e8067fe34e
adding additional data to the study details returned during validation/shield testing.
2020-08-12 17:04:59 -04:00
7bfcdd53cd
Merge branch 'dev' into cr-workflow-108
2020-08-12 10:50:19 -04:00
c4a15be90c
Change dmn files to python standard,
...
NB: this means mostly false=>False and true=>True
We may have to decide if we want to add false and true as extensions in the python namespace.
2020-08-12 10:48:59 -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
1ab765b50b
Add test for PMI problem
2020-08-06 10:29:14 -04:00
bf3dae1885
Collecting user generated study changes
2020-08-05 20:29:05 -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
04399eec2a
Accepting None for primary_investigator_id
2020-08-04 11:38:46 -06:00
cd9376cf8e
Adding back ability to update studies
2020-08-04 09:13:24 -06:00
50b207307a
Merge branch 'dev' into feature/update_study_status_latest
2020-07-31 14:26:24 -06:00
4fcba113b8
Fixing tests
2020-07-31 11:49:04 -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
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
44deee12de
Merge branch 'dev' into feature/improved_task_event_api
2020-07-30 11:28:52 -04:00
37d1ba5d5a
Merge pull request #160 from sartography/feature/ldap_lookup_script
...
Ldap lookup script
2020-07-30 11:27:38 -04:00
bf4d882519
Merge branch 'dev' into feature/ldap_lookup_script
2020-07-30 11:19:24 -04:00
2905fc6173
Merge branch 'feature/ldap_lookup_script' of github.com:sartography/cr-connect-workflow into feature/ldap_lookup_script
2020-07-30 11:17:48 -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
...
# 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
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
79adb673f2
Fixes display_name custom properties
2020-07-28 14:04:18 -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.
...
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.
...
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
51d6d6a5fa
Fixing failing tests around a notifications workflow.
2020-07-27 16:54:46 -04:00
8d42d520a0
Adding events to the study that is returned via the api.
2020-07-27 16:32:23 -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
0d2cb8c1b8
Correcting an issue with the Navigation where it did not correctly handle looking back to a previous task within the workflow.
...
In some cases the session was not getting committed, leaving rogue assignments outstanding for a workflow.
2020-07-27 12:36:20 -06:00
263ea4d00f
Adds manual task
2020-07-27 12:35:53 -06:00
6cdb9c3b3a
Exposes date in TaskEvent endpoint
2020-07-27 12:35:53 -06:00
4adb6a1b44
Adds enrollment_date to study model
2020-07-27 12:34:25 -06:00
6379b26a71
Add a few more details to the workflow metadata model.
2020-07-27 12:34:25 -06:00
cc55aed89c
Change exception name
2020-07-27 12:18:28 -04:00
70ad3872a7
Fix several bugs, most had an issue with the bpmn document
2020-07-27 12:02:34 -04:00
824582dab1
Hot fix to correct for a failing test due to updates in Spiffworkflow library,
...
and modifying the token authorization so that we can log in as different users when not in production mode.
2020-07-27 11:25:29 -04:00
a124e13c6a
Replace all legacy style calls with new calls.
...
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
...
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
842d2ee100
Supporting study status update
2020-07-23 10:58:24 -06:00
6fae89b1fc
Adds manual task
2020-07-22 14:48:36 -04:00
b87f55fbd7
Exposes date in TaskEvent endpoint
2020-07-22 14:48:10 -04:00
aa7437bfc4
Merge branch 'dev' into feature/approvals_dashboard_prototype
2020-07-22 13:08:32 -04:00
acb43cc271
Removing an unused function and addign a fix me.
2020-07-22 11:40:49 -04:00
a243c14d75
Updating to lastest spiffworkflow which uses box to support dot notation.
...
Adding a new endpoint for evaluating the results of a python expression into the tools section of the api.
2020-07-22 11:30:16 -04:00
855f5544e5
Adds enrollment_date to study model
2020-07-22 09:35:08 -04:00
41cbce8e01
Updating bpmn test
2020-07-21 21:08:08 -06:00
522f848682
Addressing feedback
2020-07-21 20:54:03 -06:00
313770d538
Ldap lookup script
2020-07-21 20:54:03 -06:00
3d9eeab502
Add a few more details to the workflow metadata model.
