9bd012c822
Clean up display_order numbers when reordering.
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This fixes the problem where we have don't have all unique display_order numbers.
I.e., 0, 1, 1, 3, 5
2021-09-08 11:16:49 -04:00
ce1af73d6e
Remove unused import
2021-09-07 15:44:15 -04:00
21987cf1f1
Remove old root definition.
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We now use the 2019 spec
2021-09-07 15:38:53 -04:00
a690535c2d
Removed script used in development
2021-09-07 15:36:50 -04:00
e630aeb94e
Add DMNDI section.
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Without it, the configurator could not parse the XML
2021-09-07 14:27:15 -04:00
6e7b549136
Change root element to use 2019 spec
2021-09-07 12:11:27 -04:00
a3b3df1bbb
Use flask send_file to return DMN file
2021-09-07 12:09:30 -04:00
1e97f0ac31
Merge pull request #368 from sartography/feature/114_read_only_expression
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#114 We just needed to allow read_only_expression
2021-09-03 14:32:56 -04:00
86c017a6a6
Merge pull request #367 from sartography/value-error-expression-428
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Value error expression #428
2021-09-03 14:32:46 -04:00
1a008499c4
Merge pull request #366 from sartography/file-id-error-info-449
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Added file_id to some error messages in api.file #449
2021-09-03 14:32:14 -04:00
93e8015ddd
Read the spreadsheet data sent from the front end. This allows pandas to see it as a file type object.
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Fixed bug where column_count wouldn't get set if there isn't an Annotation column
2021-09-03 10:37:06 -04:00
e2b70da6b7
Not returning json. Returning stream of XML
2021-09-03 10:33:12 -04:00
8677d0368b
Grab the file data from the request, not as a parameter
2021-09-03 10:32:32 -04:00
5c0d30becb
We just needed to allow read_only_expression
2021-09-03 09:48:16 -04:00
1545226e06
We no longer save the DMN file, so we don't need the workflow_spec_id
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(We will open the DMN in the editor. It will be saved there.)
2021-09-02 09:58:22 -04:00
5f3968b582
Changed script to work with a file_id
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This will all be deprecated, and we won't run this from a script
2021-09-02 09:55:31 -04:00
b5082b8fd3
Call FileService
2021-09-02 09:53:17 -04:00
4fa68bd4c0
Move business logic to FileService
2021-09-02 09:52:58 -04:00
0c31b091ee
Merge branch 'dev' into dmn-from-spreadsheet-395
2021-09-01 09:38:03 -04:00
b88daef4fa
Added task name to the error message, for configurators
2021-08-31 16:17:52 -04:00
5db5c7ca43
Added file_id to some error messages in api.file
2021-08-31 15:28:21 -04:00
ed57993f8d
Workflow spec cleanup needs a category_id
2021-08-31 12:17:25 -04:00
1140b21414
Adding a test that assures we pick up libraries on the remote system when syncing.
2021-08-31 12:07:41 -04:00
b92676ea75
Make sure we have good display_orders before adding specs and categories
2021-08-31 11:16:27 -04:00
994ce4008f
Don't let updates to workflow-spec and workflow-spec-category metadata change the display_order
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Force display_order changes to use the new reorder API endpoints
2021-08-31 10:36:22 -04:00
f6816a2e42
Move display_order cleanup to their own methods
2021-08-31 10:07:38 -04:00
d17a2c39ed
A little cleanup to assure that when we sync we correctly pick up and associate librarires with a workflow when we sync.
2021-08-30 15:46:16 -04:00
b76f45368b
Explicitly commit the changes
2021-08-30 15:29:49 -04:00
7bbb64cf27
Reorder remaining categories after delete
2021-08-30 15:20:45 -04:00
c275c01526
Reorder remaining workflow specs upon deletion
2021-08-30 14:56:26 -04:00
eb6b73fde5
Fixed typo where I returned an ApiError, instead of raising it.
2021-08-30 13:55:21 -04:00
a99818b177
Make sure we don't try to move past the top or bottom of the list.
