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Refactor how Questionnaires are generated during the $apply operation #505

Merged
merged 38 commits into from
Oct 7, 2024
Merged

Refactor how Questionnaires are generated during the $apply operation #505

merged 38 commits into from
Oct 7, 2024

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barhodes
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@barhodes barhodes commented Aug 19, 2024 •
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  • The $apply operation will now always generate a Questionnaire from any action.input elements that reference a Profile. A populated QuestionnaireResponse will be returned with the generated Questionnaire contained within it.
  • Generated Questionnaire items from StructureDefinitions that reference a CPG Feature Expression will now have an SDC Questionnaire Item Population Context extension with the expression. The expression name will be set to the name of the StructureDefinition.
  • Added support for the SDC Questionnaire Launch Context extension in the $populate operation.
  • $populate now correctly expects the subject parameter to be a Reference rather than a String.
  • $populate will use "definition-based-population" with Item Population Context when the items have definitions.
  • $extract now uses the Questionnaire item for definition based extraction, the QuestionnaireResponse definition will only be used if the Questionnaire cannot be found by the server.
  • $extract now handles answers of type decimal or integer with a Questionnaire Unit extension correctly.
  • $extract now handles multiple resources being returned by the Item Extraction Context expression.
  • Added EvaluateProcessor for the Library/$evaluate operation.
  • Fixed operation processors not using the proxy repository when endpoints are passed in.
  • Added DataRequirementsVisitor and Processor for the $data-requirements operation.
  • $data-requirements operation added for the following resources: Library, PlanDefinition, Questionnaire, ValueSet

Closes #472
Closes #481
Closes #482

@barhodes barhodes added enhancement New feature or request CDS All issues related to the CDS project labels Aug 19, 2024
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github-actions bot commented Aug 19, 2024 •
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codecov bot commented Aug 19, 2024 •
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Codecov Report

Attention: Patch coverage is 85.44251% with 176 lines in your changes missing coverage. Please review.

Project coverage is 72.95%. Comparing base (b78a391) to head (cd75a4f).
Report is 1 commits behind head on master.

Files with missing lines Patch % Lines
...s/cqf/fhir/cr/visitor/DataRequirementsVisitor.java 86.20% 7 Missing and 9 partials ⚠️
...cqf/fhir/cr/plandefinition/apply/ApplyRequest.java 72.00% 4 Missing and 10 partials ⚠️
...onnaireresponse/extract/ProcessDefinitionItem.java 87.62% 3 Missing and 9 partials ⚠️
.../opencds/cqf/fhir/cr/library/LibraryProcessor.java 60.00% 6 Missing and 4 partials ⚠️
...questionnaire/populate/ProcessItemWithContext.java 90.74% 5 Missing and 5 partials ⚠️
.../cr/inputparameters/r4/InputParameterResolver.java 84.74% 4 Missing and 5 partials ⚠️
.../cr/inputparameters/r5/InputParameterResolver.java 84.74% 4 Missing and 5 partials ⚠️
...nnaireresponse/QuestionnaireResponseProcessor.java 76.31% 4 Missing and 5 partials ⚠️
.../cqf/fhir/cr/library/evaluate/EvaluateRequest.java 75.75% 4 Missing and 4 partials ⚠️
...qf/fhir/cr/questionnaire/populate/ProcessItem.java 83.33% 4 Missing and 4 partials ⚠️
... and 22 more
Additional details and impacted files 
@@             Coverage Diff              @@
##             master     #505      +/-   ##
============================================
+ Coverage     72.87%   72.95%   +0.07%     
  Complexity       19       19              
============================================
  Files           363      365       +2     
  Lines         18710    19308     +598     
  Branches       2880     2949      +69     
============================================
+ Hits          13635    14086     +451     
- Misses         3711     3800      +89     
- Partials       1364     1422      +58

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@barhodes barhodes force-pushed the questionnaire-generation-refactor-2 branch 2 times, most recently from 3d89e07 to a9a65a8 Compare September 3, 2024 13:57
@barhodes barhodes force-pushed the questionnaire-generation-refactor-2 branch from bccea4b to 5b1495b Compare September 17, 2024 23:17
@barhodes barhodes force-pushed the questionnaire-generation-refactor-2 branch from 758811a to 8e436c3 Compare September 30, 2024 18:31
@barhodes barhodes marked this pull request as ready for review October 3, 2024 17:40
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Capt-Mac commented Oct 4, 2024

decent handful of issues flagged, don't see anything majorly critical, but I'd have a look through https://sonarcloud.io/project/issues?id=cqframework_clinical-reasoning&pullRequest=505&issueStatuses=OPEN,CONFIRMED&sinceLeakPeriod=true before merging

@barhodes
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barhodes commented Oct 7, 2024

decent handful of issues flagged, don't see anything majorly critical, but I'd have a look through https://sonarcloud.io/project/issues?id=cqframework_clinical-reasoning&pullRequest=505&issueStatuses=OPEN,CONFIRMED&sinceLeakPeriod=true before merging

Fixed all of them but the too many parameters in methods. Those will have to wait for another refactor.

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sonarcloud bot commented Oct 7, 2024

Quality Gate Passed Quality Gate passed

Issues
0 New issues
14 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

@barhodes barhodes merged commit f149779 into master Oct 7, 2024
8 checks passed
@barhodes barhodes deleted the questionnaire-generation-refactor-2 branch October 7, 2024 22:18
TahaAttari pushed a commit that referenced this pull request Oct 11, 2024
@barhodes
Refactor how Questionnaires are generated during the $apply operation (…
7bebd15 
…#505)

* Refactor Questionnaire generation during $apply operation

* Add evaluate processor

* Fix operation processors not using the proxy repository when endpoints are passed in

* $extract now uses the Questionnaire item for definition based extraction

* Handle answers of type decimal or integer with a Questionnaire Unit extension

* spotless

* Add evaluate tests

* Add support for Questionnaire Launch Context extension in $populate

* Add tests for InputParameterResolver

* Add tests

* Refactor Item generation with Case Feature Expressions

* Add list of resources already packaged to prevent duplicate recursion

* Add method to construct custom library

* fix merge issues

* Add data requirements visitor and processor

* Add tests

* cleanup

* cleanup

* Add tests

* Add tests

* Add tests

* Add ValueSetProcessor with $package and $data-requirements operations

* Add tests and cleanup

* cleanup

* cleanup

* Strip non canonical relatedArtifacts from the module-definition returned from the CQL engine

* fix merge issue

* cleanup

* cleanup

* add tests

* cleanup

* Add tests

* Add tests
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@TahaAttari TahaAttari TahaAttari left review comments

@Capt-Mac Capt-Mac Capt-Mac approved these changes

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