Merge pull request #125 from jvitrifork/spring-pr

Added spring boot example application that can be used during test ef…

.vscode/settings.json

@@ -0,0 +1,8 @@
+{
+    "files.exclude": {
+        "**/.classpath": true,
+        "**/.project": true,
+        "**/.settings": true,
+        "**/.factorypath": true
+    }
+}

pom.xml

@@ -3,6 +3,8 @@
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
 
+    <!-- one-liner to take you to the cloud with settings form the application.yaml file: -->
+    <!-- 'mvn clean package com.google.cloud.tools:jib-maven-plugin:dockerBuild -Dimage=distroless-hapi && docker run -p 8080:8080 -e spring.batch.job.enabled=false distroless-hapi' -->
     <!--
     Note: HAPI projects use the "hapi-fhir" POM as their base to provide easy management.
     You do not need to use this in your own projects, so the "parent" tag and it's
@@ -17,8 +19,13 @@
 
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>
 
+    <properties>
+        <java.version>8</java.version>
+        <spring.boot>2.3.3.RELEASE</spring.boot>
+    </properties>
+
     <prerequisites>
-        <maven>3.5.0</maven>
+        <maven>3.6.0</maven>
     </prerequisites>
 
     <packaging>war</packaging>
@@ -69,12 +76,6 @@
                 </exclusion>
             </exclusions>
         </dependency>
-        <!--
-        <dependency>
-            <groupId>javax.mail</groupId>
-            <artifactId>javax.mail-api</artifactId>
-        </dependency>
-        -->
 
         <!-- This dependency includes the core HAPI-FHIR classes -->
         <dependency>
@@ -118,7 +119,7 @@
             <artifactId>hapi-fhir-testpage-overlay</artifactId>
             <version>${project.version}</version>
             <classifier>classes</classifier>
-            <scope>provided</scope>
+
         </dependency>
 
         <!-- HAPI-FHIR uses Logback for logging support. The logback library is included automatically by Maven as a part of the hapi-fhir-base dependency, but you also need to include a logging library. Logback
@@ -240,18 +241,7 @@
             <artifactId>jetty-webapp</artifactId>
             <scope>test</scope>
         </dependency>
-        <!--
+
-        <dependency>
-            <groupId>com.helger</groupId>
-            <artifactId>ph-schematron</artifactId>
-            <exclusions>
-                <exclusion>
-                    <artifactId>Saxon-HE</artifactId>
-                    <groupId>net.sf.saxon</groupId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-			-->
 
         <!--
         For some reason JavaDoc crashed during site generation unless we have this dependency
@@ -276,6 +266,34 @@
             <scope>test</scope>
         </dependency>
 
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-autoconfigure</artifactId>
+            <version>${spring.boot}</version>
+        </dependency>
+
+
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-api</artifactId>
+            <version>5.6.2</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-engine</artifactId>
+            <version>5.6.2</version>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-test</artifactId>
+            <version>${spring.boot}</version>
+            <scope>test</scope>
+        </dependency>
+
+
     </dependencies>
 
     <build>
@@ -284,7 +302,22 @@
         <finalName>hapi-fhir-jpaserver</finalName>
 
         <plugins>
-            <!-- The following is not required for the application to build, but allows you to test it by issuing "mvn jetty:run" from the command line. -->
+            <plugin>
+                <groupId>org.springframework.boot</groupId>
+                <artifactId>spring-boot-maven-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>repackage</goal>
+                        </goals>
+                        <configuration>
+                            <mainClass>ca.uhn.fhir.jpa.starter.Application</mainClass>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+            <!-- The following is not required for the application to build, but allows you to test it by issuing "mvn package jetty:run -Dspring.batch.job.enabled=false" from the command line. -->
+            <!--
             <plugin>
                 <groupId>org.eclipse.jetty</groupId>
                 <artifactId>jetty-maven-plugin</artifactId>
@@ -296,14 +329,15 @@
                     </webApp>
                 </configuration>
             </plugin>
+            -->
 
             <!-- Tell Maven which Java source version you want to use -->
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.8.1</version>
                 <configuration>
-                    <source>1.8</source>
+                    <release>8</release>
-                    <target>1.8</target>
                 </configuration>
             </plugin>
 
@@ -323,7 +357,7 @@
                             <artifactId>hapi-fhir-testpage-overlay</artifactId>
                         </overlay>
                     </overlays>
-                    <webXml>src/main/webapp/WEB-INF/web.xml</webXml>
+                    <failOnMissingWebXml>false</failOnMissingWebXml>
                 </configuration>
             </plugin>
 
@@ -438,9 +472,51 @@
                     </ignoredResourcePatterns>
                 </configuration>
             </plugin>
-
-
         </plugins>
     </build>
 
+    <profiles>
+        <!-- Package the war for your preference. Use the boot profile if you prefer a single jar/war
+        that can be started with and embedded application server. Default is jetty as it is assumed
+        that the main users of this project already have an app server.
+        Different profiles are needed as packing it for spring boot, makes the resulting war undeployable
+        due to a class shading issue between tomcat and jetty.
+        (the error is 'java.util.ServiceConfigurationError: org.apache.juli.logging.Log: org.eclipse.jetty.apache.jsp.JuliLog not a subtype')
+
+         -->
+
+        <!-- example of how to start the server using spring boot-->
+        <!-- mvn clean package spring-boot:repackage -Pboot && java -jar target/hapi-fhir-jpaserver.war -->
+
+        <!-- Use the boot profile for development and debugging options when using your IDE -->
+        <profile>
+            <id>boot</id>
+            <dependencies>
+                <dependency>
+                    <groupId>org.springframework.boot</groupId>
+                    <artifactId>spring-boot-starter-web</artifactId>
+                    <version>2.3.3.RELEASE</version>
+                </dependency>
+            </dependencies>
+        </profile>
+        <!-- examples of how to start the server using the default profile-->
+        <!-- mvn clean package jetty:run -Dspring.batch.job.enabled=false -->
+        <!-- java -jar -Dspring.batch.job.enabled=false jetty-runner.jar target/hapi-fhir-jpaserver.war -->
+        <profile>
+            <id>jetty</id>
+            <dependencies>
+                <dependency>
+                    <groupId>org.springframework.boot</groupId>
+                    <artifactId>spring-boot-starter-web</artifactId>
+                    <version>2.3.3.RELEASE</version>
+                    <exclusions>
+                        <exclusion>
+                            <groupId>org.springframework.boot</groupId>
+                            <artifactId>spring-boot-starter-tomcat</artifactId>
+                        </exclusion>
+                    </exclusions>
+                </dependency>
+            </dependencies>
+        </profile>
+    </profiles>
 </project>

src/main/java/ca/uhn/fhir/jpa/empi/EmpiConfig.java

@@ -1,13 +1,20 @@
 package ca.uhn.fhir.jpa.empi;
 
+import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.empi.api.IEmpiSettings;
 import ca.uhn.fhir.empi.rules.config.EmpiRuleValidator;
 import ca.uhn.fhir.empi.rules.config.EmpiSettings;
-import ca.uhn.fhir.jpa.starter.HapiProperties;
+import ca.uhn.fhir.jpa.empi.config.EmpiConsumerConfig;
+import ca.uhn.fhir.jpa.empi.config.EmpiSubmitterConfig;
+import ca.uhn.fhir.jpa.starter.AppProperties;
+import ca.uhn.fhir.rest.server.util.ISearchParamRetriever;
 import com.google.common.base.Charsets;
 import org.apache.commons.io.IOUtils;
+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.Import;
 import org.springframework.core.io.DefaultResourceLoader;
 import org.springframework.core.io.Resource;
 
@@ -18,14 +25,21 @@ import java.io.IOException;
  * in 5.1.0 picks this up even if EMPI is disabled currently.
  */
 @Configuration
+@Conditional(EmpiConfigCondition.class)
+@Import({EmpiConsumerConfig.class, EmpiSubmitterConfig.class})
 public class EmpiConfig {
 
   @Bean
-  IEmpiSettings empiSettings(EmpiRuleValidator theEmpiRuleValidator) throws IOException {
+  EmpiRuleValidator empiRuleValidator(FhirContext theFhirContext, ISearchParamRetriever theSearchParamRetriever) {
+    return new EmpiRuleValidator(theFhirContext, theSearchParamRetriever);
+  }
+
+  @Bean
+  IEmpiSettings empiSettings(@Autowired EmpiRuleValidator theEmpiRuleValidator, AppProperties appProperties) throws IOException {
     DefaultResourceLoader resourceLoader = new DefaultResourceLoader();
     Resource resource = resourceLoader.getResource("empi-rules.json");
     String json = IOUtils.toString(resource.getInputStream(), Charsets.UTF_8);
-    return new EmpiSettings(theEmpiRuleValidator).setEnabled(HapiProperties.getEmpiEnabled()).setScriptText(json);
+    return new EmpiSettings(theEmpiRuleValidator).setEnabled(appProperties.getEmpi_enabled()).setScriptText(json);
   }
 
 }

src/main/java/ca/uhn/fhir/jpa/empi/EmpiConfigCondition.java

@@ -0,0 +1,13 @@
+package ca.uhn.fhir.jpa.empi;
+
+import org.springframework.context.annotation.Condition;
+import org.springframework.context.annotation.ConditionContext;
+import org.springframework.core.type.AnnotatedTypeMetadata;
+
+public class EmpiConfigCondition implements Condition {
+  @Override
+  public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
+    String property = conditionContext.getEnvironment().getProperty("hapi.fhir.empi_enabled");
+    return Boolean.parseBoolean(property);
+  }
+}

