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
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
ecff7d20d3
Adding a test for the new endpoint and cleaning up the API documenation
2021-04-21 14:00:19 -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
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
b64b52e7cb
Assure that we properly return the new status message over the api calls.
2021-03-26 19:47:31 -04:00
a08c6b794f
Updated Study Associate Endpoints
2021-03-22 17:30:49 -04:00
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
9e758c57d3
Merge branch 'dev' into bug/225_enum_lookup_same_field_name
2021-03-02 14:15:58 -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
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
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
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
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
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
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
b0dc834682
Don't error out on autocomplete_num
2021-01-04 13:41:57 -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
1f9bf72c59
Merge branch 'dev' into bug/navigation
2020-12-14 11:46:44 -05:00
6bf24cc438
fixing some failing tests related to changes in the underlying spiffworkflow library.
2020-12-14 11:27:38 -05:00
02ea414b94
Additional fixes to Navigation to allow a nested navigation structure.
2020-12-14 10:07:19 -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
93b12a8e82
updates using new navigation from spiff workflow's navigation branch, all tests passing.
2020-12-04 17:56:12 -05:00
e9979efb0d
Add some tests
2020-11-17 09:33:29 -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
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
b544334f45
1. Updating Personnel BPMN diagram to debug some issues.
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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
53d09303d8
Validating that field properties are valid - they must exist as constants on the Task model.
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Making all the lookup field names consistent.
Fixing the lookup service which was failing at times trying to find the correct field to use for building the lookup table.
Updating validation to check for additional fields and properties.
When connexion level errors occur, wrapping it in an API Error to be consistent.
2020-08-27 14:00:14 -04:00
85ad477b2b
Some minor cleanup on the study status and automatic events. I wanted to avoid having one database model automatically generating other database models as a side effect. The study service now has full responsiblity to recording study events.
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To help in running tests, adding __init__.py methods to all the test directories.
2020-08-17 14:56:00 -04:00
369fe4bb35
Automatic events refactoring
2020-08-14 08:36:46 -06:00
9a5c1d7cfb
I may have finally wrapped my head around full text search in python. Now properly using an index based on simple rather than english dictionary which has far fewer stop words and stemming processes and plays much better to the type ahead search we are trying to provide.
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Stop words are no longer excluded, so "other" is a valid search and gets a result.
2020-08-13 18:13:41 -04:00
9a31d591ae
Adds user uid and cascades study event in study model. Fixes migration to properly downgrade enums.
2020-08-12 10:13:23 -04:00
a561a5cddc
Adjusting study events attribute
2020-08-08 18:25:01 -06:00
bf3dae1885
Collecting user generated study changes
2020-08-05 20:29:05 -06:00
b4595b345a
Raises ApiError for 'display_name' extension property exception
2020-08-04 13:59:50 -04:00
50b207307a
Merge branch 'dev' into feature/update_study_status_latest
2020-07-31 14:26:24 -06:00
2c2967e633
Normalizing enum values
2020-07-31 11:19:50 -06:00
5d23223e51
New study status update
2020-07-30 21:03:11 -06:00
faba0f55ab
Adds AdminSession model and refactors impersonation methods to use it.
2020-07-30 12:40:53 -04:00
1b0ebecbf4
Uses Flask session to store impersonation state.
2020-07-30 10:17:02 -04:00
63537d7765
Adds is_admin boolean flag to user schema
2020-07-29 22:45:56 -04:00
de49397549
Adjustings tests for protocol builder status changes
2020-07-29 10:51:34 -06:00
73a6b7adf1
Fixing tests
2020-07-29 10:25:57 -06:00
6aa21638de
Updating properly study status & fixing tests
2020-07-29 10:25:57 -06:00
f897ee3aea
Merge branch 'feature/approvals_dashboard_prototype' into feature/admin_impersonations
2020-07-29 10:32:46 -04:00
0ea4c13d09
Convert protocol builder status to always be in lower case in order to better match the front end. And also fixing an issue with the multi_instance that is oddly broken suddenly, and I don't know why.
2020-07-28 17:16:48 -04:00
4d11fc04a0
dropping the "read_only" flag in favor of a "do_engine_steps" flag, which more clearly defines what is happening.
2020-07-28 13:51:29 -04:00
f15626033d
Allow the workflow to be requested without making changes to the workflow - requires that you specify a read_only flag of true, otherwise it assumes that you want a fully prepared workflow with the next ready task set to run.
