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
1052dff549
Merge remote-tracking branch 'origin/dev' into feature/python_eval
2020-08-27 14:33:16 -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
d31fd47837
Merge branch 'dev' into feature/python_eval
2020-08-25 11:08:42 -04:00
5be35e8bab
Adding a study sponsors script to return details about study sponsors
2020-08-25 10:30:46 -04:00
4dc98a6b6b
Injects current user into task data.
2020-08-21 13:34:37 -04:00
7f60a19d55
Merge pull request #189 from sartography/feature/documents_publishing
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Update github routines to use branches
2020-08-17 15:52:47 -04:00
35b1b20960
Merge remote-tracking branch 'origin/dev' into feature/documents_publishing
2020-08-17 15:19:24 -04:00
dfaffc22b5
Merge remote-tracking branch 'origin/dev' into fix/returning_failed_name_message
2020-08-17 15:18:17 -04:00
d4c5e297cc
Merge remote-tracking branch 'origin/dev' into fix/delete_workflow_endpoint
2020-08-17 15:09:11 -04:00
c09441d019
Merge branch 'dev' into fix/delete_workflow_endpoint
2020-08-17 15:07:58 -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
2bd906e96d
Update github routines to use branches
2020-08-14 11:04:22 -06:00
304ca77e3e
Fixing exception within NameError handler
2020-08-14 09:01:15 -06:00
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
79c14ad23c
Unlinking file from workflow instead of trying to delete it
2020-08-10 22:23:20 -06:00
3cfcd74a6a
Just finding a few more edge cases, all tests should pass now.
2020-08-10 15:16:53 -04:00
b53d033400
Cleaning up the delete workflow method in study service so we don't try to delete the same thing more than once)
2020-08-10 14:56:33 -04:00
56b161a234
Fixing the failing tests by passing in workflow.id rather than workflow to the delete workflow endpoint
2020-08-10 13:51:05 -04:00
d3462d2e15
Deleting all dependencies for a workflow
2020-08-10 07:42:56 -06:00
a561a5cddc
Adjusting study events attribute
2020-08-08 18:25:01 -06:00
c25536dcca
Makes Sonar happy.
2020-08-04 16:42:35 -04:00
2846bf9451
Fleshes out fake PB response, so workflows that pull from PB actually trigger validation errors
2020-08-04 15:50:29 -04:00
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
5d23223e51
New study status update
2020-07-30 21:03:11 -06:00
73699e66bd
Merge branch 'dev' into feature/admin_impersonations
2020-07-30 17:36:20 -04:00
9704cbcb26
Modifications to the ldap scripts to bring them back in line with what Kelly is doing with the evaluation process.
2020-07-30 13:35:20 -04:00
f8944da31f
Merge branch 'dev' into feature/admin_impersonations
2020-07-30 13:01:46 -04:00
faba0f55ab
Adds AdminSession model and refactors impersonation methods to use it.
2020-07-30 12:40:53 -04:00
a6ec0c92c7
Merge remote-tracking branch 'origin/dev' into cr-connect-106-augment-eval-methods
2020-07-30 11:38:47 -04:00
aa0f24bd33
Fully deletes users from g in test tearDown
2020-07-30 10:40:06 -04:00
31982f81ae
Merge branch 'dev' into feature/documents_publishing
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# Conflicts:
# Pipfile.lock
2020-07-30 10:17:08 -04:00
1b0ebecbf4
Uses Flask session to store impersonation state.
2020-07-30 10:17:02 -04:00
d301e9e6fa
Adds list_users endpoint. Adds admin impersonate uid parameter to user endpoint. Adds some utility methods to user service. Refactors authentication tests.
2020-07-29 22:47:47 -04:00
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
d617af8565
All tests are passing - may need to refactor a bit, / remove comments
2020-07-28 11:02:49 -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
70ad3872a7
Fix several bugs, most had an issue with the bpmn document
2020-07-27 12:02:34 -04:00
a124e13c6a
Replace all legacy style calls with new calls.
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Still having issues where we try to eval an empty definition, not quite sure why there is a difference from what we had before. I may need to revert some of it and determine what is going on.
2020-07-24 14:33:24 -04:00
f5ab283538
Test of adding in the ability of augmenting the workflow to include internal scripts like StudyInfo
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This is the first waypoint on a larger effort to make all of the 'special scripts' that currently require a shebang to be just another python function.
2020-07-24 12:08:46 -04:00
5ec5fcb4e4
Correcting an issue with the Navigation where it did not correctly handle looking back to a previous task within the workflow.
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In some cases the session was not getting committed, leaving rogue assignments outstanding for a workflow.
2020-07-23 12:00:24 -04:00
855f5544e5
Adds enrollment_date to study model
2020-07-22 09:35:08 -04:00
6caf44544c
Merge branch 'dev' into cr-connect-92-scripting-enhancements
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# Conflicts:
# crc/static/bpmn/ind_supplement/ind_supplement.bpmn
# tests/workflow/test_workflow_service.py
2020-07-20 13:01:23 -04:00
dd0f984347
Drop backwards compatibility of scripts. While this will cause some initial pain, it's less confusing and error prone, and we are still in the development phase of the project. Were this going straight to production we would likely want to keep this backwards compatibility.