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

@@ -0,0 +1,669 @@
+package ca.uhn.fhir.jpa.starter;
+
+
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.jpa.api.config.DaoConfig.ClientIdStrategyEnum;
+import ca.uhn.fhir.rest.api.EncodingEnum;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import com.google.common.collect.ImmutableList;
+import org.hl7.fhir.r4.model.Bundle;
+
+import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.boot.context.properties.EnableConfigurationProperties;
+import org.springframework.context.annotation.Configuration;
+
+
+@ConfigurationProperties(prefix = "hapi.fhir")
+@Configuration
+@EnableConfigurationProperties
+public class AppProperties {
+
+  private Boolean empi_enabled = false;
+  private Boolean allow_cascading_deletes = false;
+  private Boolean allow_contains_searches = true;
+  private Boolean allow_external_references = false;
+  private Boolean allow_multiple_delete = false;
+  private Boolean allow_override_default_search_params = true;
+  private Boolean allow_placeholder_references = true;
+  private Boolean auto_create_placeholder_reference_targets = true;
+  private Boolean enable_index_missing_fields = false;
+  private Boolean enforce_referential_integrity_on_delete = true;
+  private Boolean enforce_referential_integrity_on_write = true;
+  private Boolean etag_support_enabled = true;
+  private Boolean expunge_enabled = true;
+  private Boolean fhirpath_interceptor_enabled = false;
+  private Boolean filter_search_enabled = true;
+  private Boolean graphql_enabled = false;
+  private Boolean binary_storage_enabled = false;
+  private Boolean bulk_export_enabled = false;
+  private Boolean default_pretty_print = true;
+  private Integer default_page_size = 20;
+  private Integer max_binary_size = null;
+  private Integer max_page_size = Integer.MAX_VALUE;
+  private Integer defer_indexing_for_codesystems_of_size = 100;
+  private Long retain_cached_searches_mins = 60L;
+  private Long reuse_cached_search_results_millis = 60000L;
+  private String server_address = null;
+  private EncodingEnum default_encoding = EncodingEnum.JSON;
+  private FhirVersionEnum fhir_version = FhirVersionEnum.R4;
+  private ClientIdStrategyEnum client_id_strategy = ClientIdStrategyEnum.ALPHANUMERIC;
+  private List<String> supported_resource_types = new ArrayList<>();
+  private List<Bundle.BundleType> allowed_bundle_types = null;
+
+  private Validation validation = new Validation();
+  private List<Tester> tester = ImmutableList.of(new Tester());
+  private Logger logger = new Logger();
+  private Subscription subscription = new Subscription();
+  private Cors cors = null;
+  private Partitioning partitioning = null;
+  private List<ImplementationGuide> implementationGuides = null;
+
+  public Integer getDefer_indexing_for_codesystems_of_size() {
+    return defer_indexing_for_codesystems_of_size;
+  }
+
+  public void setDefer_indexing_for_codesystems_of_size(Integer defer_indexing_for_codesystems_of_size) {
+    this.defer_indexing_for_codesystems_of_size = defer_indexing_for_codesystems_of_size;
+  }
+
+  public List<ImplementationGuide> getImplementationGuides() {
+    return implementationGuides;
+  }
+
+  public void setImplementationGuides(List<ImplementationGuide> implementationGuides) {
+    this.implementationGuides = implementationGuides;
+  }
+
+  public Partitioning getPartitioning() {
+    return partitioning;
+  }
+
+  public void setPartitioning(Partitioning partitioning) {
+    this.partitioning = partitioning;
+  }
+
+  public Boolean getEmpi_enabled() {
+    return empi_enabled;
+  }
+
+  public void setEmpi_enabled(Boolean empi_enabled) {
+    this.empi_enabled = empi_enabled;
+  }
+
+
+  public Cors getCors() {
+    return cors;
+  }
+
+  public void setCors(Cors cors) {
+    this.cors = cors;
+  }
+
+  public List<Bundle.BundleType> getAllowed_bundle_types() {
+    return allowed_bundle_types;
+  }
+
+  public void setAllowed_bundle_types(List<Bundle.BundleType> allowed_bundle_types) {
+    this.allowed_bundle_types = allowed_bundle_types;
+  }
+
+  public String getServer_address() {
+    return server_address;
+  }
+
+  public void setServer_address(String server_address) {
+    this.server_address = server_address;
+  }
+
+  public Subscription getSubscription() {
+    return subscription;
+  }
+
+  public Boolean getDefault_pretty_print() {
+    return default_pretty_print;
+  }
+
+  public void setDefault_pretty_print(Boolean default_pretty_print) {
+    this.default_pretty_print = default_pretty_print;
+  }
+
+  public void setSubscription(Subscription subscription) {
+    this.subscription = subscription;
+  }
+
+  public Validation getValidation() {
+    return validation;
+  }
+
+  public void setValidation(Validation validation) {
+    this.validation = validation;
+  }
+
+  public List<String> getSupported_resource_types() {
+    return supported_resource_types;
+  }
+
+  public void setSupported_resource_types(List<String> supported_resource_types) {
+    this.supported_resource_types = supported_resource_types;
+  }
+
+  public Logger getLogger() {
+    return logger;
+  }
+
+  public void setLogger(Logger logger) {
+    this.logger = logger;
+  }
+
+  public ClientIdStrategyEnum getClient_id_strategy() {
+    return client_id_strategy;
+  }
+
+  public void setClient_id_strategy(
+    ClientIdStrategyEnum client_id_strategy) {
+    this.client_id_strategy = client_id_strategy;
+  }
+
+  public Boolean getAllow_cascading_deletes() {
+    return allow_cascading_deletes;
+  }
+
+  public void setAllow_cascading_deletes(Boolean allow_cascading_deletes) {
+    this.allow_cascading_deletes = allow_cascading_deletes;
+  }
+
+  public Boolean getAllow_contains_searches() {
+    return allow_contains_searches;
+  }
+
+  public void setAllow_contains_searches(Boolean allow_contains_searches) {
+    this.allow_contains_searches = allow_contains_searches;
+  }
+
+  public Boolean getAllow_external_references() {
+    return allow_external_references;
+  }
+
+  public void setAllow_external_references(Boolean allow_external_references) {
+    this.allow_external_references = allow_external_references;
+  }
+
+  public Boolean getAllow_multiple_delete() {
+    return allow_multiple_delete;
+  }
+
+  public void setAllow_multiple_delete(Boolean allow_multiple_delete) {
+    this.allow_multiple_delete = allow_multiple_delete;
+  }
+
+  public Boolean getAllow_override_default_search_params() {
+    return allow_override_default_search_params;
+  }
+
+  public void setAllow_override_default_search_params(
+    Boolean allow_override_default_search_params) {
+    this.allow_override_default_search_params = allow_override_default_search_params;
+  }
+
+  public Boolean getAllow_placeholder_references() {
+    return allow_placeholder_references;
+  }
+
+  public void setAllow_placeholder_references(Boolean allow_placeholder_references) {
+    this.allow_placeholder_references = allow_placeholder_references;
+  }
+
+  public Boolean getAuto_create_placeholder_reference_targets() {
+    return auto_create_placeholder_reference_targets;
+  }
+
+  public void setAuto_create_placeholder_reference_targets(
+    Boolean auto_create_placeholder_reference_targets) {
+    this.auto_create_placeholder_reference_targets = auto_create_placeholder_reference_targets;
+  }
+
+  public Integer getDefault_page_size() {
+    return default_page_size;
+  }
+
+  public void setDefault_page_size(Integer default_page_size) {
+    this.default_page_size = default_page_size;
+  }
+
+  public Boolean getEnable_index_missing_fields() {
+    return enable_index_missing_fields;
+  }
+
+  public void setEnable_index_missing_fields(Boolean enable_index_missing_fields) {
+    this.enable_index_missing_fields = enable_index_missing_fields;
+  }
+
+  public Boolean getEnforce_referential_integrity_on_delete() {
+    return enforce_referential_integrity_on_delete;
+  }
+
+  public void setEnforce_referential_integrity_on_delete(
+    Boolean enforce_referential_integrity_on_delete) {
+    this.enforce_referential_integrity_on_delete = enforce_referential_integrity_on_delete;
+  }
+
+  public Boolean getEnforce_referential_integrity_on_write() {
+    return enforce_referential_integrity_on_write;
+  }
+
+  public void setEnforce_referential_integrity_on_write(
+    Boolean enforce_referential_integrity_on_write) {
+    this.enforce_referential_integrity_on_write = enforce_referential_integrity_on_write;
+  }
+
+  public Boolean getEtag_support_enabled() {
+    return etag_support_enabled;
+  }
+
+  public void setEtag_support_enabled(Boolean etag_support_enabled) {
+    this.etag_support_enabled = etag_support_enabled;
+  }
+
+  public Boolean getExpunge_enabled() {
+    return expunge_enabled;
+  }
+
+  public void setExpunge_enabled(Boolean expunge_enabled) {
+    this.expunge_enabled = expunge_enabled;
+  }
+
+  public Boolean getFhirpath_interceptor_enabled() {
+    return fhirpath_interceptor_enabled;
+  }
+
+  public void setFhirpath_interceptor_enabled(Boolean fhirpath_interceptor_enabled) {
+    this.fhirpath_interceptor_enabled = fhirpath_interceptor_enabled;
+  }
+
+  public Boolean getFilter_search_enabled() {
+    return filter_search_enabled;
+  }
+
+  public void setFilter_search_enabled(Boolean filter_search_enabled) {
+    this.filter_search_enabled = filter_search_enabled;
+  }
+
+  public Boolean getGraphql_enabled() {
+    return graphql_enabled;
+  }
+
+  public void setGraphql_enabled(Boolean graphql_enabled) {
+    this.graphql_enabled = graphql_enabled;
+  }
+
+  public Boolean getBinary_storage_enabled() {
+    return binary_storage_enabled;
+  }
+
+  public void setBinary_storage_enabled(Boolean binary_storage_enabled) {
+    this.binary_storage_enabled = binary_storage_enabled;
+  }
+
+  public Boolean getBulk_export_enabled() {
+    return bulk_export_enabled;
+  }
+
+  public void setBulk_export_enabled(Boolean bulk_export_enabled) {
+    this.bulk_export_enabled = bulk_export_enabled;
+  }
+
+  public EncodingEnum getDefault_encoding() {
+    return default_encoding;
+  }
+
+  public void setDefault_encoding(EncodingEnum default_encoding) {
+    this.default_encoding = default_encoding;
+  }
+
+  public FhirVersionEnum getFhir_version() {
+    return fhir_version;
+  }
+
+  public void setFhir_version(FhirVersionEnum fhir_version) {
+    this.fhir_version = fhir_version;
+  }
+
+  public Integer getMax_binary_size() {
+    return max_binary_size;
+  }
+
+  public void setMax_binary_size(Integer max_binary_size) {
+    this.max_binary_size = max_binary_size;
+  }
+
+  public Integer getMax_page_size() {
+    return max_page_size;
+  }
+
+  public void setMax_page_size(Integer max_page_size) {
+    this.max_page_size = max_page_size;
+  }
+
+  public Long getRetain_cached_searches_mins() {
+    return retain_cached_searches_mins;
+  }
+
+  public void setRetain_cached_searches_mins(Long retain_cached_searches_mins) {
+    this.retain_cached_searches_mins = retain_cached_searches_mins;
+  }
+
+  public Long getReuse_cached_search_results_millis() {
+    return reuse_cached_search_results_millis;
+  }
+
+  public void setReuse_cached_search_results_millis(Long reuse_cached_search_results_millis) {
+    this.reuse_cached_search_results_millis = reuse_cached_search_results_millis;
+  }
+
+  public List<Tester> getTester() {
+    return tester;
+  }
+
+  public void setTester(List<Tester> tester) {
+    this.tester = tester;
+  }
+
+  public static class Cors {
+    private Boolean allow_Credentials = true;
+    private List<String> allowed_origin = ImmutableList.of("*");
+
+    public List<String> getAllowed_origin() {
+      return allowed_origin;
+    }
+
+    public void setAllowed_origin(List<String> allowed_origin) {
+      this.allowed_origin = allowed_origin;
+    }
+
+    public Boolean getAllow_Credentials() {
+      return allow_Credentials;
+    }
+
+    public void setAllow_Credentials(Boolean allow_Credentials) {
+      this.allow_Credentials = allow_Credentials;
+    }
+
+
+  }
+
+  public static class Logger {
+
+    private String name = "fhirtest.access";
+    private String error_format = "ERROR - ${requestVerb} ${requestUrl}";
+    private String format = "Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]";
+    private Boolean log_exceptions = true;
+
+    public String getName() {
+      return name;
+    }
+
+    public void setName(String name) {
+      this.name = name;
+    }
+
+    public String getError_format() {
+      return error_format;
+    }
+
+    public void setError_format(String error_format) {
+      this.error_format = error_format;
+    }
+
+    public String getFormat() {
+      return format;
+    }
+
+    public void setFormat(String format) {
+      this.format = format;
+    }
+
+    public Boolean getLog_exceptions() {
+      return log_exceptions;
+    }
+
+    public void setLog_exceptions(Boolean log_exceptions) {
+      this.log_exceptions = log_exceptions;
+    }
+  }
+
+
+  public static class Tester {
+
+    private String id = "home";
+    private String name = "Local Tester";
+    private String server_address = "http://localhost:8080/fhir";
+    private Boolean refuse_to_fetch_third_party_urls = true;
+    private FhirVersionEnum fhir_version = FhirVersionEnum.R4;
+
+    public FhirVersionEnum getFhir_version() {
+      return fhir_version;
+    }
+
+    public void setFhir_version(FhirVersionEnum fhir_version) {
+      this.fhir_version = fhir_version;
+    }
+
+    public String getId() {
+      return id;
+    }
+
+    public void setId(String id) {
+      this.id = id;
+    }
+
+    public String getName() {
+      return name;
+    }
+
+    public void setName(String name) {
+      this.name = name;
+    }
+
+    public String getServer_address() {
+      return server_address;
+    }
+
+    public void setServer_address(String server_address) {
+      this.server_address = server_address;
+    }
+
+    public Boolean getRefuse_to_fetch_third_party_urls() {
+      return refuse_to_fetch_third_party_urls;
+    }
+
+    public void setRefuse_to_fetch_third_party_urls(Boolean refuse_to_fetch_third_party_urls) {
+      this.refuse_to_fetch_third_party_urls = refuse_to_fetch_third_party_urls;
+    }
+  }
+
+  public static class ImplementationGuide
+  {
+    private String url;
+    private String name;
+    private String version;
+
+    public String getUrl() {
+      return url;
+    }
+
+    public void setUrl(String url) {
+      this.url = url;
+    }
+
+    public String getName() {
+      return name;
+    }
+
+    public void setName(String name) {
+      this.name = name;
+    }
+
+    public String getVersion() {
+      return version;
+    }
+
+    public void setVersion(String version) {
+      this.version = version;
+    }
+  }
+
+  public static class Validation {
+
+    private Boolean requests_enabled = false;
+    private Boolean responses_enabled = false;
+
+    public Boolean getRequests_enabled() {
+      return requests_enabled;
+    }
+
+    public void setRequests_enabled(Boolean requests_enabled) {
+      this.requests_enabled = requests_enabled;
+    }
+
+    public Boolean getResponses_enabled() {
+      return responses_enabled;
+    }
+
+    public void setResponses_enabled(Boolean responses_enabled) {
+      this.responses_enabled = responses_enabled;
+    }
+  }
+
+  public static class Partitioning {
+
+    private Boolean partitioning_include_in_search_hashes = false;
+
+
+    public Boolean getPartitioning_include_in_search_hashes() {
+      return partitioning_include_in_search_hashes;
+    }
+
+    public void setPartitioning_include_in_search_hashes(Boolean partitioning_include_in_search_hashes) {
+      this.partitioning_include_in_search_hashes = partitioning_include_in_search_hashes;
+    }
+  }
+
+  public static class Subscription {
+
+    public Boolean getResthook_enabled() {
+      return resthook_enabled;
+    }
+
+    public void setResthook_enabled(Boolean resthook_enabled) {
+      this.resthook_enabled = resthook_enabled;
+    }
+
+    public Boolean getWebsocket_enabled() {
+      return websocket_enabled;
+    }
+
+    public void setWebsocket_enabled(Boolean websocket_enabled) {
+      this.websocket_enabled = websocket_enabled;
+    }
+
+    private Boolean resthook_enabled = false;
+    private Boolean websocket_enabled = false;
+    private Email email = null;
+
+    public Email getEmail() {
+      return email;
+    }
+
+    public void setEmail(Email email) {
+      this.email = email;
+    }
+
+
+    public static class Email {
+      public String getFrom() {
+        return from;
+      }
+
+      public void setFrom(String from) {
+        this.from = from;
+      }
+
+      public String getHost() {
+        return host;
+      }
+
+      public void setHost(String host) {
+        this.host = host;
+      }
+
+      public Integer getPort() {
+        return port;
+      }
+
+      public void setPort(Integer port) {
+        this.port = port;
+      }
+
+      public String getUsername() {
+        return username;
+      }
+
+      public void setUsername(String username) {
+        this.username = username;
+      }
+
+      public String getPassword() {
+        return password;
+      }
+
+      public void setPassword(String password) {
+        this.password = password;
+      }
+
+      public Boolean getAuth() {
+        return auth;
+      }
+
+      public void setAuth(Boolean auth) {
+        this.auth = auth;
+      }
+
+      public Boolean getStartTlsEnable() {
+        return startTlsEnable;
+      }
+
+      public void setStartTlsEnable(Boolean startTlsEnable) {
+        this.startTlsEnable = startTlsEnable;
+      }
+
+      public Boolean getStartTlsRequired() {
+        return startTlsRequired;
+      }
+
+      public void setStartTlsRequired(Boolean startTlsRequired) {
+        this.startTlsRequired = startTlsRequired;
+      }
+
+      public Boolean getQuitWait() {
+        return quitWait;
+      }
+
+      public void setQuitWait(Boolean quitWait) {
+        this.quitWait = quitWait;
+      }
+
+      private String from;
+      private String host;
+      private Integer port = 25;
+      private String username;
+      private String password;
+      private Boolean auth = false;
+      private Boolean startTlsEnable = false;
+      private Boolean startTlsRequired = false;
+      private Boolean quitWait = false;
+    }
+  }
+}