2020-07-28 13:33:38 -04:00
300026cbc8
Expanding the task events endpoint to accept workflow and study ids as additional filters.
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Removing events from the study endpoint, too noisy.
2020-07-28 10:16:48 -04:00
0cb480801b
Provide event data on the Study api endpoint.
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Speed up the tests a little, because that got out of hand. Need to dig into what is causing this problem.
2020-07-27 17:05:01 -04:00
452f2c3723
Building out a user service for getting the current user, it will provide a number of functions, one of which will allow administrative users to impersonate other users in some circumstances (but will assure that we log events correctly when an impersonation occures)
2020-07-27 14:38:57 -04:00
b87f55fbd7
Exposes date in TaskEvent endpoint
2020-07-22 14:48:10 -04:00
855f5544e5
Adds enrollment_date to study model
2020-07-22 09:35:08 -04:00
3d9eeab502
Add a few more details to the workflow metadata model.
2020-07-21 15:18:08 -04:00
d67105332f
Merge branch 'dev' into feature/lanes_and_roles
2020-07-16 14:00:53 -04:00
d85ca1ce51
Whenever a workflow is loaded or updated, add events to the TaskEvent table with assignments for the next set of ready tasks, along with who should complete those tasks.
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Add the lane information to the Task model.
Drop the foreign key constraint on the user_uid in the task log, as we might create tasks for users before they ever log into the system.
Add a new endpoint to the API called task events. It should be possible to query this and get a list of all tasks that need a users attention.
The task events returned include detailed information about the workflow and study as sub-models
Rename all the actions in event log to things that are easier to pass over the api as arguments, make this backwards compatible, updating existing names in the database via the migration.
Throughly test the navigation and task details as control of the workflow is passed between two lanes.
2020-07-14 22:16:44 -04:00
9077ff3ebf
It is not possible to use task_data for an auto-complete field. It's too expensive an operation to provide that feature on the backend, and the data already fully resides on the front end anyway. Task-data can be used to populate enum fields if needed, so it can populate dropdowns, radios and checkboxes, just not auto-complete.
2020-07-14 11:38:48 -04:00
a48322ef6a
Partial work on CR Connect Roles.
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Adding checks in the API to assure the correct person is completeing a task based on the task's lane.
Adding lane to the Navigation item.
Adding a check to assure that unique user ids can be identified using task.data
Added some additional ldap entries to make testing and development easier.
Removed a big chunk of duplicate code from task_tests_api
Modified some of the helper functions to make it easier to test as specific users.
Added some additional bpmn models to the tests for testing lanes and roles.
2020-07-14 10:29:25 -04:00
b7920989ed
WIP: Adds Camunda property for retrieving enum field options from task data.
2020-07-10 14:48:38 -04:00
1f454536e3
Renames TOKEN_AUTH_SECRET_KEY to SECRET_KEY
2020-07-10 11:26:15 -04:00
7f0b35ff27
Merge branch 'dev' into feature/enum_lookup_data
2020-07-10 10:27:51 -04:00
c7b864f9c7
Cleaning up old notes
2020-07-07 08:32:20 -06:00
1d9fef380a
Merge branch 'fix/more-info-in-exceptions' into feature/enum_lookup_data
2020-07-03 14:22:11 -04:00
f344fe60c0
WIP: Adds enum field lookup option data
2020-07-03 12:20:10 -04:00
817333f26e
Adding proper exception information
2020-07-02 16:10:33 -06:00
340ae68eed
Sets PB status to Active by default
2020-07-01 11:01:36 -04:00
f183e12fe5
Provides some basic tools for getting additional information about a lookup field.
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Adds an optional 'value' parameter to the lookup endpoint so you can find a specific entry in the lookup table.
Makes sure the data attribute returned on a lookup model is a dictionary, and not a string.
Fixes a previous bug that would crop up if double spaces were used when performing a search.
2020-06-30 10:34:16 -04:00
d3ce1af1ce
Provides some basic tools for getting additional information about a lookup field.
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Adds an optional 'id' parameter to the lookup endpoint so you can find a specific entry in the lookup table.
Makes sure the data attribute returned on a lookup model is a dictionary, and not a string.
Fixes a previous bug that would crop up in double spaces were used when performing a search.
