CQL combo 2.0.0 Upgrade - Full PD$apply implementation

[vitorpamplona]

Fixes #1403, #1423, #1407, #1365, #915, #656, #718
Unlocks: #1334, #1055, #1189
Depreciates: #1395

Description

This PR brings the full functionality of the $apply operator to Android.

1. Migrates the CQL Translator, Engine, and Evaluator to version 2.0, which enables the on-device compilation of CQL as well as import/export of JSON and XML executable libraries, dependent libraries, FHIR objects, and ModelInfo.
2. Upgrades HAPI to 6.0.1 and the project to Java 11 and min SDK 26. It removes desugaring to Java 1.8 (doubling compilation speed), reorganizes the dependency stack, and creates a new module to share workflow testing assets (code and data) between androidTest and test.
3. FhirEngineRetrieveProvider now uses the existing XFhirQueryTranslator to automatically create filtering parameters based on previously-annotated context paths;
4. Completes the FhirEngineRetrieveProvider and provides testing coverage for all types of filters:
   • filters by context
   • filters by code in codes
   • filters by code in ValueSets
   • filters by id in codes
   • filters by dates
5. Completes the FhirEngineTerminologyProvider with a lookup function and reviews all other functions to behave in a similar way to a desktop version. Test cases were added to cover all desktop use cases
6. The hard-coded active=true clause for FhirEngineRetrieveProvider searches involving Patients was deleted in favor of active=true clauses in the CQL files. CQL authors are supposed to filter active records in the CQL itself, not in the provider.
7. Current test cases were reformatted to be property-order agnostic by using JSONAssert and XMLUnit libraries instead of hardcoding assertions in kotlin
8. Additional test cases were pulled from Tests for Compiling CQL with Roboelectric #1395 and CQL-Evaluator's PlanDefinition module, transformed into a fluent design and included here.

Thanks to:

• Using Jackson's XML reader instead of JAXB.unmarshal for ModelInfo files cqframework/clinical_quality_language#745
• Migrating to Java11 and Gradle 7.4 cqframework/clinical_quality_language#747
• Extract CqlCompiler from CqlTranslator cqframework/clinical_quality_language#748
• QuickFix: Upgrade commons-lang to commons-text to fix deprecation cqframework/clinical_quality_language#750
• Uses Jackson instead of JAXB to Read/Write ELM cqframework/clinical_quality_language#752
• #759: Added service loader pattern for serialization frameworks cqframework/clinical_quality_language#760
• QuickFix: Fixing the calling of static methods. cqframework/clinical_quality_language#766
• Fixes #768: Forces Woodstox on all Jackson modules cqframework/clinical_quality_language#769
• #751: Added more dynamic model info and library source provider infra… cqframework/clinical_quality_language#770
• Clean up LibrarySourceProvider API cqframework/clinical_quality_language#788
• #786: Resolve dependency cycle in cql2elm cqframework/clinical_quality_language#791
• Removes Antlr's code generation dependencies from the runtimeClasspath. cqframework/clinical_quality_language#793
• Removes jackson dependencies from the ELM module cqframework/clinical_quality_language#794
• QuickFix: { "translatorOptions" : "" } throws IllegalArgumentException cqframework/clinical_quality_language#802
• #576: CQL 2.0.0 upgrade cqframework/cql-engine#581
• Added service loader pattern for deserialization cqframework/cql-engine#587
• Rev to 2.0.0-SNAPSHOT, cleanup Library deserialization cqframework/cql-engine#601
• Removing the cql-lm schema files from the output jar cqframework/cql-engine#602
• Activate service loaders cqframework/cql-engine#603
• Forcing Woodstox on all Jackson XML modules.  cqframework/cql-engine#604
• Fixes Jackson's XML QName parser to the correct namespace cqframework/cql-engine#605
• Removing JAXB dependencies from the engine. cqframework/clinical-reasoning#73
• Updating the PlanDefinition PR based on reviewer's request cqframework/clinical-reasoning#74
• QuickFix for Empty translatorOptions cqframework/clinical-reasoning#96
• QuickFix: Adds null checks on TerminologyProviderFactory cqframework/clinical-reasoning#102
• PlanDefinition Test infrastructure overhaul and Care Plan with Questionnaires  cqframework/clinical-reasoning#103
• Update the evaluator to use the v2 translator cqframework/clinical-reasoning#107
• Dependency clean up cqframework/clinical-reasoning#138
• Engine 2.0 w jackson module upgrade cqframework/clinical-reasoning#139
• Removing heavy resources from the main fhir lib cqframework/clinical-reasoning#143
• Android compatibility checks hapifhir/hapi-fhir#4070
• Formalizes compliance with Android 8, SDK 26 (2017+) cqframework/clinical_quality_language#810
• Formalizes compliance with Android 8, SDK 26 (2017+)  cqframework/cql-engine#613
• Formalizes compliance with Android 8, SDK 26 (2017+) cqframework/clinical-reasoning#157

Alternative(s) considered
No

Type
Choose one: Feature

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).

[pld]

@Tarun-Bhardwaj can you give an update on this? since this is approved, and the failures seem to be network related, is it possible to go ahead and merge?

[vitorpamplona]

We also need more memory for the GitHub Actions machines. Either that or we need to stop running things in parallel with shared gradle deamon.

[vitorpamplona]

@jingtang10 now without the changes in the test environment (P->O), as requested.