Unit Test work - still cannot get Dstu3 working after several attempts, but included the skelton of a test to capture the effort anyways.

src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java

@@ -21,6 +21,7 @@ import org.springframework.context.annotation.Configuration;
 @EnableConfigurationProperties
 public class AppProperties {
 
+  private Boolean cql_enabled = false;
   private Boolean empi_enabled = false;
   private Boolean allow_cascading_deletes = false;
   private Boolean allow_contains_searches = true;
@@ -85,6 +86,14 @@ public class AppProperties {
     this.partitioning = partitioning;
   }
 
+  public Boolean getCql_enabled() {
+    return cql_enabled;
+  }
+
+  public void setCql_enabled(Boolean cql_enabled) {
+    this.cql_enabled = cql_enabled;
+  }
+
   public Boolean getEmpi_enabled() {
     return empi_enabled;
   }
@@ -93,7 +102,6 @@ public class AppProperties {
     this.empi_enabled = empi_enabled;
   }
 
-
   public Cors getCors() {
     return cors;
   }

src/main/java/ca/uhn/fhir/jpa/starter/Application.java

@@ -32,8 +32,8 @@ public class Application extends SpringBootServletInitializer {
     System.setProperty("spring.batch.job.enabled", "false");
     SpringApplication.run(Application.class, args);
 
-    //Server is now accessible at eg. http://localhost:8080/hapi-fhir-jpaserver/fhir/metadata
-    //UI is now accessible at http://localhost:8080/hapi-fhir-jpaserver/
+    //Server is now accessible at eg. http://localhost:8080/fhir/metadata
+    //UI is now accessible at http://localhost:8080/
   }
 
   @Override

src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java

@@ -2,6 +2,8 @@ package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.cql.provider.CqlProviderLoader;
+import ca.uhn.fhir.empi.provider.EmpiProviderLoader;
 import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.IInterceptorService;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
@@ -97,6 +99,10 @@ public class BaseJpaRestfulServer extends RestfulServer {
   @Autowired
   ApplicationContext myApplicationContext;
 
+  // These are set only if the features are enabled
+  private CqlProviderLoader cqlProviderLoader;
+  private EmpiProviderLoader empiProviderLoader;
+
   public BaseJpaRestfulServer() {
 
   }
@@ -121,10 +127,21 @@ public class BaseJpaRestfulServer extends RestfulServer {
     }
 
     setFhirContext(fhirSystemDao.getContext());
+
+    FhirVersionEnum fhirVersion = fhirSystemDao.getContext().getVersion().getVersion();
+    if (fhirVersion == FhirVersionEnum.DSTU3 || fhirVersion == FhirVersionEnum.R4) {
+      if (appProperties.getCql_enabled()) {
+        cqlProviderLoader = myApplicationContext.getBean(CqlProviderLoader.class);
+        cqlProviderLoader.loadProvider();
+      }
+      if (appProperties.getEmpi_enabled()) {
+        empiProviderLoader = myApplicationContext.getBean(EmpiProviderLoader.class);
+        empiProviderLoader.loadProvider();
+      }
+    }
     registerProviders(resourceProviders.createProviders());
     registerProvider(jpaSystemProvider);
 
-    FhirVersionEnum fhirVersion = fhirSystemDao.getContext().getVersion().getVersion();
     /*
      * The conformance provider exports the supported resources, search parameters, etc for
      * this server. The JPA version adds resourceProviders counts to the exported statement, so it

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java

@@ -4,11 +4,9 @@ import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.jpa.config.BaseJavaConfigR4;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
+import ca.uhn.fhir.jpa.starter.cql.CqlConfigR4;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Conditional;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Primary;
+import org.springframework.context.annotation.*;
 import org.springframework.core.env.ConfigurableEnvironment;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
@@ -18,6 +16,7 @@ import javax.sql.DataSource;
 
 @Configuration
 @Conditional(OnR4Condition.class)
+@Import(CqlConfigR4.class)
 public class FhirServerConfigR4 extends BaseJavaConfigR4 {
 
   @Autowired

src/main/java/ca/uhn/fhir/jpa/starter/cql/CqlConfigCondition.java

@@ -7,8 +7,8 @@ import org.springframework.core.type.AnnotatedTypeMetadata;
 public class CqlConfigCondition implements Condition {
 
   @Override
-  public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata annotatedTypeMetadata) {
-    String property = conditionContext.getEnvironment().getProperty("hapi.fhir.cql_enabled");
+  public boolean matches(ConditionContext theConditionContext, AnnotatedTypeMetadata theAnnotatedTypeMetadata) {
+    String property = theConditionContext.getEnvironment().getProperty("hapi.fhir.cql_enabled");
     boolean enabled = Boolean.parseBoolean(property);
     return enabled;
   }

src/main/java/ca/uhn/fhir/jpa/starter/cql/CqlConfigR4.java

@@ -1,13 +1,10 @@
 package ca.uhn.fhir.jpa.starter.cql;
 
 import ca.uhn.fhir.cql.config.CqlR4Config;
-import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
 import org.springframework.context.annotation.Conditional;
-import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
 
-@Configuration
-@Conditional({OnR4Condition.class, CqlConfigCondition.class})
+@Conditional({CqlConfigCondition.class})
 @Import({CqlR4Config.class})
 public class CqlConfigR4 {
 }

src/main/resources/application.yaml

@@ -29,7 +29,6 @@ hapi:
   fhir:
     ### This is the FHIR version. Choose between, DSTU2, DSTU3, R4 or R5
     fhir_version: R4
-    cql_enabled: true
 #    defer_indexing_for_codesystems_of_size: 101
 #    implementationguides:
 #      -
@@ -50,6 +49,8 @@ hapi:
 #    allow_override_default_search_params: true
 #    allow_placeholder_references: true
 #    auto_create_placeholder_reference_targets: false
+#    cql_enabled: true
+#    empi_enabled: true
 #    default_encoding: JSON
 #    default_pretty_print: true
 #    default_page_size: 20