2021-08-30 11:42:44 -04:00
070a9c9350
Code for reordering Workflow Spec Categories
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Still need to work on edge cases where you try to move past top or bottom of list
Still need to work on tests
2021-08-30 11:27:07 -04:00
f2201a3cef
Move business logic to WorkflowService
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Return ordered list of specs
2021-08-30 10:41:08 -04:00
41414e39c8
First pass at reorder spec code.
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Still need to return list of specs
Still need to work on spec categories
2021-08-27 13:02:49 -04:00
f639e101b7
Commit the skeleton API endpoints, so we can use them while developing the BPMN side of things.
2021-08-27 11:40:38 -04:00
083abd1b58
Just being consistent in the names as we named it delete_task_data in the class, but not elsewhere, and since I'm here, using the name I prefer.
2021-08-26 14:22:12 -04:00
da914be3fa
Add task_spec to data_store
2021-08-26 10:41:09 -04:00
506157d58a
Add task_spec_name to FileService.add_workflow_file, and script that calls it.
2021-08-26 10:40:47 -04:00
4c41011299
Add task_spec_name to `add_file` API call
2021-08-26 10:37:05 -04:00
3d7dadc319
Model changes and revision file for task_spec column to file and data_store models
2021-08-26 10:36:10 -04:00
ea08643bcd
Script to delete files and task_events associated with a task
2021-08-26 10:34:21 -04:00
d990a5636f
Grabbed the latest irb_documents spreadsheet, because of the new `zip` columns and updated categories
2021-08-26 08:43:11 -04:00
fb5b7f72d8
New script to created a zipped file of irb_documents for use as an email attachment.
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The script accepts a list of file_ids, and generates a list of documents from these ids.
The documents are stored in a directory structure generated from the categories in the irb_documents spreadsheet
2021-08-26 08:31:01 -04:00
961925e03e
Merge pull request #361 from sartography/430-email-enhancements
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#430 email enhancements
2021-08-25 15:02:14 -04:00
fcbbeb4735
Merge pull request #360 from sartography/423-LibraryAppearingInDashboard
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Fixes #423
2021-08-25 15:01:18 -04:00
4b9c5bd3e8
Fixing a stupid mistake.
2021-08-24 12:10:59 -04:00
0bd1c282a3
Merge branch 'dev' of github.com:sartography/cr-connect-workflow into dev
2021-08-20 13:46:08 -04:00
32c72c5a40
Modified email script and email_service to accommodate new bcc, reply_to, and attachments arguments
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Modified the email script description to add the new arguments
Cleaned up some import statements
2021-08-19 17:34:55 -04:00
ef9fd9514d
This caused a key error if we had a repeating field that was unused
2021-08-19 17:32:24 -04:00
76f8f5984e
Fixes #413
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Fixes #423 where a library was showing up in a study workflow
Alex said this used to work, but I don't see where I ever edited the code that needed a filter.
2021-08-19 10:47:13 -04:00
5692f7d377
Merge pull request #359 from sartography/413-LibraryCleanup
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413 library cleanup
2021-08-18 13:39:37 -04:00
afaecfa21c
Catching an error when variables conflict with repeating section variables.
2021-08-18 13:38:34 -04:00
feb72af32e
Update workflow.py
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Just completing a comment so I understood
2021-08-18 13:27:28 -04:00
b4ecb0f97a
Add backref cascade and make changes to the spot where we delete so it loads objects into memory and then uses the SQLAlchemy plumbing to make sure that the db object gets cleaned up.
2021-08-18 08:25:17 -04:00
032aad9bc4
Fixes #383 - Timestamp on files is UTC?
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also this includes the shield test thing for the boolean_type property whoopsie
2021-08-17 13:04:24 -04:00
7a8eeab820
Merge branch 'dev' into bug/missing_pi_name_246
2021-08-17 11:16:03 -04:00
6ce560cc2d
Made a stupid mistake in a hot fix, causing the builds to fail.
