Commit Graph

300 Commits

Author SHA1 Message Date
Kelly McDonald 9a4d167dcd Add in api changes 2020-11-11 09:44:58 -05:00
mike cullerton a78af4eab8 Run cancel task during interrupt. Currently this uses Signal event. We may change this to the Cancel event. 2020-11-04 14:37:53 -05:00
Aaron Louie 182e375fdc Adds a test for string manipulation 2020-08-21 13:46:10 -04:00
Dan Funk 66e49a347a Minor tweaks to the eval endpoint, which should take both the expression and the data as one data structure. 2020-08-20 16:13:48 -04:00
Dan Funk d4c5e297cc Merge remote-tracking branch 'origin/dev' into fix/delete_workflow_endpoint 2020-08-17 15:09:11 -04:00
Dan Funk 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.
To help in running tests, adding __init__.py methods to all the test directories.
2020-08-17 14:56:00 -04:00
Carlos Lopez 369fe4bb35 Automatic events refactoring 2020-08-14 08:36:46 -06:00
Carlos Lopez aa010272cc Automatic event creation in study creation 2020-08-14 08:36:10 -06:00
Dan Funk 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
Carlos Lopez cd9376cf8e Adding back ability to update studies 2020-08-04 09:13:24 -06:00
Carlos Lopez 50b207307a Merge branch 'dev' into feature/update_study_status_latest 2020-07-31 14:26:24 -06:00
Carlos Lopez 5d23223e51 New study status update 2020-07-30 21:03:11 -06:00
Aaron Louie f8944da31f Merge branch 'dev' into feature/admin_impersonations 2020-07-30 13:01:46 -04:00
Aaron Louie faba0f55ab Adds AdminSession model and refactors impersonation methods to use it. 2020-07-30 12:40:53 -04:00
Dan Funk 31982f81ae Merge branch 'dev' into feature/documents_publishing
# Conflicts:
#	Pipfile.lock
2020-07-30 10:17:08 -04:00
Aaron Louie 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
Aaron Louie f897ee3aea Merge branch 'feature/approvals_dashboard_prototype' into feature/admin_impersonations 2020-07-29 10:32:46 -04:00
Dan Funk 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
Dan Funk 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
Dan Funk 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
Dan Funk 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
Dan Funk 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
Dan Funk 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
Dan Funk acb43cc271 Removing an unused function and addign a fix me. 2020-07-22 11:40:49 -04:00
Dan Funk 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
Dan Funk 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
Carlos Lopez fcb772c900 Reporting to Sentry all captured exceptions and enabling multiple environments 2020-07-19 16:40:33 -06:00
Carlos Lopez 59d04feb23 Adding missing import 2020-07-17 17:08:44 -06:00
Carlos Lopez 73400ed6c7 Adding proper tests for files publishing 2020-07-17 16:59:25 -06:00
Carlos Lopez d34d08b121 Trying to force re-run to clear SonarCloud 2020-07-17 13:33:42 -06:00
Carlos Lopez 331a6c0aeb Fixing tests 2020-07-17 12:52:09 -06:00
Carlos Lopez f4eb592b87 Extracting token to env var 2020-07-17 12:31:05 -06:00
Carlos Lopez 419d06c95b Updating file by latest version 2020-07-17 12:31:05 -06:00
Carlos Lopez a10ef9066d Github integration with admin 2020-07-17 12:31:05 -06:00
Dan Funk 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
Dan Funk 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
Dan Funk 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
Dan Funk 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
Aaron Louie 9e1881ed89 Merge branch 'dev' into fix/empty_task 2020-06-29 14:43:34 -04:00
Carlos Lopez cff270071a Merge branch 'rrt/dev' into fix/empty_task 2020-06-29 08:41:21 -06:00
Dan Funk 150117587e Merge branch 'dev' into feature/parallel_multiinstance_tasks 2020-06-25 23:20:38 -04:00
Carlos Lopez 665faaa175 Send emails from service 2020-06-25 16:18:42 -06:00
Dan Funk fe5a7ddce3 Merge remote-tracking branch 'origin/rrt/dev' into feature/emails-enhancement 2020-06-25 13:29:06 -04:00
Aaron Louie 23941d73ad Fixes variable names. Updates Spiff to STG-26 branch. Updates package versions. 2020-06-25 11:02:57 -04:00
Carlos Lopez 5327b469f6 Merge branch 'rrt/dev' into feature/emails-enhancement 2020-06-24 21:46:53 -06:00
Aaron Louie a40adeca3a Merge branch 'dev' into STG-26 2020-06-22 19:57:43 -04:00
Carlos Lopez dc5ffd29d0 Refactoring shared code 2020-06-22 14:07:57 -06:00
Carlos Lopez e5541e4950 Enable CSV download 2020-06-22 09:24:58 -06:00
Dan Funk 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