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

@@ -0,0 +1,76 @@
+package ca.uhn.fhir.jpa.starter;
+
+import ca.uhn.fhir.jpa.empi.EmpiConfig;
+import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
+import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
+import ca.uhn.fhir.jpa.subscription.match.config.WebsocketDispatcherConfig;
+import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.config.AutowireCapableBeanFactory;
+import org.springframework.boot.SpringApplication;
+import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.boot.autoconfigure.elasticsearch.ElasticsearchRestClientAutoConfiguration;
+import org.springframework.boot.builder.SpringApplicationBuilder;
+import org.springframework.boot.web.servlet.ServletComponentScan;
+import org.springframework.boot.web.servlet.ServletRegistrationBean;
+import org.springframework.boot.web.servlet.support.SpringBootServletInitializer;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Import;
+import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
+import org.springframework.web.servlet.DispatcherServlet;
+
+@ServletComponentScan(basePackageClasses = {
+  JpaRestfulServer.class}, basePackages = "ca.uhn.fhir.jpa.starter")
+@SpringBootApplication(exclude = {ElasticsearchRestClientAutoConfiguration.class}, scanBasePackages = {"ca.uhn.fhir.jpa.starter"})
+@Import({SubscriptionSubmitterConfig.class, SubscriptionProcessorConfig.class, SubscriptionChannelConfig.class, WebsocketDispatcherConfig.class, EmpiConfig.class})
+public class Application extends SpringBootServletInitializer {
+
+  public static void main(String[] args) {
+
+    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/
+  }
+
+  @Override
+  protected SpringApplicationBuilder configure(
+    SpringApplicationBuilder builder) {
+    return builder.sources(Application.class);
+  }
+
+  @Autowired
+  AutowireCapableBeanFactory beanFactory;
+
+  @Bean
+  public ServletRegistrationBean hapiServletRegistration() {
+    ServletRegistrationBean servletRegistrationBean = new ServletRegistrationBean();
+    JpaRestfulServer jpaRestfulServer = new JpaRestfulServer();
+    beanFactory.autowireBean(jpaRestfulServer);
+    servletRegistrationBean.setServlet(jpaRestfulServer);
+    servletRegistrationBean.addUrlMappings("/hapi-fhir-jpaserver/fhir/*");
+    servletRegistrationBean.setLoadOnStartup(1);
+
+    return servletRegistrationBean;
+  }
+
+  @Bean
+  public ServletRegistrationBean overlayRegistrationBean() {
+
+    AnnotationConfigWebApplicationContext annotationConfigWebApplicationContext = new AnnotationConfigWebApplicationContext();
+    annotationConfigWebApplicationContext.register(FhirTesterConfig.class);
+
+    DispatcherServlet dispatcherServlet = new DispatcherServlet(
+      annotationConfigWebApplicationContext);
+    dispatcherServlet.setContextClass(AnnotationConfigWebApplicationContext.class);
+    dispatcherServlet.setContextConfigLocation(FhirTesterConfig.class.getName());
+
+    ServletRegistrationBean registrationBean = new ServletRegistrationBean();
+    registrationBean.setServlet(dispatcherServlet);
+    registrationBean.addUrlMappings("/hapi-fhir-jpaserver/*", "/*");
+    registrationBean.setLoadOnStartup(1);
+    return registrationBean;
+
+  }
+}

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

@@ -1,49 +0,0 @@
-package ca.uhn.fhir.jpa.starter;
-
-import ca.uhn.fhir.context.FhirVersionEnum;
-import ca.uhn.fhir.jpa.empi.EmpiConfig;
-import ca.uhn.fhir.jpa.empi.config.EmpiConsumerConfig;
-import ca.uhn.fhir.jpa.empi.config.EmpiSubmitterConfig;
-import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
-import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
-import ca.uhn.fhir.jpa.subscription.match.config.WebsocketDispatcherConfig;
-import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
-import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
-
-public class ApplicationContext extends AnnotationConfigWebApplicationContext {
-
-  public ApplicationContext() {
-    FhirVersionEnum fhirVersion = HapiProperties.getFhirVersion();
-    if (fhirVersion == FhirVersionEnum.DSTU2) {
-      register(FhirServerConfigDstu2.class, FhirServerConfigCommon.class);
-    } else if (fhirVersion == FhirVersionEnum.DSTU3) {
-      register(FhirServerConfigDstu3.class, FhirServerConfigCommon.class);
-    } else if (fhirVersion == FhirVersionEnum.R4) {
-      register(FhirServerConfigR4.class, FhirServerConfigCommon.class);
-    } else if (fhirVersion == FhirVersionEnum.R5) {
-      register(FhirServerConfigR5.class, FhirServerConfigCommon.class);
-    } else {
-      throw new IllegalStateException();
-    }
-
-    if (HapiProperties.getSubscriptionWebsocketEnabled()) {
-      register(WebsocketDispatcherConfig.class);
-    }
-
-    if (HapiProperties.getSubscriptionEmailEnabled()
-      || HapiProperties.getSubscriptionRestHookEnabled()
-      || HapiProperties.getSubscriptionWebsocketEnabled()) {
-      register(SubscriptionSubmitterConfig.class);
-      register(SubscriptionProcessorConfig.class);
-      register(SubscriptionChannelConfig.class);
-    }
-
-    if (HapiProperties.getEmpiEnabled()) {
-      register(EmpiSubmitterConfig.class);
-      register(EmpiConsumerConfig.class);
-      register(EmpiConfig.class);
-    }
-
-  }
-
-}

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

@@ -10,52 +10,95 @@ import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
 import ca.uhn.fhir.jpa.bulk.provider.BulkDataExportProvider;
 import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
+import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc;
+import ca.uhn.fhir.jpa.packages.PackageInstallationSpec;
 import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
 import ca.uhn.fhir.jpa.provider.GraphQLProvider;
+import ca.uhn.fhir.jpa.provider.IJpaSystemProvider;
 import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
-import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
-import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
-import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
-import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
 import ca.uhn.fhir.jpa.provider.r4.JpaConformanceProviderR4;
-import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4;
 import ca.uhn.fhir.jpa.provider.r5.JpaConformanceProviderR5;
-import ca.uhn.fhir.jpa.provider.r5.JpaSystemProviderR5;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
-import ca.uhn.fhir.model.dstu2.composite.MetaDt;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
+import ca.uhn.fhir.rest.server.ETagSupportEnum;
 import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
 import ca.uhn.fhir.rest.server.RestfulServer;
-import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.*;
-import ca.uhn.fhir.rest.server.interceptor.FhirPathFilterInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
 import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
 import ca.uhn.fhir.rest.server.tenant.UrlBaseTenantIdentificationStrategy;
 import ca.uhn.fhir.validation.IValidatorModule;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
-import org.hl7.fhir.dstu3.model.Bundle;
+import com.google.common.base.Strings;
-import org.hl7.fhir.dstu3.model.Meta;
 import org.hl7.fhir.r4.model.Bundle.BundleType;
-import org.springframework.context.ApplicationContext;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.HttpHeaders;
 import org.springframework.web.cors.CorsConfiguration;
 
 import javax.servlet.ServletException;
 import java.util.Arrays;
 import java.util.Collections;
-import java.util.HashSet;
+import java.util.List;
-import java.util.Set;
+import java.util.Optional;
-import java.util.TreeSet;
+import java.util.stream.Collectors;
 
 public class BaseJpaRestfulServer extends RestfulServer {
 
+  @Autowired
+  DaoRegistry daoRegistry;
+
+  @Autowired
+  DaoConfig daoConfig;
+
+  @Autowired
+  ISearchParamRegistry searchParamRegistry;
+
+  @Autowired
+  IFhirSystemDao fhirSystemDao;
+
+  @Autowired
+  ResourceProviderFactory resourceProviders;
+
+  @Autowired
+  IJpaSystemProvider jpaSystemProvider;
+
+  @Autowired
+  IInterceptorBroadcaster interceptorBroadcaster;
+
+  @Autowired
+  DatabaseBackedPagingProvider databaseBackedPagingProvider;
+
+  @Autowired
+  IInterceptorService interceptorService;
+
+  @Autowired
+  IValidatorModule validatorModule;
+
+  @Autowired
+  Optional<GraphQLProvider> graphQLProvider;
+
+  @Autowired
+  BulkDataExportProvider bulkDataExportProvider;
+
+  @Autowired
+  PartitionManagementProvider partitionManagementProvider;
+
+  @Autowired
+  BinaryStorageInterceptor binaryStorageInterceptor;
+
+  @Autowired
+  IPackageInstallerSvc packageInstallerSvc;
+
+  @Autowired
+  AppProperties appProperties;
+
+  public BaseJpaRestfulServer() {
+
+  }
+
   private static final long serialVersionUID = 1L;
 
   @SuppressWarnings("unchecked")
@@ -67,47 +110,19 @@ public class BaseJpaRestfulServer extends RestfulServer {
      * Create a FhirContext object that uses the version of FHIR
      * specified in the properties file.
      */
-    ApplicationContext appCtx = (ApplicationContext) getServletContext()
-      .getAttribute("org.springframework.web.context.WebApplicationContext.ROOT");
     // Customize supported resource types
-    Set<String> supportedResourceTypes = HapiProperties.getSupportedResourceTypes();
+    List<String> supportedResourceTypes = appProperties.getSupported_resource_types();
 
     if (!supportedResourceTypes.isEmpty() && !supportedResourceTypes.contains("SearchParameter")) {
       supportedResourceTypes.add("SearchParameter");
-    }
-
-    if (!supportedResourceTypes.isEmpty()) {
-      DaoRegistry daoRegistry = appCtx.getBean(DaoRegistry.class);
       daoRegistry.setSupportedResourceTypes(supportedResourceTypes);
     }
 