2020-06-30 10:00:22 -04:00
5327b469f6
Merge branch 'rrt/dev' into feature/emails-enhancement
2020-06-24 21:46:53 -06:00
6aec15cc7c
Shifting to a different model, where the TaskEvents store ONLY the form data submitted for that task.
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In order to allow proper deletion of tasks, we no longer merge data returned from the front end, we set it directly as the task_data.
When returning data to the front end, we take any previous form submission and merge it into the current task data, allowing users to keep their previous submissions.
There is now an "extract_form_data" method that does it's best job to calculate what form data might have changed from the front end.
2020-06-19 08:22:53 -04:00
e947f40ec7
Merge branch 'rrt/dev' into feature/emails-enhancement
2020-06-17 20:10:11 -06:00
896ba6b377
Email relies now on markdown content
2020-06-17 17:00:16 -06:00
2ce2dc73b5
Rendering proper content & organizing file structure for email tests
2020-06-17 16:09:38 -06:00
3b57adb84c
Continuing a major refactor. Some important points:
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* TaskEvents now contain the data for each event as it was when the task was completed.
* When loading a task for the front end, if the task was completed previously, we take that data, and overwrite it with the lastest data, allowing users to see previously entered values.
* Pulling in the Admin branch, as there are changes in that branch that are critical to seeing what is happening when we do this thing.
* Moved code for converting a workflow to an API ready data stricture into the Workflow service where it belongs, and out of the API.
* Hard resets just convert to using the latest spec, they don't try to keep the data from the last task. There is a better way.
* Moving to a previous task does not attept to keep the data from the last completed task.
* Added a function that will fix all the existing RRT data by adding critical data into the TaskEvent model. This can be called with from the flask command line tool.
2020-06-17 17:11:15 -04:00
1b9166dcb7
Cleaning up the merge, which resulted in some lost code.
2020-06-16 13:34:21 -04:00
c7d8eaff30
Merge branch 'dev' into feature/refactor_data_loading
2020-06-16 13:15:43 -04:00
706c4afda5
Create a parameter 'lane' since we are using the output from the nav-list as the input to the NavigationItem initializer.
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NB - this doesn't do anything with the lane designation, it just keeps it from blowing up.
2020-06-15 12:33:51 -04:00
561e254315
Prevents non-admin users from editing each others' tasks. Fixes bug where test user uid was not being set from token. Moves complete form and get workflow API test utility methods into BaseTest.
2020-06-12 13:46:10 -04:00
cccff9b856
Fixes broken unit tests. But still broken.
2020-06-11 11:29:58 -04:00
e9e805b2c9
Storing emails in database
2020-06-09 22:57:56 -06:00
8cf420b781
Default mail user name and password to blank.
2020-06-08 14:15:56 -04:00
6861991d8f
Allow setting the type of approvals you want back, by status.
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Some very minor performance enhancements, that will add up on the Approvers page.
2020-06-05 17:49:55 -04:00
f0db5b70fc
Adding some additional logic to the approval endpoint so that we take related approvals into account when setting the status. In addtion to prevous status options, there is a new status of "AWAITING" which means there are pending approvals before this approval that still need to be approved or canceled.
2020-06-05 14:33:00 -04:00
fed6e86f92
Trying to fix LDAP issues on production. Changing LDAP to static only methods, caching the connection and calling bind before all connection requests.
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Also assuring we don't load the documents.xls file over and over again.
2020-06-04 14:59:36 -04:00
50d2acac9c
Made a very stupid mistake with LDAP connections, pushing up quickly to production.
2020-06-04 11:57:00 -04:00
68aeaf1273
BE VERY CAREFUL where you create a new LdapService() - construction is expensive.
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Adding a few more details to the "csv" endpoint for RRT.
2020-06-04 10:33:17 -04:00
bbcbfef1ba
Fixing the migrations so I don't break the universe.
2020-06-04 10:09:36 -04:00
217ecfc911
When you can't delete a file, mark it as archived. Don't include archived files in new approval requests.
2020-06-03 17:34:27 -04:00
2424b9d78c
Don't overwrite the approval, just allow minor changes.
2020-06-02 19:36:06 -04:00
Dan Funk
Mike Cullerton
Kelly McDonald
mike cullerton
Nile Walker
Carlos Lopez
Aaron Louie