2020-07-21 15:18:08 -04:00
d01b30debc
Building the start of an endpoint that could be used by logged in / authenticated users that will evaluate basic python functions sent in via the API.
...
The hope here is that we can process these in real time for the front end, but still do it using the same evaluation engine we use everywhere else, so
the syntax for things like hide-expressions can be properly verified during workflow validation and will be assured to work during front end rendering.
Removing any all javascript code in the BPMN models.
2020-07-21 13:57:33 -04:00
73338e61d5
Merge branch 'dev' into feature/ldap_lookup_script
2020-07-20 14:56:34 -04:00
7f8c7097ef
Merge branch 'dev' into feature/ldap_lookup_script
2020-07-20 13:05:33 -04:00
6caf44544c
Merge branch 'dev' into cr-connect-92-scripting-enhancements
...
# 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.
...
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
a39cacdf00
Ldap lookup script
2020-07-19 21:53:18 -06:00
fcb772c900
Reporting to Sentry all captured exceptions and enabling multiple environments
2020-07-19 16:40:33 -06:00
59d04feb23
Adding missing import
2020-07-17 17:08:44 -06:00
73400ed6c7
Adding proper tests for files publishing
2020-07-17 16:59:25 -06:00
d34d08b121
Trying to force re-run to clear SonarCloud
2020-07-17 13:33:42 -06:00
331a6c0aeb
Fixing tests
2020-07-17 12:52:09 -06:00
f4eb592b87
Extracting token to env var
2020-07-17 12:31:05 -06:00
419d06c95b
Updating file by latest version
2020-07-17 12:31:05 -06:00
a10ef9066d
Github integration with admin
2020-07-17 12:31:05 -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.
...
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
6c6c5d315d
Fixing a stupid mistake where I used an unquoted value in the mock data for validation, which created a dict that could not be serilized.
2020-07-16 13:28:00 -04:00
6a24bcbf6f
Clears out Jinja statements to get test to pass for now
2020-07-16 09:45:11 -04:00
d0279a11e5
Fixes failing unit test
2020-07-15 17:44:46 -04:00
3fe9662f26
Updates DSP workflow
2020-07-15 16:48:32 -04:00
77948c7828
Updates Personnel workflow
2020-07-15 14:28:55 -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.
...
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
c8214a4cc4
Updates DSP
2020-07-14 14:49:04 -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.
...
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
069a9cac5e
Merge branch 'feature/enum_lookup_data' of github.com:sartography/cr-connect-workflow into feature/enum_lookup_data
2020-07-13 12:46:13 -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
32343c04d6
Merge branch 'feature/enum_lookup_data' into feature/dynamic_enum_list
2020-07-13 11:53:29 -04:00
ccb2addeb5
Fixes another one
2020-07-10 16:27:09 -04:00
743e18746b
Fixes some syntax issues
2020-07-10 16:17:49 -04:00
aea7b23aab
Removes unnecessary test workflow spec
2020-07-10 14:52:08 -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
ff7c30b879
Merge pull request #138 from sartography/fix/cleanup_todos
...
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.
...
* 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
340ae68eed
Sets PB status to Active by default
2020-07-01 11:01:36 -04:00
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.
...
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.
...
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
e03e3d9bd9
Merge branch 'dev' into fix/empty_task
2020-06-29 15:22:30 -04:00
49e80398be
Merge branch 'rrt/dev' into dev
2020-06-29 14:56:01 -04:00
9e1881ed89
Merge branch 'dev' into fix/empty_task
2020-06-29 14:43:34 -04:00
cff270071a
Merge branch 'rrt/dev' into fix/empty_task
2020-06-29 08:41:21 -06:00
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
23941d73ad
Fixes variable names. Updates Spiff to STG-26 branch. Updates package versions.
2020-06-25 11:02:57 -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
a40adeca3a
Merge branch 'dev' into STG-26
2020-06-22 19:57:43 -04:00
dd10e56d1a
Adding forgotten variables to returned dict
2020-06-22 14:56:24 -06:00
bb825f8097
Dropping old parameter from endpoint
2020-06-22 14:09:58 -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.
...
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
e6d74aaa1a
Removing extra index when parsing users info
2020-06-18 12:53:50 -06:00
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
5ce279b663
Dropping silly pdb statement
2020-06-17 17:36:15 -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
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:
...