2021-08-17 10:14:49 -04:00
c831ee7e4a
Merge pull request #357 from sartography/426-remove-hsr-number
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remove hsr number #426
2021-08-17 09:58:56 -04:00
78f79a67b7
removing exectue flag.
2021-08-17 09:52:02 -04:00
4e0e162fd6
Removing the execution flag Nile keeps adding to files.
2021-08-17 09:50:57 -04:00
77de2a8f47
Merge branch 'dev' into bug/missing_pi_name_246
2021-08-17 09:47:09 -04:00
0a2597ae36
Just a quick hot fix so that when can still report errors back to the UI even when the task_data can't be serialized, which can happen when functions are defined.
2021-08-17 09:43:08 -04:00
07ffcd7c76
Dependencies In Testing are behind this avoids that issue. https://sonarcloud.io/project/issues?id=sartography_cr-connect-workflow&pullRequest=356&resolved=false&types=BUG
2021-08-16 23:46:39 -04:00
2a2fd710c4
Merge branch 'dev' into dmn-from-spreadsheet-395
2021-08-16 14:22:02 -04:00
3f44c202ca
Merge branch '417-hsr-open-to-enrollment-bug' into 426-remove-hsr-number
2021-08-16 12:55:24 -04:00
b3fd72de8b
Remove hsr_number from Study Schema
2021-08-16 12:51:48 -04:00
1f82143aea
Remove HSR Number from models
2021-08-16 12:50:09 -04:00
46d7b13326
Start to remove HSR Number
2021-08-16 12:09:02 -04:00
0a232dace6
assertEquals -> assertEqual
2021-08-16 10:25:41 -04:00
f8dd4c3eb9
Check Study Associates Endpoint
2021-08-16 09:32:02 -04:00
bd4a9cced3
We no longer use HSRNUMBER to automatically set Study Status to `Open for Enrollment`
2021-08-13 12:06:27 -04:00
4a2581e938
get studies raises and error when invalid studies are the only studies associated with the user
2021-08-12 14:03:44 -04:00
7027392a1b
Merge remote-tracking branch 'origin/bug/missing_pi_name_246' into bug/missing_pi_name_246
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# Conflicts:
# crc/services/workflow_service.py
# tests/study/test_study_associate_script.py
2021-08-12 13:01:41 -04:00
e32c1db4c8
Merge remote-tracking branch 'origin/dev' into bug/missing_pi_name_246
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# Conflicts:
# crc/models/study.py
# crc/services/study_service.py
# crc/services/workflow_service.py
# tests/study/test_study_associate_script.py
2021-08-12 12:59:15 -04:00
000de03733
Just a quick hot fix so that when can still report errors back to the UI even when the task_data can't be serialized, which can happen when functions are defined.
2021-08-12 12:49:19 -04:00
41e27cb454
Merge remote-tracking branch 'origin/dev' into bug/missing_pi_name_246
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# Conflicts:
# crc/models/study.py
# crc/services/study_service.py
# crc/services/workflow_service.py
# tests/study/test_study_associate_script.py
2021-08-12 12:39:04 -04:00
d20b68e483
Fixed Deprecation Warnings in Test Files
2021-08-12 12:33:27 -04:00
2732071585
Merge branch 'dev' into bug/missing_pi_name_246
2021-08-12 12:07:25 -04:00
40727c7ce6
avoid erroring out when unable to calculate a value expression as a part of finding a default value.
2021-08-12 11:35:05 -04:00
adb1b74822
Merge pull request #352 from sartography/post-process-empty-field-408
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Post process empty field #408
2021-08-12 10:53:26 -04:00
d07bac27ca
Fix for hidden file data field.
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We were processing a field that didn't have a value.
Ticket 408
2021-08-11 16:43:50 -04:00
318cd34f81
bouncing to fix a bug in SpiffWorkflow that was holding outo outdated data deed within the python_script_engine.
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This caused validation to fail for valid repeat sections, so including a fix to allow that validation to continue.