Carlos Lopez e6d74aaa1a Removing extra index when parsing users info 2020-06-18 12:53:50 -06:00
Dan Funk 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
Dan Funk cf09d986ea Merge branch 'feature/admin' into feature/refactor_data_loading 2020-06-17 16:48:43 -04:00
Kelly McDonald 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
Carlos Lopez 59d66be10f Handling empty task state 2020-06-16 13:13:30 -06:00
Dan Funk c7d8eaff30 Merge branch 'dev' into feature/refactor_data_loading 2020-06-16 13:15:43 -04:00
Dan Funk 0608ffa08a Restricting the admin endpoints to be admin only, and adding a bit of configuration. 2020-06-16 12:26:25 -04:00
Aaron Louie 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
Aaron Louie 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
Aaron Louie f51e5e4e6b Adds tests for approval counts and all approvals endpoints 2020-06-11 16:39:00 -04:00
Aaron Louie 768f14b3ac Cleans up console logging 2020-06-11 13:42:44 -04:00
Aaron Louie 312eef4d40 Raises 403 error if no user found 2020-06-11 13:07:27 -04:00
Aaron Louie cccff9b856 Fixes broken unit tests. But still broken. 2020-06-11 11:29:58 -04:00
Aaron Louie 1f5554d0d8 Merge branch 'rrt/dev' into feature/swagger_admin_authentication 2020-06-11 08:55:29 -04:00
Dan Funk 777e429382 Merging production back into dev, because we got out of whack somehow. 2020-06-08 14:19:30 -04:00
Dan Funk 8cf420b781 Default mail user name and password to blank. 2020-06-08 14:15:56 -04:00
Aaron Louie 87e2379871 Merge branch 'rrt/dev' into feature/swagger_admin_authentication 2020-06-08 10:30:16 -04:00
Aaron Louie 1c8c085afe Merge branch 'rrt/dev' into rrt/testing 2020-06-07 22:39:34 -04:00
Aaron Louie 049424d01b Adds back an endpoint that returns all approvals across all statuses or users 2020-06-07 22:38:21 -04:00
Aaron Louie af1c848f65 Merge branch 'rrt/dev' into rrt/testing 2020-06-07 19:57:09 -04:00
Aaron Louie 1d3f98b381 Adds endpoint to quickly get counts of approvals in each status group for a user 2020-06-05 22:19:37 -04:00
Dan Funk 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
Carlos Lopez 57a7c7fa54 Approve/deny fixes 2020-06-05 13:39:52 -06:00
Dan Funk 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
Dan Funk 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
Dan Funk 50d2acac9c Made a very stupid mistake with LDAP connections, pushing up quickly to production. 2020-06-04 11:57:00 -04:00
Dan Funk 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
Dan Funk 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
Dan Funk 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
Dan Funk c179c7781b Do not process or return cancelled approvals via the API. 2020-06-03 16:50:47 -04:00
Dan Funk e102214809 minor cleanup of error codes. 2020-06-03 15:03:22 -04:00
Dan Funk 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
Dan Funk 4bf13b0718 Doing everything I can imagine to get a CSV dump out tomorrow. 2020-06-02 22:01:49 -04:00
Dan Funk 2424b9d78c Don't overwrite the approval, just allow minor changes. 2020-06-02 19:36:06 -04:00
Dan Funk 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
Dan Funk 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
Dan Funk c2a1b0175a Tweaks to approvals 2020-06-01 21:49:30 -04:00
Dan Funk 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
Aaron Louie cd16b984e0 Adds workflow spec title to workflow api schema 2020-05-31 22:46:56 -04:00
Aaron Louie f0bd8d4f9e Adds approvals to study schema. Adds approvals endpoint 2020-05-31 22:46:32 -04:00
Dan Funk 9c7de39b09 This adds additional file data details to the study model as well. 2020-05-31 21:15:40 -04:00
Carlos Lopez 2e54f07095 Adding more info to files and renaming approval waiting status 2020-05-31 17:24:23 -06:00
Aaron Louie 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
Aaron Louie be9b613bbb Refactors user authentication endpoints so we can use the Swagger UI in production mode 2020-05-31 16:49:39 -04:00
Dan Funk 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
Dan Funk 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
Dan Funk 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
Dan Funk 0ba2819867 Merge branch 'dev' into feature/approval_request_script 2020-05-29 04:51:50 -04:00
Dan Funk 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
Dan Funk 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
Dan Funk 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