* 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
cf09d986ea
Merge branch 'feature/admin' into feature/refactor_data_loading
2020-06-17 16:48:43 -04:00
1844c93919
STG-26 - basic test case for a looping task
...
Criteria :
task.multi_instance_type == 'looping'
to terminate, use the standard endpoint for submitting form data with a query variable of terminate_loop=true
Will likely need two buttons:
"Submit and quit"
"Submit and add another"
or something similar
2020-06-17 11:35:06 -04:00
c730a7b1ec
Sending subject and using default sender
2020-06-17 08:53:02 -06:00
40ff3b5fcb
Uses mock LDAP if LDAP_URL environment variable is 'mock'
2020-06-16 21:43:20 -04:00
2ff836019f
Sonarcloud fix
2020-06-16 18:55:18 -06:00
d4a285883f
Email script
2020-06-16 18:42:36 -06:00
59d66be10f
Handling empty task state
2020-06-16 13:13:30 -06:00
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
bd1321baf0
Merge branch 'dev' into feature/admin
2020-06-16 12:29:43 -04:00
0608ffa08a
Restricting the admin endpoints to be admin only, and adding a bit of configuration.
2020-06-16 12:26:25 -04:00
7723862530
Merge branch 'dev' of https://github.com/sartography/cr-connect-workflow into dev
2020-06-15 16:30:17 -04:00
672ed367e0
Merge branch 'rrt/dev' into feature/admin
2020-06-15 16:13:57 -04:00
706c4afda5
Create a parameter 'lane' since we are using the output from the nav-list as the input to the NavigationItem initializer.
...
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
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
691258a4fb
Fixes bug where approvals counts were off by 1. Tests CSV export and all approvals endpoints with lots of records.
2020-06-11 17:15:44 -04:00
f51e5e4e6b
Adds tests for approval counts and all approvals endpoints
2020-06-11 16:39:00 -04:00
768f14b3ac
Cleans up console logging
2020-06-11 13:42:44 -04:00
312eef4d40
Raises 403 error if no user found
2020-06-11 13:07:27 -04:00
cccff9b856
Fixes broken unit tests. But still broken.
2020-06-11 11:29:58 -04:00
1f5554d0d8
Merge branch 'rrt/dev' into feature/swagger_admin_authentication
2020-06-11 08:55:29 -04:00
e9e805b2c9
Storing emails in database
2020-06-09 22:57:56 -06:00
5c1c0f685e
Tests update
2020-06-08 16:17:41 -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
...
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
87e2379871
Merge branch 'rrt/dev' into feature/swagger_admin_authentication
2020-06-08 10:30:16 -04:00
4cf52b527c
Adding admin dashboard
2020-06-08 07:14:31 -06:00
1c8c085afe
Merge branch 'rrt/dev' into rrt/testing
2020-06-07 22:39:34 -04:00
049424d01b
Adds back an endpoint that returns all approvals across all statuses or users
2020-06-07 22:38:21 -04:00
af1c848f65
Merge branch 'rrt/dev' into rrt/testing
2020-06-07 19:57:09 -04:00
0774942b99
Merge branch 'feature/better_approval_status' into rrt/dev
2020-06-05 22:19:58 -04:00
1d3f98b381
Adds endpoint to quickly get counts of approvals in each status group for a user
2020-06-05 22:19:37 -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.
...
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.
...
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.
...
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
1324533865
Some additional cleanup - when a file is "archived" it is no longer returned for any endpoints about files, but it
...
is directly accessible via id, in the event some request is made for it at a later date.
2020-06-04 09:49:42 -04:00
f581bd9f2b
Mails for approval process
2020-06-04 00:35:59 -06:00
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
c179c7781b
Do not process or return cancelled approvals via the API.
2020-06-03 16:50:47 -04:00
e102214809
minor cleanup of error codes.
2020-06-03 15:03:22 -04:00
299ad4fc8b
Adding more details to the csv output, and assuring we don't miss people with outstanding approvals that were cancelled.
2020-06-03 07:58:48 -04:00
4bf13b0718
Doing everything I can imagine to get a CSV dump out tomorrow.
2020-06-02 22:01:49 -04:00
2424b9d78c
Don't overwrite the approval, just allow minor changes.