-    /*
+    setFhirContext(fhirSystemDao.getContext());
-     * ResourceProviders are fetched from the Spring context
-     */
-    FhirVersionEnum fhirVersion = HapiProperties.getFhirVersion();
-    ResourceProviderFactory resourceProviders;
-    Object systemProvider;
-    if (fhirVersion == FhirVersionEnum.DSTU2) {
-      resourceProviders = appCtx.getBean("myResourceProvidersDstu2", ResourceProviderFactory.class);
-      systemProvider = appCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class);
-    } else if (fhirVersion == FhirVersionEnum.DSTU3) {
-      resourceProviders = appCtx.getBean("myResourceProvidersDstu3", ResourceProviderFactory.class);
-      systemProvider = appCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class);
-    } else if (fhirVersion == FhirVersionEnum.R4) {
-      resourceProviders = appCtx.getBean("myResourceProvidersR4", ResourceProviderFactory.class);
-      systemProvider = appCtx.getBean("mySystemProviderR4", JpaSystemProviderR4.class);
-    } else if (fhirVersion == FhirVersionEnum.R5) {
-      resourceProviders = appCtx.getBean("myResourceProvidersR5", ResourceProviderFactory.class);
-      systemProvider = appCtx.getBean("mySystemProviderR5", JpaSystemProviderR5.class);
-    } else {
-      throw new IllegalStateException();
-    }
-
-    setFhirContext(appCtx.getBean(FhirContext.class));
-
     registerProviders(resourceProviders.createProviders());
-    registerProvider(systemProvider);
+    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
@@ -116,27 +131,31 @@ public class BaseJpaRestfulServer extends RestfulServer {
      * You can also create your own subclass of the conformance provider if you need to
      * provide further customization of your server's CapabilityStatement
      */
-    DaoConfig daoConfig = appCtx.getBean(DaoConfig.class);
+
-    ISearchParamRegistry searchParamRegistry = appCtx.getBean(ISearchParamRegistry.class);
+
     if (fhirVersion == FhirVersionEnum.DSTU2) {
-      IFhirSystemDao<ca.uhn.fhir.model.dstu2.resource.Bundle, MetaDt> systemDao = appCtx.getBean("mySystemDaoDstu2", IFhirSystemDao.class);
+
-      JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, systemDao, daoConfig);
+      JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, fhirSystemDao,
+        daoConfig);
       confProvider.setImplementationDescription("HAPI FHIR DSTU2 Server");
       setServerConformanceProvider(confProvider);
     } else {
       if (fhirVersion == FhirVersionEnum.DSTU3) {
-        IFhirSystemDao<Bundle, Meta> systemDao = appCtx.getBean("mySystemDaoDstu3", IFhirSystemDao.class);
+
-        JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao, daoConfig, searchParamRegistry);
+        JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, fhirSystemDao,
+          daoConfig, searchParamRegistry);
         confProvider.setImplementationDescription("HAPI FHIR DSTU3 Server");
         setServerConformanceProvider(confProvider);
       } else if (fhirVersion == FhirVersionEnum.R4) {
-        IFhirSystemDao<org.hl7.fhir.r4.model.Bundle, org.hl7.fhir.r4.model.Meta> systemDao = appCtx.getBean("mySystemDaoR4", IFhirSystemDao.class);
+
-        JpaConformanceProviderR4 confProvider = new JpaConformanceProviderR4(this, systemDao, daoConfig, searchParamRegistry);
+        JpaConformanceProviderR4 confProvider = new JpaConformanceProviderR4(this, fhirSystemDao,
+          daoConfig, searchParamRegistry);
         confProvider.setImplementationDescription("HAPI FHIR R4 Server");
         setServerConformanceProvider(confProvider);
       } else if (fhirVersion == FhirVersionEnum.R5) {
-        IFhirSystemDao<org.hl7.fhir.r5.model.Bundle, org.hl7.fhir.r5.model.Meta> systemDao = appCtx.getBean("mySystemDaoR5", IFhirSystemDao.class);
+
-        JpaConformanceProviderR5 confProvider = new JpaConformanceProviderR5(this, systemDao, daoConfig, searchParamRegistry);
+        JpaConformanceProviderR5 confProvider = new JpaConformanceProviderR5(this, fhirSystemDao,
+          daoConfig, searchParamRegistry);
         confProvider.setImplementationDescription("HAPI FHIR R5 Server");
         setServerConformanceProvider(confProvider);
       } else {
@@ -147,7 +166,10 @@ public class BaseJpaRestfulServer extends RestfulServer {
     /*
      * ETag Support
      */
-    setETagSupport(HapiProperties.getEtagSupport());
+
+    if (appProperties.getEtag_support_enabled() == false)
+      setETagSupport(ETagSupportEnum.DISABLED);
+
 
     /*
      * This server tries to dynamically generate narratives
@@ -158,12 +180,12 @@ public class BaseJpaRestfulServer extends RestfulServer {
     /*
      * Default to JSON and pretty printing
      */
-    setDefaultPrettyPrint(HapiProperties.getDefaultPrettyPrint());
+    setDefaultPrettyPrint(appProperties.getDefault_pretty_print());
 
     /*
      * Default encoding
      */
-    setDefaultResponseEncoding(HapiProperties.getDefaultEncoding());
+    setDefaultResponseEncoding(appProperties.getDefault_encoding());
 
     /*
      * This configures the server to page search results to and from
@@ -171,7 +193,8 @@ public class BaseJpaRestfulServer extends RestfulServer {
      * a performance hit when performing searches that return lots of results,
      * but makes the server much more scalable.
      */
-    setPagingProvider(appCtx.getBean(DatabaseBackedPagingProvider.class));
+
+    setPagingProvider(databaseBackedPagingProvider);
 
     /*
      * This interceptor formats the output using nice colourful
@@ -181,7 +204,7 @@ public class BaseJpaRestfulServer extends RestfulServer {
     ResponseHighlighterInterceptor responseHighlighterInterceptor = new ResponseHighlighterInterceptor();
     this.registerInterceptor(responseHighlighterInterceptor);
 
-    if (HapiProperties.isFhirPathFilterInterceptorEnabled()) {
+    if (appProperties.getFhirpath_interceptor_enabled()) {
       registerInterceptor(new FhirPathFilterInterceptor());
     }
 
@@ -189,10 +212,10 @@ public class BaseJpaRestfulServer extends RestfulServer {
      * Add some logging for each request
      */
     LoggingInterceptor loggingInterceptor = new LoggingInterceptor();
-    loggingInterceptor.setLoggerName(HapiProperties.getLoggerName());
+    loggingInterceptor.setLoggerName(appProperties.getLogger().getName());
-    loggingInterceptor.setMessageFormat(HapiProperties.getLoggerFormat());
+    loggingInterceptor.setMessageFormat(appProperties.getLogger().getFormat());
-    loggingInterceptor.setErrorMessageFormat(HapiProperties.getLoggerErrorFormat());
+    loggingInterceptor.setErrorMessageFormat(appProperties.getLogger().getError_format());
-    loggingInterceptor.setLogExceptions(HapiProperties.getLoggerLogExceptions());
+    loggingInterceptor.setLogExceptions(appProperties.getLogger().getLog_exceptions());
     this.registerInterceptor(loggingInterceptor);
 
     /*
@@ -201,8 +224,8 @@ public class BaseJpaRestfulServer extends RestfulServer {
      * this doesn't always work. If you are setting links in your search bundles that
      * just refer to "localhost", you might want to use a server address strategy:
      */
-    String serverAddress = HapiProperties.getServerAddress();
+    String serverAddress = appProperties.getServer_address();
-    if (serverAddress != null && serverAddress.length() > 0) {
+    if (!Strings.isNullOrEmpty(serverAddress)) {
       setServerAddressStrategy(new HardcodedServerAddressStrategy(serverAddress));
     }
 
@@ -214,21 +237,21 @@ public class BaseJpaRestfulServer extends RestfulServer {
      * with this feature.
      */
     if (false) { // <-- DISABLED RIGHT NOW
-      registerProvider(appCtx.getBean(TerminologyUploaderProvider.class));
+      //registerProvider(appCtx.getBean(TerminologyUploaderProvider.class));
     }
 
     // If you want to enable the $trigger-subscription operation to allow
     // manual triggering of a subscription delivery, enable this provider
     if (false) { // <-- DISABLED RIGHT NOW
-      SubscriptionTriggeringProvider retriggeringProvider = appCtx
+     /* SubscriptionTriggeringProvider retriggeringProvider = appCtx
         .getBean(SubscriptionTriggeringProvider.class);
-      registerProvider(retriggeringProvider);
+      registerProvider(retriggeringProvider);*/
     }
 
     // Define your CORS configuration. This is an example
     // showing a typical setup. You should customize this
     // to your specific needs
-    if (HapiProperties.getCorsEnabled()) {
+    if (appProperties.getCors() != null) {
       CorsConfiguration config = new CorsConfiguration();
       config.addAllowedHeader(HttpHeaders.ORIGIN);
       config.addAllowedHeader(HttpHeaders.ACCEPT);
@@ -238,17 +261,15 @@ public class BaseJpaRestfulServer extends RestfulServer {
       config.addAllowedHeader("x-fhir-starter");
       config.addAllowedHeader("X-Requested-With");
       config.addAllowedHeader("Prefer");
-      String allAllowedCORSOrigins = HapiProperties.getCorsAllowedOrigin();
+      List<String> allAllowedCORSOrigins = appProperties.getCors().getAllowed_origin();
-      Arrays.stream(allAllowedCORSOrigins.split(",")).forEach(o -> {
+      allAllowedCORSOrigins.forEach(config::addAllowedOrigin);
-        config.addAllowedOrigin(o);
+
-      });
-      config.addAllowedOrigin(HapiProperties.getCorsAllowedOrigin());
 
       config.addExposedHeader("Location");
       config.addExposedHeader("Content-Location");
       config.setAllowedMethods(
         Arrays.asList("GET", "POST", "PUT", "DELETE", "OPTIONS", "PATCH", "HEAD"));
-      config.setAllowCredentials(HapiProperties.getCorsAllowedCredentials());
+      config.setAllowCredentials(appProperties.getCors().getAllow_Credentials());
 
       // Create the interceptor and register it
       CorsInterceptor interceptor = new CorsInterceptor(config);
@@ -257,39 +278,35 @@ public class BaseJpaRestfulServer extends RestfulServer {
 
     // If subscriptions are enabled, we want to register the interceptor that
     // will activate them and match results against them
-    if (HapiProperties.getSubscriptionWebsocketEnabled() ||
+    if (appProperties.getSubscription() != null) {
-      HapiProperties.getSubscriptionEmailEnabled() ||
-      HapiProperties.getSubscriptionRestHookEnabled()) {
       // Subscription debug logging
-      IInterceptorService interceptorService = appCtx.getBean(IInterceptorService.class);
       interceptorService.registerInterceptor(new SubscriptionDebugLogInterceptor());
     }
 
     // Cascading deletes
-    DaoRegistry daoRegistry = appCtx.getBean(DaoRegistry.class);
+
-    IInterceptorBroadcaster interceptorBroadcaster = appCtx.getBean(IInterceptorBroadcaster.class);
+
-    if (HapiProperties.getAllowCascadingDeletes()) {
+    if (appProperties.getAllow_cascading_deletes()) {
-      CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(ctx, daoRegistry, interceptorBroadcaster);
+      CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(ctx,
+        daoRegistry, interceptorBroadcaster);
       getInterceptorService().registerInterceptor(cascadingDeleteInterceptor);
     }
 
     // Binary Storage
-    if (HapiProperties.isBinaryStorageEnabled()) {
+    if (appProperties.getBinary_storage_enabled()) {
-      BinaryStorageInterceptor binaryStorageInterceptor = appCtx
-        .getBean(BinaryStorageInterceptor.class);
       getInterceptorService().registerInterceptor(binaryStorageInterceptor);
     }
 
