Commit Graph

72 Commits

Author SHA1 Message Date
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
Dan Funk 6d4348d644 Fixing some failing tests. Moved the task properties into a dictionary, but moving the form field properties to a dictionary will be a larger effort that we don't want to get into on either the back or front end right this moment. 2020-05-14 14:39:14 -04:00
Dan Funk 55a1850e7c adding a navigation component to the Workflow Model.
running all extension/properties through the Jinja template processor so you can have custom display names using data, very helpful for building multi-instance displays.
Properties was returned as an array of key/value pairs, which is just mean.  Switched this to a dictionary.
2020-05-14 13:43:23 -04:00
Dan Funk da7cae51b8 Adding a new reference file that provides greater details about the investigators related to a study.
Improving the study_info script documentation to provide detailed examples of values returned based on arguments.
Making the tests a little more targetted and less subject to breaking through better mocks.
Allow all tests to pass even when ther protocol builder mock isn't running locally.
Removing the duplication of reference files in tests and static, as this seems silly to me at the moment.
2020-05-07 13:57:24 -04:00
Dan Funk 1571986c0e I had to give up and live with the idea that we can only render documentation on the current task, not on the previous or next tasks. I think this is ok. If you want to view a task, you need to make it the active task to assure all the parts and pieces are in place. 2020-05-06 13:01:38 -04:00
Dan Funk 9629b36e92 Setting JSON_SORT_KEYS to false, assuring that Flask does not resort all data returned to the front end.
Updating Spiff Workflow which has some critical behavioral changes around MultiInstance.
2020-05-06 10:59:49 -04:00
Dan Funk f1f8b91c9c Refactor the document details scripts. Now there is one script, it returns data in a consistent format, and has all the details required. The script is located in StudyInfo, with the argument documents. Make note that it returns a dictionary of ALL the documents, with a field to mark which ones are required according to the protocol builder. Others may become required if a workflow determines such, in which case the workflow will enforce this, and the document will have a count > 0, and additional details in a list of files within the document. I modified the XLS file to use lower case variable names, because it disturbed me, and we have to reference them frequently. Removed devious "as_object" variable on get_required_docs, so it behaves like the other methods all the time, and returns a dictionary. All the core business logic for finding the documents list now resides in the StudyService.
Because this changes the endpoint for all existing document details, I've modified all the test and static bpmn files to use the new format.
Shorting up the SponsorsList.xls file makes for slightly faster tests. seems senseless to load 5000 everytime we reset the data.
Tried to test all of this carefully in the test_study_details_documents.py test.
2020-04-29 15:08:11 -04:00
Dan Funk 0088364b1d Merge branch 'master' of github.com:sartography/cr-connect-workflow 2020-04-28 13:48:52 -04:00
Dan Funk 3e3a249e3c Verifying Sub-Process works, and adding a field to expose a hint as to the sub-process in which the task occurs.
Because the name field is now used to expose workflow/sub-process information on tasks, we can't use it to store the workflow_version, so that is now just stored on the database model.  Which is much cleaner and removes a duplication.
2020-04-28 13:48:44 -04:00
Aaron Louie 496e5b7719 Updates all workflow specs to match staging 2020-04-27 22:54:05 -04:00
Dan Funk 12eb039bc9 Server isn't erroring out, but can't find the lookup table id in the database, so trying to use the in-memory model instead, to give things time to get to the database. Really unsure what is happening here. Hard to see in the database. 2020-04-24 07:01:32 -04:00
Dan Funk 286af86f08 Forgot a missing bpmn file for running the tests. 2020-04-22 19:41:40 -04:00
Dan Funk 7b085c9c9d Adding an API Endpoint that will return a list of LookupValues that match a given query - can be used to populate an auto-complete table. 2020-04-22 19:40:40 -04:00
Dan Funk fd0adb1d43 Updated the study status to use a different enumeration. Migration correctly handles modifying the enum.
INCOMPLETE = 'Incomplete in Protocol Builder',
  ACTIVE = 'Active / Ready to roll',
  HOLD = 'On Hold',
  OPEN = 'Open - this study is in progress',
  ABANDONED = 'Abandoned, it got deleted in Protocol Builder'
2020-04-21 17:13:30 -04:00
Dan Funk 0a74bf8c44 We can now collect, and provide "extension properties" on a task as set in the camunda modeler.
These are provided as "properties" on a task, and are identical in structure to properties on a form field.
2020-04-21 12:07:59 -04:00
Dan Funk ee999a0f15 fixing a bunch of stupid mistakes because I am tried. 2020-04-20 20:28:12 -04:00
Dan Funk 59d400b058 Assure DMN can pick up name rather than label outputs. 2020-04-20 19:26:42 -04:00
Dan Funk 2d3402a719 Ldap Service with Test and mocks.
LDAP_URL can be set in an environment variable.
2020-04-20 15:16:33 -04:00
Dan Funk 815f40a539 forgot a critical file. 2020-04-17 15:18:03 -04:00
Dan Funk 241980f98f If you name add a file to a workflow that has the exact same name as a Task Spec's ID, and an extension of "md", it wll use that file as the markdown content, and ignore the markdown in the documentation on the task spec.
Moving the primary process id from the workflow model to the file model, and assuring it is updated properly.  This was causing a bug that would "lose" the workflow.
2020-04-17 13:30:32 -04:00
Dan Funk 3d820fcb21 Inital work on manual instance. 2020-04-16 11:07:29 -04:00
Dan Funk dc2895cb05 Allow configurators to upload xls files into a workflow for defining enumrations of values for dropdown lists in forms. Fixing lots of tests.
Found a problem where the documentation for elements was being processed BEFORE data was loaded from a script.  There still may be some issues here.

Ran into an issue with circular dependencies - handling it with a new workflow_service, and pulling computational logic out of the api_models - it was the right thing to do.
2020-04-15 11:13:32 -04:00
Dan Funk c79415a794 throw a sensible error when study is not found on get_study (don't 500)
some ugly fixes in the file_service for improving panda output from spreadsheet processing that I need to revist.
now that the spiff-workflow handles multi-instance, we can't have random multi-instance tasks around.
Improved tests around study deletion.
2020-04-08 13:28:43 -04:00
Dan Funk 697127660f Assure that all script tasks place data in a dictionary that is named exactly the same as the class - which is also the same as the Script tag. 2020-04-07 14:09:21 -04:00
Dan Funk c6b6ee5d70 Renamed the required_docs script to just "documents", and it returns all documented in the irb_documents look up table indexed on the "Code" - so details become available in the task data like "documents.IRB_INFOSEC_DOC.required".
Updated the irb_documents with shorter code names, thanks to Alex. Re-worked the DMN models so they can properly read from this new datastructure.
2020-04-06 16:56:00 -04:00
Dan Funk 60a10bb688 Marshmallow isn't the right tool when dealing with large models with lots of null values. Rather than fight the process of mamaging the Study Details, I'm letting that fall through, and we can test on an individual value or maybe set up a constants array when that becomes meaningful. 2020-04-03 16:24:38 -04:00
Dan Funk c7d2c28178 Vastly more informative ApiError model that provides details on the underlying task where the error occured.
Added a validate_workflow_specification endpoint that allows you to check if the workflow will execute from beginning to end using random data.
Minor fixes to existing bpmns to allow them to pass.
All scripts must include a "do_task_validate_only" that restricts external calls and database modifications, but performs as much logic as possible.
2020-03-27 08:29:31 -04:00