2020-06-02 19:36:06 -04:00
c7484267e1
For the main approval endpoints - we now group the approvals by study. So you get one record back for each study, but it may have other approvals along with it as "related_approvals".
...
We now cache the LDAP records - so we look in our own database for the record before calling out to ldap for the details when given a straight up computing id like dhf8r.
Added "date_approved" to the approval model.
And moved the approver and primary investigator into real associated models to make it easier to dump.
Fixed a problem with the validation that was causing it to throw incorrect errors on valid workflows. Getting it to behave a little more like the front end behaves, and respecting the read-only fields. But it was mainly to do with always returning all the data with each form submission.
2020-06-02 18:17:00 -04:00
59e91ec414
Don't add an empty approval record.
2020-06-02 08:35:19 -04:00
d8329e9eff
I completely missed pushing up my changes last night before handing back over to Carlos. Sorry about that.
...
Added checks to assure the approver matches g.uid of the current user - otherwise don't modify the approval record.
2020-06-02 07:43:19 -04:00
4090667a5d
Missed committing a pile of changes last night.
2020-06-02 07:08:29 -04:00
a78db8834c
Merge pull request #99 from sartography/feature/sentry
...
Enabling Sentry for boxes with the flag set
2020-06-02 06:28:06 -04:00
d0918e9ed3
Merge pull request #98 from sartography/fix/approvals-info
...
Approval info addition
2020-06-02 06:26:56 -04:00
95a3b22bf0
Enabling Sentry for boxes with the flag set
2020-06-01 19:59:55 -06:00
c2a1b0175a
Tweaks to approvals
2020-06-01 21:49:30 -04:00
1db9401166
Don't put all the data into Spiff Tasks on a reload or backtrack, just store the data that gets submitted each time in the task log, and use that.
...
This should correct issues with parallel tasks and other complex areas - so we don't have tasks seeing data that isn't along their path.
2020-06-01 17:42:39 -04:00
3c2849f40d
Approval info addition
2020-06-01 15:29:59 -06:00
51accc350c
Updates doc template
2020-06-01 13:37:44 -04:00
885ce5668e
Updates RRT workflow spec files
2020-06-01 13:29:57 -04:00
c790737bf0
The complete_template script might not grab the correct document when validating, fixed.
...
Updated to latest RRT files, and passing.
2020-06-01 12:33:58 -04:00
b6bf843f6e
used 'name' rather than 'value' in the lookup options during validation, causing a disconnect with how this is processed on the front end.
2020-06-01 11:00:56 -04:00
7c8b7829ea
Merge branch 'rrt/dev' into feature/approvals_enhancements
2020-06-01 00:41:51 -04:00
1702ab2576
Fixes decision tables that were causing failing tests
2020-06-01 00:36:25 -04:00
ea441dbff5
More updates
2020-06-01 00:28:37 -04:00
8092bbe682
Wrong file in wrong place.
2020-06-01 00:17:20 -04:00
7351dc4a43
Updates RRT workflow spec files for reals this time
2020-06-01 00:14:09 -04:00
2d5eb740ef
Updates RRTworkflow spec files
2020-06-01 00:07:50 -04:00
bec11980eb
Fixing broken test by using proper FileSchema
2020-05-31 22:00:52 -06:00
b2e56f797b
Converting ApprovalModel to Approval in order to serialize properly the result
2020-05-31 21:02:47 -06:00
cd16b984e0
Adds workflow spec title to workflow api schema
2020-05-31 22:46:56 -04:00
f0bd8d4f9e
Adds approvals to study schema. Adds approvals endpoint
2020-05-31 22:46:32 -04:00
9c7de39b09
This adds additional file data details to the study model as well.
2020-05-31 21:15:40 -04:00
dd6c1d2b42
Renaming approval files
2020-05-31 18:16:42 -06:00
2e54f07095
Adding more info to files and renaming approval waiting status
2020-05-31 17:24:23 -06:00
c4a84ac509
Work in progress: Trying to get Swagger to use verify_token_admin to protect admin endpoints. Not working for some reason, though.