     // Validation
-    IValidatorModule validatorModule = appCtx.getBean(IValidatorModule.class);
+
     if (validatorModule != null) {
-      if (HapiProperties.getValidateRequestsEnabled()) {
+      if (appProperties.getValidation().getRequests_enabled()) {
         RequestValidatingInterceptor interceptor = new RequestValidatingInterceptor();
         interceptor.setFailOnSeverity(ResultSeverityEnum.ERROR);
         interceptor.setValidatorModules(Collections.singletonList(validatorModule));
         registerInterceptor(interceptor);
       }
-      if (HapiProperties.getValidateResponsesEnabled()) {
+      if (appProperties.getValidation().getResponses_enabled()) {
         ResponseValidatingInterceptor interceptor = new ResponseValidatingInterceptor();
         interceptor.setFailOnSeverity(ResultSeverityEnum.ERROR);
         interceptor.setValidatorModules(Collections.singletonList(validatorModule));
@@ -298,40 +315,46 @@ public class BaseJpaRestfulServer extends RestfulServer {
     }
 
     // GraphQL
-    if (HapiProperties.getGraphqlEnabled()) {
+    if (appProperties.getGraphql_enabled()) {
       if (fhirVersion.isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
-        registerProvider(appCtx.getBean(GraphQLProvider.class));
+        registerProvider(graphQLProvider.get());
       }
     }
 
-    if (!HapiProperties.getAllowedBundleTypes().isEmpty()) {
+    if (appProperties.getAllowed_bundle_types() != null) {
-      String allowedBundleTypesString = HapiProperties.getAllowedBundleTypes();
+      daoConfig.setBundleTypesAllowedForStorage(appProperties.getAllowed_bundle_types().stream().map(BundleType::toCode).collect(Collectors.toSet()));
-      Set<String> allowedBundleTypes = new HashSet<>();
-      Arrays.stream(allowedBundleTypesString.split(",")).forEach(o -> {
-        BundleType type = BundleType.valueOf(o);
-        allowedBundleTypes.add(type.toCode());
-      });
-      DaoConfig config = daoConfig;
-      config.setBundleTypesAllowedForStorage(
-        Collections.unmodifiableSet(new TreeSet<>(allowedBundleTypes)));
     }
 
+    daoConfig.setDeferIndexingForCodesystemsOfSize(appProperties.getDefer_indexing_for_codesystems_of_size());
+
     // Bulk Export
-    if (HapiProperties.getBulkExportEnabled()) {
+    if (appProperties.getBulk_export_enabled()) {
-      registerProvider(appCtx.getBean(BulkDataExportProvider.class));
+      registerProvider(bulkDataExportProvider);
     }
 
     // Partitioning
-    if (HapiProperties.getPartitioningMultitenancyEnabled()) {
+    if (appProperties.getPartitioning() != null) {
       registerInterceptor(new RequestTenantPartitionInterceptor());
       setTenantIdentificationStrategy(new UrlBaseTenantIdentificationStrategy());
-      registerProviders(appCtx.getBean(PartitionManagementProvider.class));
+      registerProviders(partitionManagementProvider);
     }
 
-    if (HapiProperties.getClientIdStrategy() == DaoConfig.ClientIdStrategyEnum.ANY) {
+    if (appProperties.getClient_id_strategy() == DaoConfig.ClientIdStrategyEnum.ANY) {
       daoConfig.setResourceServerIdStrategy(DaoConfig.IdStrategyEnum.UUID);
-      daoConfig.setResourceClientIdStrategy(HapiProperties.getClientIdStrategy());
+      daoConfig.setResourceClientIdStrategy(appProperties.getClient_id_strategy());
+    }
+
+    if (appProperties.getImplementationGuides() != null) {
+      List<AppProperties.ImplementationGuide> guides = appProperties.getImplementationGuides();
+      for (AppProperties.ImplementationGuide guide : guides) {
+        packageInstallerSvc.install(new PackageInstallationSpec()
+          .setPackageUrl(guide.getUrl())
+          .setName(guide.getName())
+          .setVersion(guide.getVersion())
+          .setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL));
+      }
     }
   }
 
+
 }

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

@@ -0,0 +1,92 @@
+package ca.uhn.fhir.jpa.starter;
+
+import org.springframework.core.env.CompositePropertySource;
+import org.springframework.core.env.ConfigurableEnvironment;
+import org.springframework.core.env.EnumerablePropertySource;
+import org.springframework.core.env.PropertySource;
+
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Properties;
+
+public class EnvironmentHelper {
+
+  public static Properties getHibernateProperties(ConfigurableEnvironment environment) {
+    Properties properties = new Properties();
+    if (environment.getProperty("spring.jpa.properties", String.class) == null) {
+      properties.put("hibernate.dialect", "org.hibernate.dialect.H2Dialect");
+      properties.put("hibernate.search.model_mapping", "ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory");
+      properties.put("hibernate.format_sql", "false");
+      properties.put("hibernate.show_sql", "false");
+      properties.put("hibernate.hbm2ddl.auto", "update");
+      properties.put("hibernate.jdbc.batch_size", "20");
+      properties.put("hibernate.cache.use_query_cache", "false");
+      properties.put("hibernate.cache.use_second_level_cache", "false");
+      properties.put("hibernate.cache.use_structured_entries", "false");
+      properties.put("hibernate.cache.use_minimal_puts", "false");
+      properties.put("hibernate.search.default.directory_provider", "filesystem");
+      properties.put("hibernate.search.default.indexBase", "target/lucenefiles");
+      properties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");
+    } else {
+      Arrays.asList(environment.getProperty("spring.jpa.properties", String.class).split(" ")).stream().forEach(s ->
+      {
+        String[] values = s.split("=");
+        properties.put(values[0], values[1]);
+      });
+    }
+    return properties;
+  }
+
+  public static Map<String, Object> getPropertiesStartingWith(ConfigurableEnvironment aEnv,
+                                                              String aKeyPrefix) {
+    Map<String, Object> result = new HashMap<>();
+
+    Map<String, Object> map = getAllProperties(aEnv);
+
+    for (Map.Entry<String, Object> entry : map.entrySet()) {
+      String key = entry.getKey();
+
+      if (key.startsWith(aKeyPrefix)) {
+        result.put(key, entry.getValue());
+      }
+    }
+
+    return result;
+  }
+
+  public static Map<String, Object> getAllProperties(ConfigurableEnvironment aEnv) {
+    Map<String, Object> result = new HashMap<>();
+    aEnv.getPropertySources().forEach(ps -> addAll(result, getAllProperties(ps)));
+    return result;
+  }
+
+  public static Map<String, Object> getAllProperties(PropertySource<?> aPropSource) {
+    Map<String, Object> result = new HashMap<>();
+
+    if (aPropSource instanceof CompositePropertySource) {
+      CompositePropertySource cps = (CompositePropertySource) aPropSource;
+      cps.getPropertySources().forEach(ps -> addAll(result, getAllProperties(ps)));
+      return result;
+    }
+
+    if (aPropSource instanceof EnumerablePropertySource<?>) {
+      EnumerablePropertySource<?> ps = (EnumerablePropertySource<?>) aPropSource;
+      Arrays.asList(ps.getPropertyNames()).forEach(key -> result.put(key, ps.getProperty(key)));
+      return result;
+    }
+
+    return result;
+
+  }
+
+  private static void addAll(Map<String, Object> aBase, Map<String, Object> aToBeAdded) {
+    for (Map.Entry<String, Object> entry : aToBeAdded.entrySet()) {
+      if (aBase.containsKey(entry.getKey())) {
+        continue;
+      }
+
+      aBase.put(entry.getKey(), entry.getValue());
+    }
+  }
+}

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

@@ -8,17 +8,14 @@ import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory;
 import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
 import ca.uhn.fhir.jpa.subscription.match.deliver.email.JavaMailEmailSender;
-import org.apache.commons.dbcp2.BasicDataSource;
+import com.google.common.base.Strings;
 import org.hl7.fhir.dstu2.model.Subscription;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Lazy;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
-import org.thymeleaf.util.Validate;
 
-import java.lang.reflect.InvocationTargetException;
+import java.util.Optional;
-import java.sql.Driver;
 
 /**
  * This is the primary configuration file for the example server
@@ -29,57 +26,34 @@ public class FhirServerConfigCommon {
 
   private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirServerConfigCommon.class);
 
-  private Boolean enableIndexMissingFields = HapiProperties.getEnableIndexMissingFields();
-  private Boolean autoCreatePlaceholderReferenceTargets = HapiProperties.getAutoCreatePlaceholderReferenceTargets();
-  private Boolean enforceReferentialIntegrityOnWrite = HapiProperties.getEnforceReferentialIntegrityOnWrite();
-  private Boolean enforceReferentialIntegrityOnDelete = HapiProperties.getEnforceReferentialIntegrityOnDelete();
-  private Boolean allowContainsSearches = HapiProperties.getAllowContainsSearches();
-  private Boolean allowMultipleDelete = HapiProperties.getAllowMultipleDelete();
-  private Boolean allowExternalReferences = HapiProperties.getAllowExternalReferences();
-  private Boolean expungeEnabled = HapiProperties.getExpungeEnabled();
-  private Boolean allowPlaceholderReferences = HapiProperties.getAllowPlaceholderReferences();
-  private Boolean subscriptionRestHookEnabled = HapiProperties.getSubscriptionRestHookEnabled();
-  private Boolean subscriptionEmailEnabled = HapiProperties.getSubscriptionEmailEnabled();
-  private Boolean allowOverrideDefaultSearchParams = HapiProperties.getAllowOverrideDefaultSearchParams();
-  private String emailFrom = HapiProperties.getEmailFrom();
-  private Boolean emailEnabled = HapiProperties.getEmailEnabled();
-  private String emailHost = HapiProperties.getEmailHost();
-  private Integer emailPort = HapiProperties.getEmailPort();
-  private String emailUsername = HapiProperties.getEmailUsername();
-  private String emailPassword = HapiProperties.getEmailPassword();
-  private Boolean emailAuth = HapiProperties.getEmailAuth();
-  private Boolean emailStartTlsEnable = HapiProperties.getEmailStartTlsEnable();
-  private Boolean emailStartTlsRequired = HapiProperties.getEmailStartTlsRequired();
-  private Boolean emailQuitWait = HapiProperties.getEmailQuitWait();
-  @Autowired
-  private ApplicationContext myAppCtx;
 
-  public FhirServerConfigCommon() {
+  public FhirServerConfigCommon(AppProperties appProperties) {
-    ourLog.info("Server configured to " + (this.allowContainsSearches ? "allow" : "deny") + " contains searches");
+    ourLog.info("Server configured to " + (appProperties.getAllow_contains_searches() ? "allow" : "deny") + " contains searches");
-    ourLog.info("Server configured to " + (this.allowMultipleDelete ? "allow" : "deny") + " multiple deletes");
+    ourLog.info("Server configured to " + (appProperties.getAllow_multiple_delete() ? "allow" : "deny") + " multiple deletes");
-    ourLog.info("Server configured to " + (this.allowExternalReferences ? "allow" : "deny") + " external references");
+    ourLog.info("Server configured to " + (appProperties.getAllow_external_references() ? "allow" : "deny") + " external references");
-    ourLog.info("Server configured to " + (this.expungeEnabled ? "enable" : "disable") + " expunges");
+    ourLog.info("Server configured to " + (appProperties.getExpunge_enabled() ? "enable" : "disable") + " expunges");
-    ourLog.info("Server configured to " + (this.allowPlaceholderReferences ? "allow" : "deny") + " placeholder references");
+    ourLog.info("Server configured to " + (appProperties.getAllow_placeholder_references() ? "allow" : "deny") + " placeholder references");
-    ourLog.info("Server configured to " + (this.allowOverrideDefaultSearchParams ? "allow" : "deny") + " overriding default search params");
+    ourLog.info("Server configured to " + (appProperties.getAllow_override_default_search_params() ? "allow" : "deny") + " overriding default search params");
 
-    if (this.emailEnabled) {
+    if (appProperties.getSubscription().getEmail() != null) {
-      ourLog.info("Server is configured to enable email with host '" + this.emailHost + "' and port " + this.emailPort.toString());
+      AppProperties.Subscription.Email email = appProperties.getSubscription().getEmail();
-      ourLog.info("Server will use '" + this.emailFrom + "' as the from email address");
+      ourLog.info("Server is configured to enable email with host '" + email.getHost() + "' and port " + email.getPort());
+      ourLog.info("Server will use '" + email.getFrom() + "' as the from email address");
 
