Merge tag 'image/v7.6.0' into update-to-v7.6.0

pom.xml

@@ -14,7 +14,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>hapi-fhir</artifactId>
-        <version>7.4.0</version>
+        <version>7.6.0</version>
     </parent>
 
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>
@@ -44,15 +44,7 @@
     <dependencyManagement>
        <dependencies>
 
-            <!-- Temporarily override CR depedencies for debugging -->
-<!--            <dependency>-->
-<!--                <groupId>org.opencds.cqf.fhir</groupId>-->
-<!--                <artifactId>cqf-fhir-bom</artifactId>-->
-<!--                <version>3.4.0</version>-->
-<!--                <type>pom</type>-->
-<!--                <scope>import</scope>-->
-<!--            </dependency>-->
-           <dependency>
+            <dependency>
                <groupId>org.glassfish.jaxb</groupId>
                <artifactId>jaxb-runtime</artifactId>
                <version>2.3.8</version>
@@ -381,6 +373,14 @@
             <version>1.13.3</version>
         </dependency>
 
+        <!-- https://mvnrepository.com/artifact/io.micrometer/micrometer-registry-prometheus-simpleclient -->
+        <dependency>
+            <groupId>io.micrometer</groupId>
+            <artifactId>micrometer-registry-prometheus-simpleclient</artifactId>
+            <version>1.13.3</version>
+        </dependency>
+
+
         <dependency>
             <groupId>com.zaxxer</groupId>
             <artifactId>HikariCP</artifactId>

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

@@ -83,6 +83,7 @@ public class AppProperties {
   private Subscription subscription = new Subscription();
   private Cors cors = null;
   private Partitioning partitioning = null;
+  private Boolean validate_resource_status_for_package_upload = true;
   private Boolean install_transitive_ig_dependencies = true;
   private Map<String, PackageInstallationSpec> implementationGuides = null;
 
@@ -106,7 +107,11 @@ public class AppProperties {
   private final List<String> custom_interceptor_classes = new ArrayList<>();
 
 	private final List<String> custom_provider_classes = new ArrayList<>();
+	private Boolean upliftedRefchains_enabled = false;
 
+	private boolean userRequestRetryVersionConflictsInterceptorEnabled = false;
+
+	private List<Integer> search_prefetch_thresholds = new ArrayList<>();
 
 	public List<String> getCustomInterceptorClasses() {
     return custom_interceptor_classes;
@@ -613,6 +618,14 @@ public void setInstall_transitive_ig_dependencies(boolean install_transitive_ig_
 		this.install_transitive_ig_dependencies = install_transitive_ig_dependencies;
 	}
 
+  public Boolean getValidate_resource_status_for_package_upload() {
+		return validate_resource_status_for_package_upload;
+	}
+
+	public void setValidate_resource_status_for_package_upload(Boolean validate_resource_status_for_package_upload) {
+		this.validate_resource_status_for_package_upload = validate_resource_status_for_package_upload;
+	}
+
 	public Integer getBundle_batch_pool_size() {
 		return this.bundle_batch_pool_size;
 	}
@@ -670,6 +683,30 @@ public void setLanguage_search_parameter_enabled(Boolean language_search_paramet
 		this.language_search_parameter_enabled = language_search_parameter_enabled;
 	}
 
