stuff into new file
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Make changes to api naming scheme
add some error checking around endpoints for missing/invalid endpoints
2020-12-10 10:46:23 -05:00
a8203ed01d
save changes before refactor
2020-12-10 10:06:21 -05:00
e377a05dea
Add some punctuation
2020-12-09 13:50:52 -05:00
c57b17df1e
Add a robust way of adding an API key, update examples and documentation for swagger API and add the ability to completely sync the local system from the remote system.
2020-12-09 12:13:17 -05:00
32c5060a31
No longer use eval on the email address. It is already parsed.
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Tests for single and multiple emails, and email error checking.
Still need to figure out how to implement multiple emails.
2020-12-09 12:11:46 -05:00
0e1aa59fa1
Make a change to make sure that if there is a new file locally that is not present remotely when we pull from the remote, the new local file gets deleted.
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Also: add several things to the requirements.txt that should have been there in the first place.
2020-12-08 13:42:01 -05:00
730d0ca18f
Email script now uses an email address instead of a UVA LDAP user_id.
2020-12-07 16:23:41 -05:00
44c72115ae
Make sure we get the file we intended
2020-12-07 08:50:20 -05:00
f26a8615a4
Get more file details so we can fill out everything locally and also add a method to download the file by md5_hash
2020-12-07 08:49:38 -05:00
93b12a8e82
updates using new navigation from spiff workflow's navigation branch, all tests passing.
2020-12-04 17:56:12 -05:00
cad613cf63
Fix problem when method is run for a workflow that is non-existant locally
2020-12-04 12:00:02 -05:00
d41d018fe3
For a given workflow - find the files that are different from a remote endpoint for the same workflow
2020-12-04 11:49:07 -05:00
3e8d4ca7c9
Add some inline documentation to make the process more clear
2020-12-04 10:23:03 -05:00
10dce542ec
documentation change
2020-12-03 15:27:45 -05:00
0f59d3de09
add endpoint that gets a record for all changed /new workflow_specs at a remote endpoint
2020-12-03 14:45:57 -05:00
bcb45a59c8
allow cors
2020-12-03 08:46:34 -05:00
0e8913434a
refactor a bit
2020-12-03 08:44:15 -05:00
92aa1b971d
commit before removing big long SQL
2020-12-02 16:04:00 -05:00
aca1fb366b
Fixing a failing test and updating the personnel.
2020-12-01 15:47:27 -05:00
e15130e09c
Merge pull request #203 from sartography/151-data-store-exclusive-branch-expression
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Added the ability to use the custom functions within a decision/flow …
2020-12-01 14:44:27 -05:00
801c5df75e
Merge pull request #201 from sartography/verify-end-event-#105
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Verify end event #105
2020-12-01 14:24:12 -05:00
e0c28cbc7d
Make it easer to start things up.
2020-12-01 11:17:07 -05:00
94662c560e
Added the ability to use the custom functions within a decision/flow coming off of an exclusive join
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Altered previous test to test this feature
2020-12-01 09:13:12 -05:00
73e01b347b
Ticket #105 . Verify End Event Documentation. Added explicit call to _process_documentation at end of crc.services.workflow_service.test_spec for the end event
2020-11-24 16:51:18 -05:00
071c98d72e
Some minor config tweaks to try and deal with some database timeout issues.
2020-11-19 11:25:58 -05:00
b8a91a513b
Merge pull request #196 from sartography/128-data-store
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128 data store
2020-11-18 18:55:33 -05:00
b83ab1bcd1
Move data store base into its own file.
2020-11-18 15:34:50 -05:00
d198f124d7
Committing a merge from dev
2020-11-18 15:33:44 -05:00
66693d9f3a
Removing datastore script, as it isn't used in the api at all.
2020-11-18 15:06:28 -05:00
c62b73a539
drop some of the test-only api endpints and rework the tests so they aren't needed
2020-11-18 15:04:36 -05:00
16313609ec
removed call to signal (changed to cancel_notify)
2020-11-18 13:55:30 -05:00
72ade3c367
Add crosstalk test
2020-11-17 10:29:49 -05:00
e9979efb0d
Add some tests
2020-11-17 09:33:29 -05:00
a2dc3c4812
Use Cancel Event
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New title 'New Title'
2020-11-16 09:59:22 -05:00
70425eee0d
Add last_updated field - change the api signature to be closer to what we need going forward, but retain the old methods for testing the script get/set through the API
2020-11-13 12:03:29 -05:00
7c2c725840
save before changing how API works
2020-11-13 09:58:21 -05:00
acaf633b45
Added ID as pk
2020-11-11 11:36:25 -05:00
9a4d167dcd
Add in api changes
2020-11-11 09:44:58 -05:00
cef221be32
Refactor to reuse code
2020-11-10 11:32:59 -05:00
3ba11f5e6b
add user_data_get/set and alter test so that it ensures that we don't grab study_data stuff from the user_data calls
...
change the test to mock up the user.
2020-11-10 10:32:37 -05:00
245124779e
Add mostly-working elements of the data-store, compare with dev to see why db is not working after running tests
2020-11-10 08:21:46 -05:00
e598994d34
Change the study_sponsors script so that we can actually call it :
...
var = study_info('sponsors')
to keep it more in line with other scripts that we have
2020-11-05 10:31:47 -05:00
1815a4b657
Merge branch '117-save-restore' into dev
2020-11-05 08:24:18 -05:00
a78af4eab8
Run cancel task during interrupt. Currently this uses Signal event. We may change this to the Cancel event.
2020-11-04 14:37:53 -05:00
2931f45187
Add 'sponsors' to study_info call
2020-11-04 14:34:10 -05:00
849a4e9f94
Made changes to how soft_reset works so it is backward compatible - essentially, we use the file if we are doing a soft-reset or a new workflow. NB, this may actually still have problems if we have a workflow with P/SMI and we do a soft-reset on it even if there are no structural changes.
...
Also, change how default_value is interpreted, looking at the object attribute rather than the properties list.
2020-10-09 11:00:33 -04:00
8b23cdc05c
commit changes before switching branches
2020-10-09 08:46:14 -04:00
b2aede2b8d
Glob on windows seems to return directories where in linux it does not, so now assuring we don't try to add files from the sub-directory.
2020-10-05 17:35:35 -04:00
014a4d9757
Fixing a failing test and updating the personnel.
2020-09-02 08:24:48 -04:00
b544334f45
1. Updating Personnel BPMN diagram to debug some issues.
...
2. Disabling the token timeout for now, to see if this corrects the issues Alex is having with lost work.
3. Raising more thoughtful error messages for unknown lookup options.
4. Providing better validation of default values and injecting the correct value for defaults related to enum lists of all types.
5. Bumping Spiffworkflow library which contains some better error messages and checks.
2020-09-01 15:58:50 -04:00
Kelly McDonald
mike cullerton
Dan
Mike Cullerton
Nile Walker