-      if (this.emailUsername != null && this.emailUsername.length() > 0) {
+      if (!Strings.isNullOrEmpty(email.getUsername())) {
-        ourLog.info("Server is configured to use username '" + this.emailUsername + "' for email");
+        ourLog.info("Server is configured to use username '" + email.getUsername() + "' for email");
       }
 
-      if (this.emailPassword != null && this.emailPassword.length() > 0) {
+      if (!Strings.isNullOrEmpty(email.getPassword())) {
         ourLog.info("Server is configured to use a password for email");
       }
     }
 
-    if (this.subscriptionRestHookEnabled) {
+    if (appProperties.getSubscription().getResthook_enabled()) {
       ourLog.info("REST-hook subscriptions enabled");
     }
 
-    if (this.subscriptionEmailEnabled) {
+    if (appProperties.getSubscription().getEmail() != null) {
       ourLog.info("Email subscriptions enabled");
     }
   }
@@ -88,56 +62,60 @@ public class FhirServerConfigCommon {
    * Configure FHIR properties around the the JPA server via this bean
    */
   @Bean()
-  public DaoConfig daoConfig() {
+  public DaoConfig daoConfig(AppProperties appProperties) {
     DaoConfig retVal = new DaoConfig();
 
-    retVal.setIndexMissingFields(this.enableIndexMissingFields ? DaoConfig.IndexEnabledEnum.ENABLED : DaoConfig.IndexEnabledEnum.DISABLED);
+    retVal.setIndexMissingFields(appProperties.getEnable_index_missing_fields() ? DaoConfig.IndexEnabledEnum.ENABLED : DaoConfig.IndexEnabledEnum.DISABLED);
-    retVal.setAutoCreatePlaceholderReferenceTargets(this.autoCreatePlaceholderReferenceTargets);
+    retVal.setAutoCreatePlaceholderReferenceTargets(appProperties.getAuto_create_placeholder_reference_targets());
-    retVal.setEnforceReferentialIntegrityOnWrite(this.enforceReferentialIntegrityOnWrite);
+    retVal.setEnforceReferentialIntegrityOnWrite(appProperties.getEnforce_referential_integrity_on_write());
-    retVal.setEnforceReferentialIntegrityOnDelete(this.enforceReferentialIntegrityOnDelete);
+    retVal.setEnforceReferentialIntegrityOnDelete(appProperties.getEnforce_referential_integrity_on_delete());
-    retVal.setAllowContainsSearches(this.allowContainsSearches);
+    retVal.setAllowContainsSearches(appProperties.getAllow_contains_searches());
-    retVal.setAllowMultipleDelete(this.allowMultipleDelete);
+    retVal.setAllowMultipleDelete(appProperties.getAllow_multiple_delete());
-    retVal.setAllowExternalReferences(this.allowExternalReferences);
+    retVal.setAllowExternalReferences(appProperties.getAllow_external_references());
-    retVal.setExpungeEnabled(this.expungeEnabled);
+    retVal.setExpungeEnabled(appProperties.getExpunge_enabled());
-    retVal.setAutoCreatePlaceholderReferenceTargets(this.allowPlaceholderReferences);
+    retVal.setAutoCreatePlaceholderReferenceTargets(appProperties.getAllow_placeholder_references());
-    retVal.setEmailFromAddress(this.emailFrom);
+    if(appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null)
+      retVal.setEmailFromAddress(appProperties.getSubscription().getEmail().getFrom());
 
-    Integer maxFetchSize = HapiProperties.getMaximumFetchSize();
+    Integer maxFetchSize =  appProperties.getMax_page_size();
     retVal.setFetchSizeDefaultMaximum(maxFetchSize);
     ourLog.info("Server configured to have a maximum fetch size of " + (maxFetchSize == Integer.MAX_VALUE ? "'unlimited'" : maxFetchSize));
 
-    Long reuseCachedSearchResultsMillis = HapiProperties.getReuseCachedSearchResultsMillis();
+    Long reuseCachedSearchResultsMillis = appProperties.getReuse_cached_search_results_millis();
     retVal.setReuseCachedSearchResultsForMillis(reuseCachedSearchResultsMillis);
     ourLog.info("Server configured to cache search results for {} milliseconds", reuseCachedSearchResultsMillis);
 
-    Long retainCachedSearchesMinutes = HapiProperties.getExpireSearchResultsAfterMins();
+
+    Long retainCachedSearchesMinutes = appProperties.getRetain_cached_searches_mins();
     retVal.setExpireSearchResultsAfterMillis(retainCachedSearchesMinutes * 60 * 1000);
 
+    if(appProperties.getSubscription() != null) {
       // Subscriptions are enabled by channel type
-    if (HapiProperties.getSubscriptionRestHookEnabled()) {
+      if (appProperties.getSubscription().getResthook_enabled()) {
         ourLog.info("Enabling REST-hook subscriptions");
         retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.RESTHOOK);
       }
-    if (HapiProperties.getSubscriptionEmailEnabled()) {
+      if (appProperties.getSubscription().getEmail() != null) {
         ourLog.info("Enabling email subscriptions");
         retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.EMAIL);
       }
-    if (HapiProperties.getSubscriptionWebsocketEnabled()) {
+      if (appProperties.getSubscription().getWebsocket_enabled()) {
         ourLog.info("Enabling websocket subscriptions");
         retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.WEBSOCKET);
       }
+    }
 
-    retVal.setFilterParameterEnabled(HapiProperties.getFilterSearchEnabled());
+    retVal.setFilterParameterEnabled(appProperties.getFilter_search_enabled());
 
     return retVal;
   }
 
   @Bean
-  public PartitionSettings partitionSettings() {
+  public PartitionSettings partitionSettings(AppProperties appProperties) {
     PartitionSettings retVal = new PartitionSettings();
 
     // Partitioning
-    if (HapiProperties.getPartitioningMultitenancyEnabled()) {
+    if (appProperties.getPartitioning() != null) {
       retVal.setPartitioningEnabled(true);
     }
 
@@ -146,19 +124,20 @@ public class FhirServerConfigCommon {
 
 
   @Bean
-  public ModelConfig modelConfig() {
+  public ModelConfig modelConfig(AppProperties appProperties) {
     ModelConfig modelConfig = new ModelConfig();
-    modelConfig.setAllowContainsSearches(this.allowContainsSearches);
+    modelConfig.setAllowContainsSearches(appProperties.getAllow_contains_searches());
-    modelConfig.setAllowExternalReferences(this.allowExternalReferences);
+    modelConfig.setAllowExternalReferences(appProperties.getAllow_external_references());
-    modelConfig.setDefaultSearchParamsCanBeOverridden(this.allowOverrideDefaultSearchParams);
+    modelConfig.setDefaultSearchParamsCanBeOverridden(appProperties.getAllow_override_default_search_params());
-    modelConfig.setEmailFromAddress(this.emailFrom);
+    if(appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null)
+      modelConfig.setEmailFromAddress(appProperties.getSubscription().getEmail().getFrom());
 
     // You can enable these if you want to support Subscriptions from your server
-    if (this.subscriptionRestHookEnabled) {
+    if (appProperties.getSubscription() != null && appProperties.getSubscription().getResthook_enabled() != null) {
       modelConfig.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.RESTHOOK);
     }
 
-    if (this.subscriptionEmailEnabled) {
+    if (appProperties.getSubscription()  != null && appProperties.getSubscription().getEmail() != null) {
       modelConfig.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.EMAIL);
     }
 
@@ -171,7 +150,7 @@ public class FhirServerConfigCommon {
    * <p>
    * A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
    */
-  @Bean(destroyMethod = "close")
+  /*@Bean(destroyMethod = "close")
   public BasicDataSource dataSource() throws ClassNotFoundException, NoSuchMethodException, IllegalAccessException, InvocationTargetException, InstantiationException {
     BasicDataSource retVal = new BasicDataSource();
     Driver driver = (Driver) Class.forName(HapiProperties.getDataSourceDriver()).getConstructor().newInstance();
@@ -181,38 +160,37 @@ public class FhirServerConfigCommon {
     retVal.setPassword(HapiProperties.getDataSourcePassword());
     retVal.setMaxTotal(HapiProperties.getDataSourceMaxPoolSize());
     return retVal;
-  }
+  }*/
 
   @Lazy
   @Bean
-  public IBinaryStorageSvc binaryStorageSvc() {
+  public IBinaryStorageSvc binaryStorageSvc(AppProperties appProperties) {
     DatabaseBlobBinaryStorageSvcImpl binaryStorageSvc = new DatabaseBlobBinaryStorageSvcImpl();
 
-    if (HapiProperties.getMaxBinarySize() != null) {
+    if (appProperties.getMax_binary_size() != null) {
-      binaryStorageSvc.setMaximumBinarySize(HapiProperties.getMaxBinarySize());
+      binaryStorageSvc.setMaximumBinarySize(appProperties.getMax_binary_size());
     }
 
     return binaryStorageSvc;
   }
 
   @Bean()
-  public IEmailSender emailSender() {
+  public IEmailSender emailSender(AppProperties appProperties, Optional<SubscriptionDeliveryHandlerFactory> subscriptionDeliveryHandlerFactory) {
-    if (this.emailEnabled) {
+    if (appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null) {
       JavaMailEmailSender retVal = new JavaMailEmailSender();
 
-      retVal.setSmtpServerHostname(this.emailHost);
+      AppProperties.Subscription.Email email = appProperties.getSubscription().getEmail();
-      retVal.setSmtpServerPort(this.emailPort);
+      retVal.setSmtpServerHostname(email.getHost());
-      retVal.setSmtpServerUsername(this.emailUsername);
+      retVal.setSmtpServerPort(email.getPort());
-      retVal.setSmtpServerPassword(this.emailPassword);
+      retVal.setSmtpServerUsername(email.getUsername());
-      retVal.setAuth(this.emailAuth);
+      retVal.setSmtpServerPassword(email.getPassword());
-      retVal.setStartTlsEnable(this.emailStartTlsEnable);
+      retVal.setAuth(email.getAuth());
-      retVal.setStartTlsRequired(this.emailStartTlsRequired);
+      retVal.setStartTlsEnable(email.getStartTlsEnable());
-      retVal.setQuitWait(this.emailQuitWait);
+      retVal.setStartTlsRequired(email.getStartTlsRequired());
-
+      retVal.setQuitWait(email.getQuitWait());
-      SubscriptionDeliveryHandlerFactory subscriptionDeliveryHandlerFactory = myAppCtx.getBean(SubscriptionDeliveryHandlerFactory.class);
-      Validate.notNull(subscriptionDeliveryHandlerFactory, "No subscription delivery handler");
-      subscriptionDeliveryHandlerFactory.setEmailSender(retVal);
 
+      if(subscriptionDeliveryHandlerFactory.isPresent())
+       subscriptionDeliveryHandlerFactory.get().setEmailSender(retVal);
 
       return retVal;
     }

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java

@@ -7,13 +7,20 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Primary;
+import org.springframework.context.annotation.Profile;
+import org.springframework.core.env.ConfigurableEnvironment;
+import org.springframework.core.env.Environment;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
 import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Properties;
 
 @Configuration
+@Profile("dstu2")
 public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
 
   @Autowired
@@ -24,14 +31,20 @@ public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
    * the default/max page sizes for search results. You can set these however
    * you want, although very large page sizes will require a lot of RAM.
    */
+  @Autowired
+  AppProperties appProperties;
+
   @Override
   public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
     DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();
-        pagingProvider.setDefaultPageSize(HapiProperties.getDefaultPageSize());
+    pagingProvider.setDefaultPageSize(appProperties.getDefault_page_size());
-        pagingProvider.setMaximumPageSize(HapiProperties.getMaximumPageSize());
+    pagingProvider.setMaximumPageSize(appProperties.getMax_page_size());
     return pagingProvider;
   }
 
+  @Autowired
+  private ConfigurableEnvironment configurableEnvironment;
+
   @Override
   @Bean()
   public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
@@ -43,8 +56,7 @@ public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
     } catch (Exception e) {
       throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
     }
-
+    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment));
-        retVal.setJpaProperties(HapiProperties.getJpaProperties());
     return retVal;
   }
 
@@ -56,4 +68,5 @@ public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
     return retVal;
   }
 