+	public List<Integer> getSearch_prefetch_thresholds() {
+		return this.search_prefetch_thresholds;
+	}
+
+	public void  setSearch_prefetch_thresholds(List<Integer> thePrefetchThresholds) {
+		this.search_prefetch_thresholds = thePrefetchThresholds;
+	}
+
+	public boolean getUpliftedRefchains_enabled() {
+		return upliftedRefchains_enabled;
+	}
+
+	public void setUpliftedRefchains_enabled(boolean upliftedRefchains_enabled) {
+		this.upliftedRefchains_enabled = upliftedRefchains_enabled;
+	}
+
+	public Boolean getUserRequestRetryVersionConflictsInterceptorEnabled() {
+		return userRequestRetryVersionConflictsInterceptorEnabled;
+	}
+
+	public void setUserRequestRetryVersionConflictsInterceptorEnabled(Boolean userRequestRetryVersionConflictsInterceptorEnabled) {
+		this.userRequestRetryVersionConflictsInterceptorEnabled = userRequestRetryVersionConflictsInterceptorEnabled;
+	}
+
 	public static class Cors {
     private Boolean allow_Credentials = true;
     private List<String> allowed_origin = List.of("*");
@@ -689,8 +726,6 @@ public Boolean getAllow_Credentials() {
     public void setAllow_Credentials(Boolean allow_Credentials) {
       this.allow_Credentials = allow_Credentials;
     }
-
-
   }
 
   public static class Oauth {
@@ -951,6 +986,7 @@ public static class Partitioning {
 
     private Boolean partitioning_include_in_search_hashes = false;
     private Boolean allow_references_across_partitions = false;
+    private Boolean conditional_create_duplicate_identifiers_enabled = false;
 
     public Boolean getPartitioning_include_in_search_hashes() {
       return partitioning_include_in_search_hashes;
@@ -966,6 +1002,14 @@ public Boolean getAllow_references_across_partitions() {
     public void setAllow_references_across_partitions(Boolean allow_references_across_partitions) {
       this.allow_references_across_partitions = allow_references_across_partitions;
     }
+
+    public Boolean getConditional_create_duplicate_identifiers_enabled() {
+      return conditional_create_duplicate_identifiers_enabled;
+    }
+
+    public void setConditional_create_duplicate_identifiers_enabled(Boolean conditional_create_duplicate_identifiers_enabled) {
+      this.conditional_create_duplicate_identifiers_enabled = conditional_create_duplicate_identifiers_enabled;
+    }
   }
 
   public static class Subscription {

src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigCommon.java

@@ -151,7 +151,12 @@ public JpaStorageSettings jpaStorageSettings(AppProperties appProperties) {
 		jpaStorageSettings.setDeleteExpungeEnabled(appProperties.getDelete_expunge_enabled());
 		jpaStorageSettings.setExpungeEnabled(appProperties.getExpunge_enabled());
 		jpaStorageSettings.setLanguageSearchParameterEnabled(appProperties.getLanguage_search_parameter_enabled());
+		jpaStorageSettings.setValidateResourceStatusForPackageUpload(appProperties.getValidate_resource_status_for_package_upload());
+		jpaStorageSettings.setIndexOnUpliftedRefchains(appProperties.getUpliftedRefchains_enabled());
 
+		if (!appProperties.getSearch_prefetch_thresholds().isEmpty()) {
+			jpaStorageSettings.setSearchPreFetchThresholds(appProperties.getSearch_prefetch_thresholds());
+		}
 
 		Integer maxFetchSize = appProperties.getMax_page_size();
 		jpaStorageSettings.setFetchSizeDefaultMaximum(maxFetchSize);
@@ -244,6 +249,8 @@ public PartitionSettings partitionSettings(AppProperties appProperties) {
 			} else {
 				retVal.setAllowReferencesAcrossPartitions(CrossPartitionReferenceMode.NOT_ALLOWED);
 			}
+			retVal.setConditionalCreateDuplicateIdentifiersEnabled(
+				appProperties.getPartitioning().getConditional_create_duplicate_identifiers_enabled());
 		}
 
 		return retVal;

src/main/java/ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.java

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.jpa.starter.common;
 