2020-05-31 18:01:08 -04:00
be9b613bbb
Refactors user authentication endpoints so we can use the Swagger UI in production mode
2020-05-31 16:49:39 -04:00
26809d1470
Waiting status renaming
2020-05-31 13:35:42 -06:00
2bc735a3f0
Kelly wrote a beautiful method for resetting the workflow that doesn't loose data when reset inside a parallel task, all I needed to do was use it.
...
Catching TypeErrors and reporting them back to the UI so we don't 500 in a bad way (but we still 500)
2020-05-31 13:48:00 -04:00
98fb305868
Run the validation process twice, each time it is requested, first populating everything, and then a second time
...
using on the required form fields.
2020-05-30 18:43:20 -04:00
1f0e8741ba
Run the validation twice, once completing all of the data, and a second time, completing only the required fields.
...
Also, add a helper method to reduce boiler plate code around Workflow Exceptions.
2020-05-30 17:26:27 -04:00
860c475b29
Fill out repeating sections during validation process.
...
Also, when returning error messages, attempt to include the task data for the task that caused the error.
Also, when attempting to delete any file, respond with an API error explaining the issue, and log the details.
2020-05-30 15:37:04 -04:00
d51fbe51e0
Merge branch 'dev' of github.com:sartography/cr-connect-workflow into dev
2020-05-29 15:18:41 -04:00
4e4cc7884c
Better ldap searching.
2020-05-29 15:17:51 -04:00
34b812b74e
Updates RRT workflow spec files
2020-05-29 10:49:47 -04:00
895d2f8852
Slight change to the way the approval model is connected.
2020-05-29 05:04:18 -04:00
0ba2819867
Merge branch 'dev' into feature/approval_request_script
2020-05-29 04:51:50 -04:00
afb6be7c60
re-working the way the redirects function, so we pass arguments as a get parameter. Just trying to get rid of the weird lag on production.
...
I noticed the validation sometimes looks ahead for files, so looking at all the tasks now, not just the ready tasks for the lookup field.
Ran into an issue with validation where a workflow model was required, so I create one and delete it. Another refactor for another day.
2020-05-29 04:42:48 -04:00
11413838a7
Faster lookup fields. We were parsing the spec each time to get details about how to search. We're just grabbing the workflow id and task id now and building that straight into the full text search index for faster lookups. Should be peppy.
...
Another speed improvement - data in the FileDataModel is deferred, and not queried until it is specifically used, as the new data structures need to use this model frequently.
2020-05-29 01:39:39 -04:00
aea78de066
Merge remote-tracking branch 'origin/dev' into feature/file_refactor_part2
2020-05-28 20:06:32 -04:00
dba41f4759
Ludicrously stupid launch in a refactor of the way all files work in the system at a time where I crave sleep and peace above all other things.
...
Added a File class, that we wrap around the FileModel so the api endpoints don't change, but File no longer holds refences to versions or dates of the file_data model, we
figure this out based on a clean database structure.
The ApprovalFile is directly related to the file_data_model - so no chance that a reviewer would review the incorrect version of a file.py
Noticed that our FileType enum called "bpmn" "bpmm", hope this doesn't screw someone up.
Workflows are directly related to the data_models that create the workflow spec it needs. So the files should always be there. There are no more hashes, and thus no more hash errors where it can't find the files to rebuild the workflow.py
Not much to report here, other than I broke every single test in the system at one point. So I'm super concerned about this, and will be testing it a lot before creating the pull request.
2020-05-28 20:03:50 -04:00
dedec02d48
Updates RRT workflow spec files
2020-05-28 10:43:03 -04:00
41b26e28bd
Merge branch 'dev' into feature/approval_request_script
2020-05-28 08:11:31 -06:00
cd7f67ab48
A major refactor of how we search and store files, as there was a lot of confusing bits in here.
...
From an API point of view you can do the following (and only the following)
/files?workflow_spec_id=x
* You can find all files associated with a workflow_spec_id, and add a file with a workflow_spec_id
/files?workflow_id=x
* You can find all files associated with a workflow_id, and add a file that is directly associated with the workflow
/files?workflow_id=x&form_field_key=y
* You can find all files associated with a form element on a running workflow, and add a new file.
Note: you can add multiple files to the same form_field_key, IF they have different file names. If the same name, the original file is archived,
and the new file takes its place.
The study endpoints always return a list of the file metadata associated with the study. Removed /studies-files, but there is an
endpoint called
/studies/all - that returns all the studies in the system, and does include their files.