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Don't parse on spaces if this is python code, so we avoid any errors in processing - spaces should be valid.
2020-07-20 12:26:34 -04:00
b85869905b
Merge branch 'cr-connect-92-scripting-enhancements' of github.com:sartography/cr-connect-workflow into cr-connect-92-scripting-enhancements
2020-07-20 11:40:10 -04:00
06430550c8
Dropping the RRT-Data-Fix, it should have come out already, but had a failing test, so pulling it out now rather than delve into what is going wrong with obsolete code.
2020-07-20 11:39:50 -04:00
f415f22ccb
Add warning message when we fail due to syntax error and then we try to look up the class as a backup
2020-07-20 10:12:15 -04:00
fcb772c900
Reporting to Sentry all captured exceptions and enabling multiple environments
2020-07-19 16:40:33 -06:00
73400ed6c7
Adding proper tests for files publishing
2020-07-17 16:59:25 -06:00
e82532aad8
Updates IND workflow spec. Fixes validation process to return lookups for enum values.
2020-07-17 11:51:21 -04:00
de54b63e20
Process scripts with no shebang (#!) as a regular python script. If there is a shebang, we look up the class as we did before.
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I've also made it so that it falls back if we accidentally forget to add a shebang to a study as this would be a breaking change.
With the fallback feature, it should work with unmodified bpmn documents.
2020-07-17 10:56:04 -04:00
ab5771024e
Check in for sanity check
2020-07-17 09:24:53 -04:00
d67105332f
Merge branch 'dev' into feature/lanes_and_roles
2020-07-16 14:00:53 -04:00
d0279a11e5
Fixes failing unit test
2020-07-15 17:44:46 -04:00
08fba1a4dc
Merge branch 'dev' into feature/dynamic_enum_list
2020-07-15 13:09:02 -04:00
c7662315aa
Assure that any errors that occur during the do_engine_steps is correctly captured and returned to the end user or configurator with enough information for them to act on.
2020-07-15 11:16:35 -04:00
fa7608053a
fixing a failed test.
2020-07-14 22:23:54 -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
d71ff80eac
Adds end and start events
2020-07-14 13:42:52 -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
463660f185
Merge branch 'dev' into feature/dynamic_enum_list
2020-07-13 17:47:56 -04:00
07066b8a16
Looks up enum options from task data
2020-07-13 17:46:28 -04:00
9e29a43785
Correct for a race condition where multiple lookup tables are built for the same field and workflow specification, causing it to appear that the models are not updating correctly.
2020-07-13 12:45:51 -04:00
b7920989ed
WIP: Adds Camunda property for retrieving enum field options from task data.
2020-07-10 14:48:38 -04:00
7f0b35ff27
Merge branch 'dev' into feature/enum_lookup_data
2020-07-10 10:27:51 -04:00
ff7c30b879
Merge pull request #138 from sartography/fix/cleanup_todos
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Cleanup pending TODOs
2020-07-10 08:26:47 -04:00
6a79fb3581
There may be multiple investigators of the same type that come back from the protocol builder, adding some tests and additional code to handle this, but still keep the list flat, currently appends a number to the investigator type when there is more than one.
2020-07-07 17:16:33 -04:00
64f9bd2ca7
Tiny leftover
2020-07-07 08:38:33 -06:00
b4e127b3b7
Cleaning properly previous versions
2020-07-07 08:32:41 -06:00
a302208890
Updating test for study with approvals
2020-07-07 08:32:41 -06:00
c7b864f9c7
Cleaning up old notes
2020-07-07 08:32:20 -06:00
517cd8fc91
Merge branch 'dev' into feature/enum_lookup_data
2020-07-06 16:31:19 -04:00
bb4000ff6d
Don't attept to load up the workflows for abandoned studies.
2020-07-06 16:01:43 -04:00
8a66128189
Bug fixes after bumping the version of Spiffworlflow to the latest - which has fixes for sequential multi-instance.
2020-07-06 15:34:24 -04:00
419c05e46c
Merge branch 'dev' into fix/more-info-in-exceptions
2020-07-06 12:51:24 -04:00
a5cef8775e
* Modifying the StudyInfo script to return both "investigators" and "roles", the investigators argument will return only the current active investigators according to the protocol builder. The "roles" argument returns all possible roles - it is what "investigators" use to be.
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* The Task.title returned to the front end will now attempt to process the "display_name" property for dot-notation syntax, making it possible to use this for multi-instance tasks,
but will work in all cases where we want he title to change based on values in the data model.
* Fixing a bug the test_study_api where it wasn't updated when we made recent changes to the different states of a study.
*
2020-07-06 12:09:21 -04:00
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
84973d2351
resolving comments from pull request.
2020-06-30 12:24:48 -04:00
93bf46354b
A last minute change to make the API a little clearer and cleaner broke some tests.
