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
182e375fdc
Adds a test for string manipulation
2020-08-21 13:46:10 -04:00
4dc98a6b6b
Injects current user into task data.
2020-08-21 13:34:37 -04:00
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
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
8f5488d910
Don't raise an error when validating workflows that use the ldap script.
2020-08-17 15:45:37 -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
32d47c1417
Merge remote-tracking branch 'origin/dev' into fix/delete_workflow_endpoint
2020-08-17 15:08:44 -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
aa010272cc
Automatic event creation in study creation
2020-08-14 08:36:10 -06:00
c57ac6d302
Merge pull request #185 from sartography/feature/107_current_user_info
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calling ldap with no argument will return information about the curre…
2020-08-14 09:18:10 -04:00
08c24b7441
Merge pull request #184 from sartography/PMI_fix
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Pmi fix
2020-08-14 09:17:58 -04:00
c12e2b97f3
calling ldap with no argument will return information about the current user.
2020-08-13 21:09:52 -04:00
1a963cf940
Merge branch 'dev' into PMI_fix
2020-08-13 20:49:45 -04:00
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
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,
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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
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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
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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
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.
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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
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.
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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,
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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.
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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
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.
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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.
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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
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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
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.
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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
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.
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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
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.
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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
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
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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
Dan Funk
Aaron Louie
Carlos Lopez
Kelly McDonald