+import ca.uhn.fhir.batch2.config.Batch2JobRegisterer;
 import ca.uhn.fhir.batch2.coordinator.JobDefinitionRegistry;
 import ca.uhn.fhir.batch2.jobs.export.BulkDataExportProvider;
 import ca.uhn.fhir.batch2.jobs.imprt.BulkDataImportProvider;
@@ -28,6 +29,7 @@
 import ca.uhn.fhir.jpa.delete.ThreadSafeResourceDeleterSvc;
 import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
 import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
+import ca.uhn.fhir.jpa.interceptor.UserRequestRetryVersionConflictsInterceptor;
 import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingInterceptor;
 import ca.uhn.fhir.jpa.ips.provider.IpsOperationProvider;
 import ca.uhn.fhir.jpa.model.config.SubscriptionSettings;
@@ -50,7 +52,6 @@
 import ca.uhn.fhir.jpa.starter.interceptor.SmartWellKnownInterceptor;
 import ca.uhn.fhir.jpa.starter.ig.IImplementationGuideOperationProvider;
 import ca.uhn.fhir.jpa.starter.util.EnvironmentHelper;
-import ca.uhn.fhir.jpa.starter.ig.IImplementationGuideOperationProvider;
 import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChain;
@@ -71,6 +72,8 @@
 import com.google.common.base.Strings;
 import jakarta.persistence.EntityManagerFactory;
 import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.NoSuchBeanDefinitionException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
@@ -94,7 +97,7 @@
 @Import(ThreadPoolFactoryConfig.class)
 public class StarterJpaConfig {
 
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(StarterJpaConfig.class);
+	private static final Logger ourLog = LoggerFactory.getLogger(StarterJpaConfig.class);
 
 	@Bean
 	public IFulltextSearchSvc fullTextSearchSvc() {
@@ -196,11 +199,11 @@ public LoggingInterceptor loggingInterceptor(AppProperties appProperties) {
 	@Primary
 	@Conditional(OnImplementationGuidesPresent.class)
 	public IPackageInstallerSvc packageInstaller(
-			AppProperties appProperties,
-			JobDefinition<ReindexJobParameters> reindexJobParametersJobDefinition,
-			JobDefinitionRegistry jobDefinitionRegistry,
-			IPackageInstallerSvc packageInstallerSvc) {
-		jobDefinitionRegistry.addJobDefinitionIfNotRegistered(reindexJobParametersJobDefinition);
+		AppProperties appProperties,
+		IPackageInstallerSvc packageInstallerSvc,
+		Batch2JobRegisterer batch2JobRegisterer) {
+
+		batch2JobRegisterer.start();
 
 		if (appProperties.getImplementationGuides() != null) {
 			Map<String, PackageInstallationSpec> guides = appProperties.getImplementationGuides();
@@ -481,6 +484,10 @@ public RestfulServer restfulServer(
 			fhirServer.registerProvider(theIpsOperationProvider.get());
 		}
 
+		if (appProperties.getUserRequestRetryVersionConflictsInterceptorEnabled() ) {
+			fhirServer.registerInterceptor(new UserRequestRetryVersionConflictsInterceptor());
+		}
+
 		// register custom providers
 		registerCustomProviders(fhirServer, appContext, appProperties.getCustomProviderClasses());
 

src/main/java/ca/uhn/fhir/jpa/starter/cr/CareGapsProperties.java

@@ -1,22 +1,22 @@
 package ca.uhn.fhir.jpa.starter.cr;
 
 public class CareGapsProperties {
-    private String reporter = "default";
+	private String reporter = "default";
 	private String section_author = "default";
 
-    public String getReporter() {
-        return reporter;
-    }
+	public String getReporter() {
+		return reporter;
+	}
 
-    public void setReporter(String reporter) {
-        this.reporter = reporter;
-    }
+	public void setReporter(String reporter) {
+		this.reporter = reporter;
+	}
 
-    public String getSection_author() {
-        return section_author;
-    }
+	public String getSection_author() {
+		return section_author;
+	}
 
