Commit Graph

97 Commits

Author SHA1 Message Date
Kelly McDonald d617af8565 All tests are passing - may need to refactor a bit, / remove comments 2020-07-28 11:02:49 -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
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
Dan Funk 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
Aaron Louie e82532aad8 Updates IND workflow spec. Fixes validation process to return lookups for enum values. 2020-07-17 11:51:21 -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
Aaron Louie 6a24bcbf6f Clears out Jinja statements to get test to pass for now 2020-07-16 09:45:11 -04:00
Aaron Louie 3fe9662f26 Updates DSP workflow 2020-07-15 16:48:32 -04:00
Aaron Louie 77948c7828 Updates Personnel workflow 2020-07-15 14:28:55 -04:00
Aaron Louie c8214a4cc4 Updates DSP 2020-07-14 14:49:04 -04:00
Aaron Louie ccb2addeb5 Fixes another one 2020-07-10 16:27:09 -04:00
Aaron Louie 743e18746b Fixes some syntax issues 2020-07-10 16:17:49 -04:00
Aaron Louie aea7b23aab Removes unnecessary test workflow spec 2020-07-10 14:52:08 -04:00
Aaron Louie f344fe60c0 WIP: Adds enum field lookup option data 2020-07-03 12:20:10 -04:00
Carlos Lopez 5c1c0f685e Tests update 2020-06-08 16:17:41 -06:00
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
Carlos Lopez 57a7c7fa54 Approve/deny fixes 2020-06-05 13:39:52 -06:00
Carlos Lopez 4fc1b51cbc Approve/denied emails 2020-06-05 12:08:31 -06:00
Carlos Lopez 4727d87adb Hooking up emails into process - start 2020-06-04 20:37:28 -06:00
Carlos Lopez f581bd9f2b Mails for approval process 2020-06-04 00:35:59 -06:00
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
Aaron Louie 51accc350c Updates doc template 2020-06-01 13:37:44 -04:00
Aaron Louie 885ce5668e Updates RRT workflow spec files 2020-06-01 13:29:57 -04:00
Dan Funk 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
Aaron Louie 1702ab2576 Fixes decision tables that were causing failing tests 2020-06-01 00:36:25 -04:00
Aaron Louie ea441dbff5 More updates 2020-06-01 00:28:37 -04:00
Aaron Louie 8092bbe682 Wrong file in wrong place. 2020-06-01 00:17:20 -04:00
Aaron Louie 7351dc4a43 Updates RRT workflow spec files for reals this time 2020-06-01 00:14:09 -04:00
Aaron Louie 2d5eb740ef Updates RRTworkflow spec files 2020-06-01 00:07:50 -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
Aaron Louie 34b812b74e Updates RRT workflow spec files 2020-05-29 10:49:47 -04:00
Aaron Louie dedec02d48 Updates RRT workflow spec files 2020-05-28 10:43:03 -04:00
Dan Funk 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
Dan Funk 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
Aaron Louie 481a9ed04c Gets image ids from task data and Injects images into jinja docx 2020-05-19 21:51:54 -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 b7c11fd893 Merge branch 'master' into feature/investigators_reference_file 2020-05-11 17:36:37 -04:00
Dan Funk 02f8764056 Updated to use the latest script engine / evaluation engine that creates a single location where all values used in BPMN/DMN are processed. Right now this is a python based interpreter, but we will eventually base this on FEEL expressions.
The validation process needs to take the api model into account so we catch errors with bad file names.
2020-05-11 17:04:05 -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 8ded625c7d Merge remote-tracking branch 'origin/chore/update_specs' into feature/previous_task
# Conflicts:
#	Pipfile.lock

Assuring that all documents from the xls spreadsheet are loaded when doing validations.
Fixing some failed tests.
2020-05-06 11:46:19 -04:00
Dan Funk 07e58e923d Merge remote-tracking branch 'origin/chore/update_specs' into feature/previous_task
# Conflicts:
#	Pipfile.lock

Assuring that all documents from the xls spreadsheet are loaded when doing validations.
2020-05-06 11:25:50 -04:00
Aaron Louie 6c36a32411 Adds DSP 2020-05-06 10:37:43 -04:00
Aaron Louie a8827d78c4 Fixes typo 2020-05-05 20:49:07 -04:00
Aaron Louie 4ecb0cb3a3 Updates BPMN files 2020-05-05 16:15:38 -04:00
Dan Funk ce76b0d3e8 Merge branch 'feature/protocol_status' into feature/previous_task 2020-05-04 11:12:12 -04:00
Dan Funk 714b5f3be0 Merge branch 'feature/protocol_status' into feature/previous_task
# Conflicts:
#	crc/services/study_service.py
2020-05-04 11:08:36 -04:00
Aaron Louie 098cf10926 Fixes Jinja code to match new structure of StudyInfo documents 2020-05-01 22:49:52 -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