Commit Graph

98 Commits

Author SHA1 Message Date
Dan Funk 08c24b7441
Merge pull request #184 from sartography/PMI_fix
Pmi fix
2020-08-14 09:17:58 -04:00
Dan Funk 1a963cf940 Merge branch 'dev' into PMI_fix 2020-08-13 20:49:45 -04:00
Dan Funk 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.
Stop words are no longer excluded, so "other" is a valid search and gets a result.
2020-08-13 18:13:41 -04:00
Kelly McDonald 7bfcdd53cd Merge branch 'dev' into cr-workflow-108 2020-08-12 10:50:19 -04:00
Kelly McDonald 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
Kelly McDonald 623ecbae8e Add IRB test 2020-08-07 09:59:53 -04:00
Aaron Louie 2846bf9451 Fleshes out fake PB response, so workflows that pull from PB actually trigger validation errors 2020-08-04 15:50:29 -04:00
Aaron Louie c8881cbf91 Merge branch 'dev' into feature/approvals_dashboard_prototype 2020-07-31 12:17:22 -04:00
Dan Funk 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
Dan Funk a6ec0c92c7 Merge remote-tracking branch 'origin/dev' into cr-connect-106-augment-eval-methods 2020-07-30 11:38:47 -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
Aaron Louie 79adb673f2 Fixes display_name custom properties 2020-07-28 14:04:18 -04:00
Kelly McDonald 70ad3872a7 Fix several bugs, most had an issue with the bpmn document 2020-07-27 12:02:34 -04:00
Kelly McDonald 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
Kelly McDonald 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
Carlos Lopez 522f848682 Addressing feedback 2020-07-21 20:54:03 -06:00
Dan Funk 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
Kelly McDonald 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
Kelly McDonald ab5771024e Check in for sanity check 2020-07-17 09:24:53 -04:00
Aaron Louie 7cbafe966e Adds form key and pool name 2020-07-16 17:59:56 -04:00
Aaron Louie d67105332f Merge branch 'dev' into feature/lanes_and_roles 2020-07-16 14:00:53 -04:00
Aaron Louie 08fba1a4dc Merge branch 'dev' into feature/dynamic_enum_list 2020-07-15 13:09:02 -04:00
Dan Funk 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
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
Aaron Louie 07066b8a16 Looks up enum options from task data 2020-07-13 17:46:28 -04:00
Dan Funk 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
Dan Funk 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
Aaron Louie fe61333b7b Fixes typo 2020-06-26 12:31:15 -04:00
Dan Funk 150117587e Merge branch 'dev' into feature/parallel_multiinstance_tasks 2020-06-25 23:20:38 -04:00
Carlos Lopez a0d877e02f Feedback from PR addressed 2020-06-24 22:23:31 -06:00
Carlos Lopez e6d74aaa1a Removing extra index when parsing users info 2020-06-18 12:53:50 -06:00
Kelly McDonald 479f6d9647 STG-26
Do rename per conversation, continue to look for ways to implement looping in a way that is re-entrant
2020-06-18 12:01:02 -04:00
Carlos Lopez 4db815a999 Handling incoming values from processor 2020-06-17 21:11:47 -06:00
Carlos Lopez e947f40ec7 Merge branch 'rrt/dev' into feature/emails-enhancement 2020-06-17 20:10:11 -06:00
Carlos Lopez 896ba6b377 Email relies now on markdown content 2020-06-17 17:00:16 -06:00
Carlos Lopez 2ce2dc73b5 Rendering proper content & organizing file structure for email tests 2020-06-17 16:09:38 -06:00
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 d4a285883f Email script 2020-06-16 18:42:36 -06:00
Kelly McDonald 0d3105fe7e Make changes to the workflow names so that they are placed in the correct order - I made workflows go in order of the name rather than in the order they appear in the XML to allow more control over the way the nav list is displayed. 2020-06-15 12:32:19 -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 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 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
Dan Funk 77f72e408f Lookup Service now raises exact matches to the top. Very hackish, but it works. 2020-05-27 14:36:10 -04:00
Dan Funk d5e075db82 Order search results by relevancy in the lookup service. 2020-05-27 09:47:44 -04:00
Dan Funk d1606ffb1a forgot to include the new empty master workflow, which allows the tests to all pass. 2020-05-22 15:31:38 -04:00
Dan Funk 951710d762 ldap lookup.
Refactored calls into a new lookup_service to keep things tidy.

New keys for all enum/auto-complete fields:
    PROP_OPTIONS_FILE = "spreadsheet.name"
    PROP_OPTIONS_VALUE_COLUMN = "spreadsheet.value.column"
    PROP_OPTIONS_LABEL_COL = "spreadsheet.label.column"
    PROP_LDAP_LOOKUP = "ldap.lookup"
    FIELD_TYPE_AUTO_COMPLETE = "autocomplete"
2020-05-19 16:11:43 -04:00
Dan Funk 7a380fdeb4 Forgot to fix another test and to add the example file used for a previous test. 2020-05-16 15:38:15 -04:00
Dan Funk 53255ef35e massive overhaul of the Workflow API endpoint.
No Previous Task, No Last Task, No Task List.  Just the current task, and the Navigation.
Use the token endpoint to set the current task, even if it is a "READY" task in the api.
Previous Task can be set by identifying the prior task in the Navigation (I'm hoping)
Prefering camel case to snake case on all new apis.  Maybe clean the rest up later.
2020-05-15 15:54:53 -04:00