-    public void setSection_author(String section_author) {
-        this.section_author = section_author;
-    }
+	public void setSection_author(String section_author) {
+		this.section_author = section_author;
+	}
 }

src/main/java/ca/uhn/fhir/jpa/starter/cr/CqlCompilerProperties.java

@@ -5,7 +5,7 @@
 import org.cqframework.cql.cql2elm.LibraryBuilder;
 
 public class CqlCompilerProperties {
-    private Boolean validate_units = true;
+	private Boolean validate_units = true;
 	private Boolean verify_only = false;
 	private String compatibility_level = "1.5";
 	private CqlCompilerException.ErrorSeverity error_level = CqlCompilerException.ErrorSeverity.Info;
@@ -27,7 +27,6 @@ public class CqlCompilerProperties {
 	private Boolean require_from_keyword = false;
 	private Boolean disable_default_model_info_load = false;
 
-
 	public boolean isValidateUnits() {
 		return validate_units;
 	}
@@ -194,5 +193,5 @@ public CqlTranslator.Format getTranslatorFormat() {
 
 	public void setTranslatorFormat(CqlTranslator.Format translatorFormat) {
 		this.translator_format = translatorFormat;
-	}  
+	}
 }

src/main/java/ca/uhn/fhir/jpa/starter/cr/CqlProperties.java

@@ -5,49 +5,49 @@
 
 public class CqlProperties {
 
-    private Boolean use_embedded_libraries = true;
-    private CqlCompilerProperties compiler = new CqlCompilerProperties();
-    private CqlRuntimeProperties runtime = new CqlRuntimeProperties();
-    private TerminologySettings terminology = new TerminologySettings();
-    private RetrieveSettings data = new RetrieveSettings();
-    
-    public Boolean getUse_embedded_libraries() {
-        return use_embedded_libraries;
-    }
-
-    public void setUse_embedded_libraries(Boolean use_embedded_libraries) {
-        this.use_embedded_libraries = use_embedded_libraries;
-    }
-
-    public CqlCompilerProperties getCompiler() {
-        return compiler;
-    }
-
-    public void setCompiler(CqlCompilerProperties compiler) {
-        this.compiler = compiler;
-    }
-
-    public CqlRuntimeProperties getRuntime() {
-        return runtime;
-    }
-    
-    public void setRuntime(CqlRuntimeProperties runtime) {
-        this.runtime = runtime;
-    }
-
-    public TerminologySettings getTerminology() {
-        return terminology;
-    }
-
-    public void setTerminology(TerminologySettings terminology) {
-        this.terminology = terminology;
-    }
-
-    public RetrieveSettings getData() {
-        return data;
-    }
-
-    public void setData(RetrieveSettings data) {
-        this.data = data;
-    }
+	private Boolean use_embedded_libraries = true;
+	private CqlCompilerProperties compiler = new CqlCompilerProperties();
+	private CqlRuntimeProperties runtime = new CqlRuntimeProperties();
+	private TerminologySettings terminology = new TerminologySettings();
+	private RetrieveSettings data = new RetrieveSettings();
+
+	public Boolean getUse_embedded_libraries() {
+		return use_embedded_libraries;
+	}
+
+	public void setUse_embedded_libraries(Boolean use_embedded_libraries) {
+		this.use_embedded_libraries = use_embedded_libraries;
+	}
+
+	public CqlCompilerProperties getCompiler() {
+		return compiler;
+	}
+
+	public void setCompiler(CqlCompilerProperties compiler) {
+		this.compiler = compiler;
+	}
+
+	public CqlRuntimeProperties getRuntime() {
+		return runtime;
+	}
+
+	public void setRuntime(CqlRuntimeProperties runtime) {
+		this.runtime = runtime;
+	}
+
+	public TerminologySettings getTerminology() {
+		return terminology;
+	}
+
+	public void setTerminology(TerminologySettings terminology) {
+		this.terminology = terminology;
+	}
+
+	public RetrieveSettings getData() {
+		return data;
+	}
+
+	public void setData(RetrieveSettings data) {
+		this.data = data;
+	}
 }