On a deeper level:
The File model no longer contains:
- study_id,
- task_id,
- form_field_key
Instead, if the file is associated with workflow - then that is the one way it is connected to the study, and we use this relationship to find files for a study.
A file is never associated with a task_id, as these change when the workflow is reloaded.
The form_field_key must match the irb_doc_code, so when requesting files for a form field, we just look up the irb_doc_code.
2020-05-28 08:27:26 -04:00
97cdbfce94
Deletes extra line break
2020-05-27 23:48:48 -04:00
77f72e408f
Lookup Service now raises exact matches to the top. Very hackish, but it works.
2020-05-27 14:36:10 -04:00
54640988a7
Update endpoint fixes
2020-05-27 12:06:32 -06:00
d5e075db82
Order search results by relevancy in the lookup service.
2020-05-27 09:47:44 -04:00
397cb23b52
Is true "true", yes it is true. So true, is "false", so true, it is true.
2020-05-26 23:38:57 -04:00
0025931a2e
Trying hard to figure out why the DCOS servers think the protocol builder is enabled.
2020-05-26 23:18:14 -04:00
7869fa596e
Protocol Builder isn't disabled on the dcos servers, trying to figure out why, and assure it isn't some sort of weird race condition.
2020-05-26 22:42:49 -04:00
eb15d172c1
I absolutely must fix our cascade deletes, but I sort of like the horror such chunks of code cause, we really need to protect these endpoints, and assure they never get called under normal circumstances, and raise some thoughtful errors.
2020-05-26 21:18:09 -04:00
ccbf374b40
Loads of bug fixes.
...
Modifed the request_approval to take a list of arguments, which works better for us... today.
UpdateStudy correctly handles validation.
WorkflowService correctly populates random values from lookup tables.
And several fixes down in Spiffworkflow, including a big bug where only the last item in a decision table made it through.
2020-05-26 20:06:50 -04:00
987790164e
use redirect, not redirect_url.
2020-05-26 15:09:57 -04:00
7ed9411c74
Handling unavailability of ldap connection
2020-05-26 11:29:24 -06:00
72b59deeaf
Completing tests
2020-05-26 10:21:36 -06:00
a14168362a
Merge branch 'feature/support_ui_dashboard' into dev
2020-05-25 21:31:16 -04:00
1231b963d0
Enabling ldap lookup
2020-05-25 17:30:16 -06:00
727274ae33
Using full approval payload to update record
2020-05-25 15:40:24 -06:00
13186176ba
Improved LDAP searches, allow filtering on last name as well as uva id.
2020-05-25 16:00:36 -04:00
be057e8758
Adding an "UpdateStudy" task that is able to update the data on the study model, useful for setting core data points on the model, such as setting the Primary Investigator, or altering the Study Title.
...
Fixing a bug where the validation of forms did not correctly process auto-complete fields.
Fixing a bug where the approvals script and the update study script could not process dot notation correctly.
Moved populate_random_data into the WorkflowService where it makes more sense.
2020-05-25 15:30:06 -04:00
6cd4ef64d1
Fixing add_study api endpoint, so you can actually add a new "Study" with just some basic information.
...
Using the LDAP service for checking user details in development mode - even if you are using the back door.
Added a new Flask fucntion load-example-rrt-data that loads the rrt workflow, and not the CRC wrokflows.
Modified the "load-example-data" in the tests to use some test data, rather than loading up all the workflows[
in CRC each time, with a parameter to load crc data if that is required - which is enabled for just a handful of tests.
(Tests run in 1/4 the time now)
2020-05-25 12:29:05 -04:00
971d9a58e9
As we now have an approval_service.py, I moved all the business logic into this service and out of the request_approval.py script. And moved all tests for these features into a test file for the service. Will make it easier to cross reference what is happening, as everything all happens in one file.
...
As many of the scripts need to know the workflow, and it's down in a weird parameter, moved this so it is passed in each time.
2020-05-24 16:13:15 -04:00
e9bd19b112
Fixing broken test
2020-05-24 01:22:14 -06:00
49eb4b3f98
Making working endpoints for approvals
2020-05-23 23:53:48 -06:00
Dan Funk
Kelly McDonald
Aaron Louie
Carlos Lopez