2021-08-11 14:21:23 -04:00
05e7f5e253
Worksheet for Alex
2021-08-11 10:06:12 -04:00
19e0caa700
API endpoint for creating a DMN table from a spreadsheet
2021-08-11 08:55:10 -04:00
848c2e622f
Always use a schema to define what is being returned, it enforces consistency of the API and internally we can depend on well defined objects.
2021-08-10 16:16:08 -04:00
913c12c02d
Merge branch 'dev' into bug/pi_name_missing_246
2021-08-10 15:06:52 -04:00
dce95189cb
Merge branch 'dev' into dmn-from-spreadsheet-395
2021-08-10 09:39:42 -04:00
960d302c03
Finish #367 - Make sure that we only use a primary_id if it is in the workflow that we are currently working on - otherwise it is a library and might have its own primary id.
2021-08-10 09:15:38 -04:00
c153c5e344
Another test spreadsheet
2021-08-09 13:27:58 -04:00
deebc49a82
Removed test files - don't need under version control
2021-08-03 12:20:25 -04:00
0e20480f52
Removed test files - don't need under version control
2021-08-03 12:17:54 -04:00
64576ee8fd
It now adds the dmn file to the DB.
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Added annotations.
Still need to move it out of a script.
Maybe a new API endpoint and a new method in file_service
2021-08-03 11:55:50 -04:00
6e1fedb704
Add tests for libraries, remove an API endpoint that didn't make sense after recent changes and remove some commented out sections that were not needed after some decisions about the api endpoints were made
2021-08-03 10:02:22 -04:00
deb16740f6
First attempt at creating dmn from spreadsheet.
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xml template and example spreadsheet
2021-08-02 10:04:25 -04:00
e1aee0f635
First attempt at creating dmn table from spreadsheet.
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Starting as a script
2021-08-02 10:03:10 -04:00
41ad7935f8
Merge branch 'dev' into 367-Call-Activity
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# 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 -
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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
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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
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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.
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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.
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We now return an empty dictionary
2021-07-22 10:44:41 -04:00
48516e4009
Parent side working
2021-07-22 10:23:05 -04:00
2455495457
got library side working - still need to have parent working
2021-07-22 10:20:34 -04:00
3906580604
Merges getStudyAssociates() endpoint
2021-07-20 14:25:01 -04:00
a263447806
Merges getStudyAssociates() endpoint
2021-07-20 13:57:32 -04:00
4632c6374f
Merge branch 'dev' into bug/missing_pi_name_246
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# Conflicts:
# crc/api.yml
# crc/services/study_service.py
2021-07-20 11:44:11 -04:00
354e20c34b
Use the data_store_service to set the data_store, rather than access DB directly.
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Pass the label explicitly (as the value)
2021-07-15 13:09:40 -04:00
dd67a5e650
Never set the date to datetime.utcnow() on DateTime fields. We want this to fall back on the func.now() method and allow the database to set the time on insert.
2021-07-12 15:58:32 -04:00
522ca9d164
Merge pull request #340 from sartography/bug/better_errors_on_scheduled_tasks
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Assure we log reasonably clear errors when executing scheduled tasks …
2021-07-12 10:13:02 -04:00
d1bf370a39
Merge pull request #339 from sartography/restrict-loaded-studies-374
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Restrict loaded studies #374
2021-07-12 10:11:34 -04:00
7070761089
Merge pull request #338 from sartography/document-spreadsheet-name-380
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Document spreadsheet name #380
2021-07-12 10:11:16 -04:00
f982745d32
fixing a failing test, don't assume the study and workflow ids will always be 1.
2021-07-12 10:00:39 -04:00
1916c4ff54
Assure we log reasonably clear errors when executing scheduled tasks in the background, so that sentry can pick them up and they can be addressed effectively.
2021-07-12 09:43:12 -04:00
690c059335
get_studies_for_user is no longer a static method
2021-07-09 10:37:57 -04:00
dad2de9f0c
get_user_studies now checks study_details['REVIEW_TYPE'] before displaying a study.
