sartography/cr-connect-workflow
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159 Commits

Author SHA1 Message Date
Dan
e44ea6e13c merging in from dev. 2022-03-18 16:22:33 -04:00
mike cullerton
f4d6b07467 In get study, only process categories when we ask 2022-03-18 16:03:50 -04:00
Dan
a401c41b23 Setting a minimum date for which to import studies. 
Merging in code to improve performance of calculating percent complete for a study.
Assureing we have a primary investigator for the front page (another merge)
 2022-03-18 15:27:45 -04:00
Dan
b36ff02517 Merge remote-tracking branch 'origin/chore/study-progress' into staging-500-error 2022-03-18 15:07:14 -04:00
alicia pritchett
3c5a75c976 Change study progress resulting from a query 2022-03-18 14:42:03 -04:00
Dan
405c63aaef Merge remote-tracking branch 'origin/chore/study-progress' into staging-500-error 2022-03-18 12:59:31 -04:00
Dan
b7489aea43 merging in PI Name changes from Alicia's #499 PR. 2022-03-18 12:30:20 -04:00
alicia pritchett
12a0e26ee1 Include the PI name on the study model 2022-03-18 11:03:06 -04:00
Dan
ef5aca4fe4 ReviewType now comes back with the user studies, so we don't need to make an additional query to get it. 2022-03-18 09:59:10 -04:00
alicia pritchett
2ab96b16a0 Update the study model to include a progress (integer) 2022-03-17 17:20:42 -04:00
mike cullerton
15750beb10 Added a comment on why we moved the session.add(study) line 2022-03-17 15:18:49 -04:00
mike cullerton
be2b7c07ef add the new study to the session after we run update_from_protocol_builder 2022-03-17 14:29:38 -04:00
alicia pritchett
c18bc6f876 fix study service 2022-03-16 16:21:02 -04:00
alicia pritchett
5b7e71d42d meta field for categories 2022-03-16 12:49:35 -04:00
alicia pritchett
829c810807 wip 2022-03-15 13:21:58 -04:00
alicia pritchett
37d92c6a5f WIP ~ adding a category metadata object 2022-03-15 10:49:41 -04:00
Dan
483d7e858b Improved Errors - Pick up on the new task_trace information in WorkflowException and pass it on through the api. 
Also:  All script tasks should raise WorkflowTaskExecExceptions - NOT APIExceptions - this is because our scripts are executed by Spiff (not the other way around)  so the errors need to pass fluidly through spiff, and come back to use THEN we can convert them to APIErrors.  Otherwise we lose all kinds of good information about the error.
 2022-03-14 16:00:53 -04:00
Dan
4ab314c7b8 Be sure to delete the data store items when you delete a study. 2022-03-12 13:38:09 -05:00
Dan
3944d00e88 Removing an unused / rogue variable. 
Adding a logger warning for very large workflow json data.
 2022-02-25 09:59:41 -05:00
Dan
e61ca471db remove all the @timeit from method calls. 2022-02-24 21:06:22 -05:00
Dan
dde8873c9e 1. defer the loading of the bpmn_json when loading the workflow model. It can be stupidly larger. (see models/workflow.py) 
2. Shave a little more time off the reset by not re-creating the whole WorkflowProcessor