+
 }

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java

@@ -7,6 +7,8 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Primary;
+import org.springframework.context.annotation.Profile;
+import org.springframework.core.env.ConfigurableEnvironment;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
@@ -14,6 +16,7 @@ import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
 @Configuration
+@Profile("dstu3")
 public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
 
   @Autowired
@@ -24,14 +27,20 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
    * the default/max page sizes for search results. You can set these however
    * you want, although very large page sizes will require a lot of RAM.
    */
+  @Autowired
+  AppProperties appProperties;
+
   @Override
   public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
     DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();
-        pagingProvider.setDefaultPageSize(HapiProperties.getDefaultPageSize());
+    pagingProvider.setDefaultPageSize(appProperties.getDefault_page_size());
-        pagingProvider.setMaximumPageSize(HapiProperties.getMaximumPageSize());
+    pagingProvider.setMaximumPageSize(appProperties.getMax_page_size());
     return pagingProvider;
   }
 
+  @Autowired
+  private ConfigurableEnvironment configurableEnvironment;
+  
   @Override
   @Bean
   public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
@@ -44,7 +53,7 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
       throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
     }
 
-        retVal.setJpaProperties(HapiProperties.getJpaProperties());
+    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment));
     return retVal;
   }
 

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

@@ -7,13 +7,19 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Primary;
+import org.springframework.context.annotation.Profile;
+import org.springframework.core.env.ConfigurableEnvironment;
+import org.springframework.core.env.Environment;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
 import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
+import java.util.Arrays;
+import java.util.Properties;
 
 @Configuration
+@Profile("r4")
 public class FhirServerConfigR4 extends BaseJavaConfigR4 {
 
   @Autowired
@@ -24,14 +30,20 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
    * the default/max page sizes for search results. You can set these however
    * you want, although very large page sizes will require a lot of RAM.
    */
+  @Autowired
+  AppProperties appProperties;
+
   @Override
   public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
     DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();
-        pagingProvider.setDefaultPageSize(HapiProperties.getDefaultPageSize());
+    pagingProvider.setDefaultPageSize(appProperties.getDefault_page_size());
-        pagingProvider.setMaximumPageSize(HapiProperties.getMaximumPageSize());
+    pagingProvider.setMaximumPageSize(appProperties.getMax_page_size());
     return pagingProvider;
   }
 
+  @Autowired
+  private ConfigurableEnvironment configurableEnvironment;
+
   @Override
   @Bean()
   public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
@@ -44,7 +56,7 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
       throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
     }
 
-        retVal.setJpaProperties(HapiProperties.getJpaProperties());
+    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment));
     return retVal;
   }
 

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java

@@ -7,6 +7,8 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Primary;
+import org.springframework.context.annotation.Profile;
+import org.springframework.core.env.ConfigurableEnvironment;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
@@ -14,6 +16,7 @@ import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
 @Configuration
+@Profile("r5")
 public class FhirServerConfigR5 extends BaseJavaConfigR5 {
 
   @Autowired
@@ -24,14 +27,20 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 {
    * the default/max page sizes for search results. You can set these however
    * you want, although very large page sizes will require a lot of RAM.
    */
+  @Autowired
+  AppProperties appProperties;
+
   @Override
   public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
     DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();
-        pagingProvider.setDefaultPageSize(HapiProperties.getDefaultPageSize());
+    pagingProvider.setDefaultPageSize(appProperties.getDefault_page_size());
-        pagingProvider.setMaximumPageSize(HapiProperties.getMaximumPageSize());
+    pagingProvider.setMaximumPageSize(appProperties.getMax_page_size());
     return pagingProvider;
   }
 
+  @Autowired
+  private ConfigurableEnvironment configurableEnvironment;
+
   @Override
   @Bean()
   public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
@@ -44,7 +53,7 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 {
       throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
     }
 
-        retVal.setJpaProperties(HapiProperties.getJpaProperties());
+    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment));
     return retVal;
   }
 

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

@@ -1,11 +1,10 @@
 package ca.uhn.fhir.jpa.starter;
 
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Import;
-
 import ca.uhn.fhir.to.FhirTesterMvcConfig;
 import ca.uhn.fhir.to.TesterConfig;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
 
 //@formatter:off
 /**
@@ -35,15 +34,19 @@ public class FhirTesterConfig {
 	 * you might want to use that instead of using the variable.
 	 */
   @Bean
-	public TesterConfig testerConfig() {
+  public TesterConfig testerConfig(AppProperties appProperties) {
     TesterConfig retVal = new TesterConfig();
+    appProperties.getTester().stream().forEach(t -> {
       retVal
         .addServer()
-				.withId(HapiProperties.getServerId())
+        .withId(t.getId())
-				.withFhirVersion(HapiProperties.getFhirVersion())
+        .withFhirVersion(t.getFhir_version())
-				.withBaseUrl(HapiProperties.getServerAddress())
+        .withBaseUrl(t.getServer_address())
-				.withName(HapiProperties.getServerName());
+        .withName(t.getName());
-		retVal.setRefuseToFetchThirdPartyUrls(HapiProperties.getTesterConfigRefustToFetchThirdPartyUrls());
+      retVal.setRefuseToFetchThirdPartyUrls(
+        t.getRefuse_to_fetch_third_party_urls());
+
+    });
     return retVal;
   }
 

