Update Clinical Reasoning plugin (#692)

* Reproducing issues with CR/HAPI cds-hooks processing

* Add new $questionnaire operation

* Update StarterIpsConfig.java

* Update pom.xml

* Fixes for configuration properties

* Update VS Code launch properties

* Fixes for CQL logging

* Update pom.xml

* Remove unused threaded option

* Update to 7.1.7

* Fix some CR defaults

* Update to new snapshot

* Update pom.xml

* Fix test settings

* Do not make prefetch calls if all items are present

* Add alternative application.yaml for CDS settings.

* Add CdsHook tests and documentation

* Comment out custom prefetch until it is more mature

* Removal of DataEndpoint parameter is not longer needed

* Fix debug logging setting being overwritten

* Revert change

* Remove unused class

* Adding Rec10 Test

* Disable test until fixed

* fix tests

---------

Co-authored-by: c-schuler <hoofschu@gmail.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>

src/main/resources/application.yaml

@@ -29,7 +29,6 @@ management:
 spring:
   main:
     allow-circular-references: true
-    #allow-bean-definition-overriding: true
   flyway:
     enabled: false
     baselineOnMigrate: true
@@ -78,9 +77,50 @@ hapi:
     ### Flag is false by default, can be passed as command line argument to override.
     cr:
       enabled: false
+      caregaps:
+        reporter: "default"
+        section_author: "default"
+      cql:
+        use_embedded_libraries: true
+        compiler:
+          ### These are low-level compiler options.
+          ### They are not typically needed by most users.
+          # validate_units: true
+          # verify_only: false
+          # compatibility_level: "1.5"
+          error_level: Info
+          signature_level: All
+          # analyze_data_requirements: false
+          # collapse_data_requirements: false
+          # translator_format: JSON
+          # enable_date_range_optimization: true
+          enable_annotations: true
+          enable_locators: true
+          enable_results_type: true
+          enable_detailed_errors: true
+          # disable_list_traversal: false
+          # disable_list_demotion: false
+          # enable_interval_demotion: false
+          # enable_interval_promotion: false
+          # disable_method_invocation: false
+          # require_from_keyword: false
+          # disable_default_model_info_load: false
+        runtime:
+          debug_logging_enabled: false
+          # enable_validation: false
+          # enable_expression_caching: true
+        terminology:
+          valueset_preexpansion_mode: REQUIRE # USE_IF_PRESENT, REQUIRE, IGNORE
+          valueset_expansion_mode: PERFORM_NAIVE_EXPANSION # AUTO, USE_EXPANSION_OPERATION, PERFORM_NAIVE_EXPANSION
+          valueset_membership_mode: USE_EXPANSION # AUTO, USE_VALIDATE_CODE_OPERATION, USE_EXPANSION
+          code_lookup_mode: USE_VALIDATE_CODE_OPERATION # AUTO, USE_VALIDATE_CODE_OPERATION, USE_CODESYSTEM_URL
+        data:
+          search_parameter_mode: FILTER_IN_MEMORY # AUTO, USE_SEARCH_PARAMETERS, FILTER_IN_MEMORY
+          terminology_parameter_mode: FILTER_IN_MEMORY #  AUTO, USE_VALUE_SET_URL, USE_INLINE_CODES, FILTER_IN_MEMORY
+          profile_mode: DECLARED # ENFORCED, DECLARED, OPTIONAL, TRUST, OFF
 
     cdshooks:
-      enabled: true
+      enabled: false
       clientIdHeaderName: client_id
 
     ### This enables the swagger-ui at /fhir/swagger-ui/index.html as well as the /fhir/api-docs (see https://hapifhir.io/hapi-fhir/docs/server_plain/openapi.html)