Migrates Workflow to CQL Evaluator 3.0.0-PRE9-SNAPSHOT

[vitorpamplona]

Migrates the workflow, knowledge, workflow-testing, and workflow/benchmark to the new Clinical Reasoning API.

This PR should cover most if not all of the current uses of the workflow module with updated test cases.

Done:

• Adjusted dependencies to the new version. Deleted most of the old hacks that were necessary to work (caffeine).
• Migrated FhirDal implementations to Repostiory implementations
• Deleted Content, Terminology, and Retrieve Providers; and merges some of their code into Repository.
• Migrated Test cases to the new testing and repository structure.
• Created a new IGInputStream Repository using Android resources to simulate the IGFile Repository of test cases from upstream.
• Updates all test cases that were originally from upstream to make them run on AndroidJunit

TODO (next PRs):

• Implement FHIR Operators (lookup/expand/in) that were in the outdated Terminology Provider
• Fully implement the Repository interface's Search function with nested AND/OR conditionals.
• Better merge the Engine's Search interface with the new Search interface from HAPI (search param interface vs client search param interface)
• Update the ProxyRepository to use FhirEngine and Knowledge repository for terminology (split by type instead of trying one after another)
• Make sure the new Repository classes cover all of the outdated Retrieve Provider implementations
• Review OpioidRec10PatientView test case
• Delete the list(null) hack in the measureEvaluate function when this is fixed: Population Measure crashes when subjectIds is null or empty cqframework/clinical-reasoning#358
• Create a Gradle Task to automatically generate the contents.txt file in every test repository being used
• Fix Jackson's multi-version dependency scheme due to the need to support minSDK 24 and newer versions of Jackson at the same time
• Merge the UcumService property of SimpleWorkerContext and the correct caching of StructureDefinitions from HapiWorkerContext to replace today's DualHapiWorkerContext
• Expose just one Ucum service from Commons -> UnitConverter.ucumService for all engine and workflow needs
• Fix an upstream bug that incorrectly returns 2022-12-31T00:00:00 instead of 2021-12-31T23:59:59 in some measure evaluates

Type
Feature

Screenshots (if applicable)

Checklist

• I have read and acknowledged the Code of conduct.
• I have read the Contributing page.
• I have signed the Google Individual CLA, or I am covered by my company's Corporate CLA.
• I have discussed my proposed solution with code owners in the linked issue(s) and we have agreed upon the general approach.
• I have run ./gradlew spotlessApply and ./gradlew spotlessCheck to check my code follows the style guide of this project.
• I have run ./gradlew check and ./gradlew connectedCheck to test my changes locally.
• I have built and run the demo app(s) to verify my change fixes the issue and/or does not break the demo app(s).

[omarismail94]

@vitorpamplona , there are two Instrumentation tests that are failing:

• com.google.android.fhir.workflow.CqlBuilderAndroidTest.shouldCompileAndAssembleImmunityCheck
• com.google.android.fhir.workflow.PlanDefinitionProcessorAndroidTest.testANCDT17

the errors are due to the expected and the actual values being the same, but not in order.

I've figure out the code to resolve this. In CQLBuilder, change line 200 to:

      JSONAssert.assertEquals(expectedElmJsonAsset, translator.toJson(), false)

and in XMLAssert change line 30 to:

        .withNodeMatcher(DefaultNodeMatcher(ElementSelectors.byNameAndAllAttributes))

can you make those changes on your end please?

[omarismail94]

@vitorpamplona my bad, testANCDT17 is not resolved by what I suggested. It fails locally as well when I run the test on my device

[jingtang10]

what a monumental effort! thanks @vitorpamplona!