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This corresponds to REVIEWTYPENAME being `Full Committee`, `Expedited`, `Non-UVA IRB Full Board`, or `Non-UVA IRB Expedited`
2021-07-09 10:37:25 -04:00
79c69037dd
Filter out Library categories from the list returned
2021-07-08 08:57:40 -04:00
d6f9b013f7
Change `irb_documents` to `documents`
2021-07-07 12:54:03 -04:00
23180908c8
Undo change. Wrong branch
2021-07-07 12:43:51 -04:00
c39e08972d
Change irb_documents to documents
2021-07-07 12:42:01 -04:00
3c52453c26
Merge branch 'dev' into add-name-error-hint-8
2021-07-07 11:35:24 -04:00
2ed436327f
Merge pull request #333 from sartography/check-study-script-273
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Check study script #273
2021-07-07 11:28:32 -04:00
db9b228735
Merge pull request #334 from sartography/WaitingEventsHotPatch
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Make a change so that anything that has a waiting event is labeled in…
2021-07-07 11:27:10 -04:00
2a45f2fcda
Merge branch 'dev' into add-name-error-hint-8
2021-07-07 11:24:00 -04:00
b0cf74fa3d
Merge branch 'dev' into add-by-user-61
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# Conflicts:
# tests/files/test_files_api.py
2021-07-07 10:46:50 -04:00
c11b5cfb29
Add user_uid to api output
2021-07-07 08:18:02 -04:00
fb54edac1c
Adding additional details to error messages, and cleaning up the cruft around these messages to keep them clear and succinct.
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Most noteable is the addition of the line on which the error occurs for script tasks. It will report the line number and pass back the content of
the line that failed.
The validator only returns the first error it encounters, as it's clear that all we ever get right now is two of the same error.
Did a lot of work between this and spiffworkflow to remove all the places where we obfuscate or drop details as we converted between workflowExceptions and APIExceptions.
Dropped the python levenshtein dependency, in favor of just rolling a simple one ourselves in Spiffworkflow.
2021-07-07 00:53:49 -04:00
894377a607
Add user_uid to FileDataModel calls
2021-07-06 17:09:00 -04:00
23be257db0
Add user_uid column to file_data table
2021-07-06 17:07:47 -04:00
a9805ad40c
Adding some documentation for clarity.
2021-07-06 14:40:20 -04:00
cafdc4d100
Removing an unneeded modification to the database structure for lookup tables.
2021-07-06 14:02:07 -04:00
04842aa66b
Undo change to 1 minute.
2021-07-06 13:13:07 -04:00
7aa4b0833c
Merge remote-tracking branch 'origin/dev' into feature/documents_xls_refactor
2021-07-06 13:11:08 -04:00
1b1a994360
Refactoring Reference files to use the lookup table, rather than parsing the results directly out of the spreadsheet, or attempting to cache them.
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Adding a DocumentService to clean up the FileService, and get Documents well seperated, as it seems likely be pulled out or seperated in the future, there is now a Documents api file as well, for the same reason.
Some other minor changes are just fixing white space to assure our code is linting correctly.
I removed _create_study_workflow_approvals from the base test, as we don't use approvals like this anymore.
2021-07-06 13:10:20 -04:00
9803a04d6d
Make a change so that anything that has a waiting event is labeled in the database as waiting, even if it is sitting around waiting on a user input task that is ready
2021-07-06 11:46:47 -04:00
dce1d86e93
commit changes before looking at something else
2021-07-06 10:34:57 -04:00
f647390e1c
Added description and validate_only
2021-07-02 15:51:24 -04:00
9690c69b6c
added check_study method to protocol_builder service for new endpoint
2021-07-02 15:25:33 -04:00
cd26654b3a
Script to call new pb mock api endpoint `check_study`
2021-07-02 15:21:35 -04:00
db44882733
When we encounter a name error running a script, look in the task data and see if there is a variable with a similar name.
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If a variable with a similar name exists, add it to the ApiError as a hint
2021-07-01 15:38:45 -04:00
98d641f54d
Merge branch 'dev' into partial_testing
2021-06-30 16:13:31 -04:00
mike cullerton
Dan Funk
Mike Cullerton
Kelly McDonald
Leashys
nilez