2020-06-30 11:12:28 -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
e650a46073
Fixes local testing bug where working directory was sometimes wrong.
2020-06-29 16:41:42 -04:00
49e80398be
Merge branch 'rrt/dev' into dev
2020-06-29 14:56:01 -04:00
a996c81508
Gets mi_index out of Spiff task internal data
2020-06-28 11:35:35 -04:00
d4bcb9af65
Proper error handling in csv/dumps for approvals
2020-06-27 13:59:04 -06:00
848ad563d3
Only filters by mi_index if task has a mult_instance_index
2020-06-26 12:47:42 -04:00
f9f3003ef0
Filters by multi-instance index, if applicable
2020-06-26 12:31:37 -04:00
150117587e
Merge branch 'dev' into feature/parallel_multiinstance_tasks
2020-06-25 23:20:38 -04:00
665faaa175
Send emails from service
2020-06-25 16:18:42 -06:00
44995e3813
Merge branch 'feature/emails-enhancement' of github.com:sartography/cr-connect-workflow into feature/emails-enhancement
2020-06-25 14:37:04 -06:00
c3ceda4c2f
Replaces xml.etree with lxml.etree
2020-06-25 14:02:16 -04:00
7116b582e8
Splitting commands properly without losing double quoted strings
2020-06-25 12:01:24 -06:00
fe5a7ddce3
Merge remote-tracking branch 'origin/rrt/dev' into feature/emails-enhancement
2020-06-25 13:29:06 -04:00
5d1ae402b6
Slight refactor on data passed to template rendering
2020-06-24 22:43:44 -06:00
a0d877e02f
Feedback from PR addressed
2020-06-24 22:23:31 -06:00
5327b469f6
Merge branch 'rrt/dev' into feature/emails-enhancement
2020-06-24 21:46:53 -06:00
dd10e56d1a
Adding forgotten variables to returned dict
2020-06-22 14:56:24 -06:00
dc5ffd29d0
Refactoring shared code
2020-06-22 14:07:57 -06:00
e5541e4950
Enable CSV download
2020-06-22 09:24:58 -06:00
b8d60ca944
Spreadsheet generation
2020-06-22 07:14:00 -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
4db815a999
Handling incoming values from processor
2020-06-17 21:11:47 -06:00
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
da048d358e
Merge branch 'dev' into feature/refactor_data_loading
2020-06-17 17:14:30 -04:00
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
40ff3b5fcb
Uses mock LDAP if LDAP_URL environment variable is 'mock'
2020-06-16 21:43:20 -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
92580ee867
adding an additional error check for invalid json returned from the Protocol builder.
2020-06-15 12:26:53 -04:00
eec4b579a7
Don't error out if we don't have a valid study id when doing validation.
2020-06-15 11:27:28 -04:00
5f13b96079
More enhancements
2020-06-12 12:17:08 -06:00
2a84d5196a
filter, not filter_by
2020-06-12 14:13:27 -04:00
e3126620b3
Eschews obfuscation
2020-06-12 14:09:08 -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
e9e805b2c9
Storing emails in database
2020-06-09 22:57:56 -06:00
777e429382
Merging production back into dev, because we got out of whack somehow.
2020-06-08 14:19:30 -04:00
8cf420b781
Default mail user name and password to blank.
2020-06-08 14:15:56 -04:00
e370148380
Merge pull request #112 from sartography/rrt/dev
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Rrt/dev
2020-06-08 13:18:41 -04:00
0351b3548a
Adding bcc to all emails sent
2020-06-08 11:17:17 -06:00
f91fbf76b9
Capturing explicit errors from mails
2020-06-08 09:16:26 -06:00
af1c848f65
Merge branch 'rrt/dev' into rrt/testing
2020-06-07 19:57:09 -04:00
213d3f3501
Merge branch 'feature/better_approval_status' into rrt/dev
2020-06-05 19:11:16 -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
f0904e75a6
Sets main approval status after related approvals have been populated
2020-06-05 15:54:53 -04:00
663da57d8b
Config can read smtp values from environment now
2020-06-05 13:54:37 -06:00
57a7c7fa54
Approve/deny fixes
2020-06-05 13:39:52 -06:00
1f32a99efe
Some approval statuses coming back as null., fixed
2020-06-05 14:55:49 -04:00
16ca4fa2c0
Merge branch 'rrt/dev' into feature/mail-system
2020-06-05 12:35:05 -06:00
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
4fc1b51cbc
Approve/denied emails
2020-06-05 12:08:31 -06:00
4727d87adb
Hooking up emails into process - start
2020-06-04 20:37:28 -06:00
b6abb0cbe2
using a restartable strategy to get around login errors
2020-06-04 18:03:59 -04:00
9cfe00dfd0
Don't bind all the time.
2020-06-04 15:38:45 -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
8c36d9f367
Email calls outline
2020-06-04 11:43:10 -06:00
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
Dan Funk
Aaron Louie
Carlos Lopez
Kelly McDonald