cleaning up all the firsttime/sincetime statements.
 2022-02-24 20:56:57 -05:00
Dan
3442655bd1 Performance Improvements: 
1. Avoid ever re-generating the list of scripts that can be used in a script task.  Terribly expensive as we call eval constantly, and it never ever changes once the app starts. (see script.py changes, and comments)
2. Cache the DocumentStatus list in the flask session, so we calculate it at most once per API Call.  It's at least .25 seconds per call.  (see study_sevice)
3. We called UserFileService.get_files_for_study (which runs a db query EVERY time) for every possible document type.  Now we run the query once (study service line 321)
4. When returning a workflow, we looped through every single task in that workflow's navigation, and called the expensive spiff_task_to_api_task just to figure out it's proper display name. We run a much faster and more efficient method to calculate the display name naow (see workflow_service on lie 680, and 799)
5. A hellton of @timeit and sincetime() calls, that I want to leave in, to help debug any slowness on production.
 2022-02-24 14:25:42 -05:00
Dan
3704279f20 Quick fix, assure we can reset studies. 2022-02-17 14:07:33 -05:00
Dan
3993297360 minor fixes to the study api to get things working locally when we pull down a database from testing. 2022-02-10 18:19:57 -05:00
Dan
eb7760fa55 Adding the migration - very destructive, but required for running the app. 
minor fixes - there is still some weird problems with study id and user id being null that I need to track down, but the issue is sporadic, and hard to track down.
 2022-02-10 11:50:31 -05:00
Dan
de6d7eee84 nearly all study tests work. 2022-02-09 12:03:45 -05:00
Dan
cc915ac25a refactoring the study service. 2022-02-09 08:50:00 -05:00
mike cullerton
65d6728be7 pass specs to _add_all_workflow_specs_to_study 2022-02-08 15:03:00 -05:00
Dan
2383c7d76d WIP - lots of random changes, trying to swtich over 2022-02-04 14:50:31 -05:00
Dan
4ec6e403f5 1. Created a UserFileService, so it's clear what we use when for File Services, UserFiles, SpecFiles, and ReferenceFiles each function differently. 
2. Reference Files and Spec Files are written to disk, they do not exist in the database at all.
 2022-02-02 12:59:56 -05:00
mike cullerton
68820c67cb Removed (almost) all references to WorkflowSpecDependencyFile 
(There is still a call in the lookup service, but we need to decide how to fix that)
 2022-01-19 16:12:54 -05:00
mike cullerton
9cc91f92c3 *** WIP *** 
cleanup - removing commented code
 2022-01-11 15:55:08 -05:00
mike cullerton
dc27f795c8 *** WIP *** 
Committing because it is Friday afternoon, and my computer is acting flaky
 2022-01-07 15:34:51 -05:00
mike cullerton
9cd5022bf0 Set progress_status to in_progress when creating a new study. 
-- I'm not sure if this is what we want.
 2021-12-10 16:00:33 -05:00
mike cullerton
8813098190 Updated to use new ProtocolBuilderCreatorStudy model and schema 2021-12-06 14:37:42 -05:00
Dan
455c1035f1 Performance upgrade to script.py - reduce the number of times we generate the augmented list of script functions for running python evals. 
Performance upgrade to study_service.py - Don't query on the whole WorkflowModel, just get the status that we need.  Saves lots of complex joins.
Performance upgrade to SpiffWorkflow - don't convert to box unless we have to do so.
 2021-11-29 17:48:05 -05:00
mike cullerton
a8b7cd8bba Merge branch 'dev' into test-protocol-builder-519 2021-11-10 16:32:34 -05:00
alicia pritchett
aa1ba59bb1 Delete Task log model when deleting a study 
just a minor fix
 2021-11-09 10:42:47 -05:00
mike cullerton
b193f56f35 Minor cleanup for readability. 2021-11-08 10:13:07 -05:00
mike cullerton
6f09b0d7dd Added comment to _is_valid_study. 
Fixed get_required_docs. The data returned for get_required_dcs from UVA PB was *very* different than what we had.
 2021-11-05 14:37:41 -04:00
mike cullerton
6d548c2a74 *** WIP *** 
Committing to work on another ticket
There are TODOs in study_service
 2021-11-05 09:59:14 -04:00
Dan
fdce91507c Improve the warning messages that come back when running the master workflow spec. 2021-10-07 14:43:38 -04:00
mike cullerton
10abf51f70 Added workflow_spec_id to WorkflowMetadata model, because the id is the workflow id, not the workflow_spec id. 
Then, we use workflow_spec_id in StudyService when looking for workflow status.
 2021-10-07 10:02:13 -04:00
mike cullerton
572ca1db6b Fixes for backend code after removing name column from workflow_spec and workflow_spec_category tables 2021-10-05 14:17:41 -04:00
Dan
19104303de Refactor of the way we store and return details about users - All the details about a user, or individual associated with a study is returned within in an Ldap model. I've removed duplication between these models. This required some cleanup of the tests, and a migration that will drop the user details. 2021-09-22 13:16:25 -04:00
Dan
4b591a076f Adding importlib-resournces as a dependency, which is suddenly failing on Travis, likely due to different versions of Python as I try to upgrade to 3.9 2021-09-21 14:36:57 -04:00
Kelly McDonald
76f8f5984e Fixes #413 
Fixes #423 where a library was showing up in a study workflow

Alex said this used to work, but I don't see where I ever edited the code that needed a filter.
 2021-08-19 10:47:13 -04:00
Dan
7a8eeab820 Merge branch 'dev' into bug/missing_pi_name_246 2021-08-17 11:16:03 -04:00
mike cullerton
bd4a9cced3 We no longer use HSRNUMBER to automatically set Study Status to Open for Enrollment 2021-08-13 12:06:27 -04:00
nilez
4a2581e938 get studies raises and error when invalid studies are the only studies associated with the user 2021-08-12 14:03:44 -04:00