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

@@ -1,535 +0,0 @@
-package ca.uhn.fhir.jpa.starter;
-
-import ca.uhn.fhir.context.ConfigurationException;
-import ca.uhn.fhir.context.FhirVersionEnum;
-import ca.uhn.fhir.jpa.api.config.DaoConfig;
-import ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder;
-import ca.uhn.fhir.rest.api.EncodingEnum;
-import ca.uhn.fhir.rest.server.ETagSupportEnum;
-import com.google.common.annotations.VisibleForTesting;
-import org.apache.commons.lang3.StringUtils;
-import org.hibernate.search.elasticsearch.cfg.ElasticsearchIndexStatus;
-import org.hibernate.search.elasticsearch.cfg.IndexSchemaManagementStrategy;
-import org.jetbrains.annotations.NotNull;
-
-import javax.annotation.Nonnull;
-import java.io.FileInputStream;
-import java.io.InputStream;
-import java.util.Arrays;
-import java.util.Locale;
-import java.util.Properties;
-import java.util.Set;
-import java.util.Map;
-import java.util.stream.Collectors;
-
-import static org.apache.commons.lang3.StringUtils.defaultString;
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-import static org.apache.commons.lang3.StringUtils.trim;
-
-public class HapiProperties {
-  static final String ENABLE_INDEX_MISSING_FIELDS = "enable_index_missing_fields";
-  static final String AUTO_CREATE_PLACEHOLDER_REFERENCE_TARGETS = "auto_create_placeholder_reference_targets";
-  static final String ENFORCE_REFERENTIAL_INTEGRITY_ON_WRITE = "enforce_referential_integrity_on_write";
-  static final String ENFORCE_REFERENTIAL_INTEGRITY_ON_DELETE = "enforce_referential_integrity_on_delete";
-  static final String BINARY_STORAGE_ENABLED = "binary_storage.enabled";
-  static final String ALLOW_EXTERNAL_REFERENCES = "allow_external_references";
-  static final String ALLOW_MULTIPLE_DELETE = "allow_multiple_delete";
-  static final String ALLOW_PLACEHOLDER_REFERENCES = "allow_placeholder_references";
-  static final String REUSE_CACHED_SEARCH_RESULTS_MILLIS = "reuse_cached_search_results_millis";
-  static final String DATASOURCE_DRIVER = "datasource.driver";
-  static final String DATASOURCE_MAX_POOL_SIZE = "datasource.max_pool_size";
-  static final String DATASOURCE_PASSWORD = "datasource.password";
-  static final String DATASOURCE_URL = "datasource.url";
-  static final String DATASOURCE_USERNAME = "datasource.username";
-  static final String DEFAULT_ENCODING = "default_encoding";
-  static final String DEFAULT_PAGE_SIZE = "default_page_size";
-  static final String DEFAULT_PRETTY_PRINT = "default_pretty_print";
-  static final String ETAG_SUPPORT = "etag_support";
-  static final String FHIR_VERSION = "fhir_version";
-  static final String ALLOW_CASCADING_DELETES = "allow_cascading_deletes";
-  static final String HAPI_PROPERTIES = "hapi.properties";
-  static final String LOGGER_ERROR_FORMAT = "logger.error_format";
-  static final String LOGGER_FORMAT = "logger.format";
-  static final String LOGGER_LOG_EXCEPTIONS = "logger.log_exceptions";
-  static final String LOGGER_NAME = "logger.name";
-  static final String MAX_FETCH_SIZE = "max_fetch_size";
-  static final String MAX_PAGE_SIZE = "max_page_size";
-  static final String SERVER_ADDRESS = "server_address";
-  static final String SERVER_ID = "server.id";
-  static final String SERVER_NAME = "server.name";
-  static final String SUBSCRIPTION_EMAIL_ENABLED = "subscription.email.enabled";
-  static final String SUBSCRIPTION_RESTHOOK_ENABLED = "subscription.resthook.enabled";
-  static final String SUBSCRIPTION_WEBSOCKET_ENABLED = "subscription.websocket.enabled";
-  static final String EMPI_ENABLED = "empi.enabled";
-  static final String PARTITIONING_ENABLED = "partitioning.enabled";
-  static final String PARTITIONING_CROSS_PARTITION_REFERENCE_MODE = "partitioning.cross_partition_reference_mode";
-  static final String ALLOWED_BUNDLE_TYPES = "allowed_bundle_types";
-  static final String TEST_PORT = "test.port";
-  static final String TESTER_CONFIG_REFUSE_TO_FETCH_THIRD_PARTY_URLS = "tester.config.refuse_to_fetch_third_party_urls";
-  static final String CORS_ENABLED = "cors.enabled";
-  static final String CORS_ALLOWED_ORIGIN = "cors.allowed_origin";
-  static final String CORS_ALLOW_CREDENTIALS = "cors.allowCredentials";
-  static final String ALLOW_CONTAINS_SEARCHES = "allow_contains_searches";
-  static final String ALLOW_OVERRIDE_DEFAULT_SEARCH_PARAMS = "allow_override_default_search_params";
-  static final String EMAIL_FROM = "email.from";
-  static final String VALIDATE_REQUESTS_ENABLED = "validation.requests.enabled";
-  static final String VALIDATE_RESPONSES_ENABLED = "validation.responses.enabled";
-  static final String FILTER_SEARCH_ENABLED = "filter_search.enabled";
-  static final String GRAPHQL_ENABLED = "graphql.enabled";
-  static final String BULK_EXPORT_ENABLED = "bulk.export.enabled";
-  static final String EXPIRE_SEARCH_RESULTS_AFTER_MINS = "retain_cached_searches_mins";
-  static final String MAX_BINARY_SIZE = "max_binary_size";
-  static final String PARTITIONING_MULTITENANCY_ENABLED = "partitioning.multitenancy.enabled";
-  private static final String PARTITIONING_INCLUDE_PARTITION_IN_SEARCH_HASHES = "partitioning.partitioning_include_in_search_hashes";
-  static final String CLIENT_ID_STRATEGY = "daoconfig.client_id_strategy";
-  private static Properties ourProperties;
-
-  public static boolean isElasticSearchEnabled() {
-    return HapiProperties.getPropertyBoolean("elasticsearch.enabled", false);
-  }
-
-  /*
-   * Force the configuration to be reloaded
-   */
-  public static void forceReload() {
-    ourProperties = null;
-    getProperties();
-  }
-
-  /**
-   * This is mostly here for unit tests. Use the actual properties file
-   * to set values
-   */
-  @VisibleForTesting
-  public static void setProperty(String theKey, String theValue) {
-    getProperties().setProperty(theKey, theValue);
-  }
-
-  public static Properties getJpaProperties() {
-    Properties retVal = loadProperties();
-
-    if (isElasticSearchEnabled()) {
-      ElasticsearchHibernatePropertiesBuilder builder = new ElasticsearchHibernatePropertiesBuilder();
-      builder.setRequiredIndexStatus(getPropertyEnum("elasticsearch.required_index_status", ElasticsearchIndexStatus.class, ElasticsearchIndexStatus.YELLOW));
-      builder.setRestUrl(getProperty("elasticsearch.rest_url"));
-      builder.setUsername(getProperty("elasticsearch.username"));
-      builder.setPassword(getProperty("elasticsearch.password"));
-      builder.setIndexSchemaManagementStrategy(getPropertyEnum("elasticsearch.schema_management_strategy", IndexSchemaManagementStrategy.class, IndexSchemaManagementStrategy.CREATE));
-      builder.setDebugRefreshAfterWrite(getPropertyBoolean("elasticsearch.debug.refresh_after_write", false));
-      builder.setDebugPrettyPrintJsonLog(getPropertyBoolean("elasticsearch.debug.pretty_print_json_log", false));
-      builder.apply(retVal);
-    }
-
-    return retVal;
-  }
-
-  private static Properties getProperties() {
-    if (ourProperties == null) {
-      Properties properties = loadProperties();
-      HapiProperties.ourProperties = properties;
-    }
-
-    return ourProperties;
-  }
-
-  @NotNull
-  private static Properties loadProperties() {
-    // Load the configurable properties file
-    Properties properties;
-    try (InputStream in = HapiProperties.class.getClassLoader().getResourceAsStream(HAPI_PROPERTIES)) {
-      properties = new Properties();
-      properties.load(in);
-    } catch (Exception e) {
-      throw new ConfigurationException("Could not load HAPI properties", e);
-    }
-
-    Properties overrideProps = loadOverrideProperties();
-    if (overrideProps != null) {
-      properties.putAll(overrideProps);
-    }
-    properties.putAll(System.getenv().entrySet()
-                                     .stream()
-                                     .filter(e -> e.getValue() != null && properties.containsKey(e.getKey()))
-                                     .collect(Collectors.toMap(Map.Entry::getKey, Map.Entry::getValue)));
-    return properties;
-  }
-
-  /**
-   * If a configuration file path is explicitly specified via -Dhapi.properties=<path>, the properties there will
-   * be used to override the entries in the default hapi.properties file (currently under WEB-INF/classes)
-   *
-   * @return properties loaded from the explicitly specified configuraiton file if there is one, or null otherwise.
-   */
-  private static Properties loadOverrideProperties() {
-    String confFile = System.getProperty(HAPI_PROPERTIES);
-    if (confFile != null) {
-      try {
-        Properties props = new Properties();
-        props.load(new FileInputStream(confFile));
-        return props;
-      } catch (Exception e) {
-        throw new ConfigurationException("Could not load HAPI properties file: " + confFile, e);
-      }
-    }
-
-    return null;
-  }
-
-  private static String getProperty(String propertyName) {
-    String env = "HAPI_" + propertyName.toUpperCase(Locale.US);
-    env = env.replace(".", "_");
-    env = env.replace("-", "_");
-
-    String propertyValue = System.getenv(env);
-    if (propertyValue != null) {
-      return propertyValue;
-    }
-
-    Properties properties = HapiProperties.getProperties();
-    if (properties != null) {
-      propertyValue = properties.getProperty(propertyName);
-    }
-
-    return propertyValue;
-  }
-
-  private static String getProperty(String propertyName, String defaultValue) {
-    String value = getProperty(propertyName);
-
-    if (value != null && value.length() > 0) {
-      return value;
-    }
-
-    return defaultValue;
-  }
-
-  private static Boolean getBooleanProperty(String propertyName, Boolean defaultValue) {
-    String value = HapiProperties.getProperty(propertyName);
-
-    if (value == null || value.length() == 0) {
-      return defaultValue;
-    }
-
-    return Boolean.parseBoolean(value);
-  }
-
-  private static boolean getBooleanProperty(String propertyName, boolean defaultValue) {
-    return getBooleanProperty(propertyName, Boolean.valueOf(defaultValue));
-  }
-
-  private static Integer getIntegerProperty(String propertyName, Integer defaultValue) {
-    String value = HapiProperties.getProperty(propertyName);
-
-    if (value == null || value.length() == 0) {
-      return defaultValue;
-    }
-
-    return Integer.parseInt(value);
-  }
-
-  public static FhirVersionEnum getFhirVersion() {
-    String fhirVersionString = HapiProperties.getProperty(FHIR_VERSION);
-
-    if (fhirVersionString != null && fhirVersionString.length() > 0) {
-      return FhirVersionEnum.valueOf(fhirVersionString);
-    }
-
-    return FhirVersionEnum.DSTU3;
-  }
-
-  public static boolean isBinaryStorageEnabled() {
-    return HapiProperties.getBooleanProperty(BINARY_STORAGE_ENABLED, true);
-  }
-
-  public static ETagSupportEnum getEtagSupport() {
-    String etagSupportString = HapiProperties.getProperty(ETAG_SUPPORT);
-
-    if (etagSupportString != null && etagSupportString.length() > 0) {
-      return ETagSupportEnum.valueOf(etagSupportString);
-    }
-
-    return ETagSupportEnum.ENABLED;
-  }
-
-  public static DaoConfig.ClientIdStrategyEnum getClientIdStrategy() {
-    String idStrategy = HapiProperties.getProperty(CLIENT_ID_STRATEGY);
-
-    if (idStrategy != null && idStrategy.length() > 0) {
-      return DaoConfig.ClientIdStrategyEnum.valueOf(idStrategy);
-    }
-
-    return DaoConfig.ClientIdStrategyEnum.ALPHANUMERIC;
-  }
-
-  public static EncodingEnum getDefaultEncoding() {
-    String defaultEncodingString = HapiProperties.getProperty(DEFAULT_ENCODING);
-
-    if (defaultEncodingString != null && defaultEncodingString.length() > 0) {
-      return EncodingEnum.valueOf(defaultEncodingString);
-    }
-
-    return EncodingEnum.JSON;
-  }
-
-  public static Boolean getDefaultPrettyPrint() {
-    return HapiProperties.getBooleanProperty(DEFAULT_PRETTY_PRINT, true);
-  }
-
-  public static String getServerAddress() {
-    return HapiProperties.getProperty(SERVER_ADDRESS);
-  }
-
-  public static Integer getDefaultPageSize() {
-    return HapiProperties.getIntegerProperty(DEFAULT_PAGE_SIZE, 20);
-  }
-
-  public static Integer getMaximumPageSize() {
-    return HapiProperties.getIntegerProperty(MAX_PAGE_SIZE, 200);
-  }
-
-  public static Integer getMaximumFetchSize() {
-    return HapiProperties.getIntegerProperty(MAX_FETCH_SIZE, Integer.MAX_VALUE);
-  }
-
-  public static String getLoggerName() {
-    return HapiProperties.getProperty(LOGGER_NAME, "fhirtest.access");
-  }
-
-  public static String getLoggerFormat() {
-    return HapiProperties.getProperty(LOGGER_FORMAT, "Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]");
-  }
-
-  public static String getLoggerErrorFormat() {
-    return HapiProperties.getProperty(LOGGER_ERROR_FORMAT, "ERROR - ${requestVerb} ${requestUrl}");
-  }
-
-  public static Boolean getLoggerLogExceptions() {
-    return HapiProperties.getBooleanProperty(LOGGER_LOG_EXCEPTIONS, true);
-  }
-
-  public static String getDataSourceDriver() {
-    return HapiProperties.getProperty(DATASOURCE_DRIVER, "org.apache.derby.jdbc.EmbeddedDriver");
-  }
-
-  public static Integer getDataSourceMaxPoolSize() {
-    return HapiProperties.getIntegerProperty(DATASOURCE_MAX_POOL_SIZE, 10);
-  }
-
-  public static String getDataSourceUrl() {
-    return HapiProperties.getProperty(DATASOURCE_URL, "jdbc:derby:directory:target/jpaserver_derby_files;create=true");
-  }
-
-  public static String getDataSourceUsername() {
-    return HapiProperties.getProperty(DATASOURCE_USERNAME);
-  }
-
-  public static String getDataSourcePassword() {
-    return HapiProperties.getProperty(DATASOURCE_PASSWORD);
-  }
-
-  public static Boolean getAllowMultipleDelete() {
-    return HapiProperties.getBooleanProperty(ALLOW_MULTIPLE_DELETE, false);
-  }
-
-  public static Boolean getAllowCascadingDeletes() {
-    return HapiProperties.getBooleanProperty(ALLOW_CASCADING_DELETES, false);
-  }
-
-  public static Boolean getAllowExternalReferences() {
-    return HapiProperties.getBooleanProperty(ALLOW_EXTERNAL_REFERENCES, false);
-  }
-
-  public static Boolean getExpungeEnabled() {
-    return HapiProperties.getBooleanProperty("expunge_enabled", true);
-  }
-
-  public static Boolean getTesterConfigRefustToFetchThirdPartyUrls() {
-    return HapiProperties.getBooleanProperty(TESTER_CONFIG_REFUSE_TO_FETCH_THIRD_PARTY_URLS, false);
-  }
-
-  public static Boolean getCorsEnabled() {
-    return HapiProperties.getBooleanProperty(CORS_ENABLED, true);
-  }
-
-  public static String getCorsAllowedOrigin() {
-    return HapiProperties.getProperty(CORS_ALLOWED_ORIGIN, "*");
-  }
-
-  public static String getAllowedBundleTypes() {
-    return HapiProperties.getProperty(ALLOWED_BUNDLE_TYPES, "");
-  }
-
-  @Nonnull
-  public static Set<String> getSupportedResourceTypes() {
-    String[] types = defaultString(getProperty("supported_resource_types")).split(",");
-    return Arrays.stream(types)
-      .map(StringUtils::trim)
-      .filter(StringUtils::isNotBlank)
-      .collect(Collectors.toSet());
-  }
-
-  public static String getServerName() {
-    return HapiProperties.getProperty(SERVER_NAME, "Local Tester");
-  }
-
-  public static String getServerId() {
-    return HapiProperties.getProperty(SERVER_ID, "home");
-  }
-
-  public static Boolean getAllowPlaceholderReferences() {
-    return HapiProperties.getBooleanProperty(ALLOW_PLACEHOLDER_REFERENCES, true);
-  }
-
-  public static Boolean getSubscriptionEmailEnabled() {
-    return HapiProperties.getBooleanProperty(SUBSCRIPTION_EMAIL_ENABLED, false);
-  }
-
-  public static Boolean getSubscriptionRestHookEnabled() {
-    return HapiProperties.getBooleanProperty(SUBSCRIPTION_RESTHOOK_ENABLED, false);
-  }
-
-  public static Boolean getSubscriptionWebsocketEnabled() {
-    return HapiProperties.getBooleanProperty(SUBSCRIPTION_WEBSOCKET_ENABLED, false);
-  }
-
-  public static Boolean getEmpiEnabled() {
-    return HapiProperties.getBooleanProperty(EMPI_ENABLED, false);
-  }
-
-  public static Boolean getPartitioningEnabled() {
-    return HapiProperties.getBooleanProperty(PARTITIONING_ENABLED, false);
-  }
-
-
-  public static String getPartitioningCrossPartitionReferenceMode() {
-    return HapiProperties.getProperty(PARTITIONING_CROSS_PARTITION_REFERENCE_MODE, "NOT_ALLOWED");
-  }
-
-  public static Boolean getIncludePartitionInSearchHashes() {
-    return HapiProperties.getBooleanProperty(PARTITIONING_INCLUDE_PARTITION_IN_SEARCH_HASHES, true);
-  }
-
-  public static Boolean getAllowContainsSearches() {
-    return HapiProperties.getBooleanProperty(ALLOW_CONTAINS_SEARCHES, true);
-  }
-
-  public static Boolean getAllowOverrideDefaultSearchParams() {
-    return HapiProperties.getBooleanProperty(ALLOW_OVERRIDE_DEFAULT_SEARCH_PARAMS, true);
-  }
-
-  public static String getEmailFrom() {
-    return HapiProperties.getProperty(EMAIL_FROM, "some@test.com");
-  }
-
-  public static Boolean getEmailEnabled() {
-    return HapiProperties.getBooleanProperty("email.enabled", false);
-  }
-
-  public static String getEmailHost() {
-    return HapiProperties.getProperty("email.host");
-  }
-
-  public static Integer getEmailPort() {
-    return HapiProperties.getIntegerProperty("email.port", 0);
-  }
-
-  public static String getEmailUsername() {
-    return HapiProperties.getProperty("email.username");
-  }
-
-  public static String getEmailPassword() {
-    return HapiProperties.getProperty("email.password");
-  }
-
-  // Defaults from https://javaee.github.io/javamail/docs/api/com/sun/mail/smtp/package-summary.html
-  public static Boolean getEmailAuth() {
-    return HapiProperties.getBooleanProperty("email.auth", false);
-  }
-
-  public static Boolean getEmailStartTlsEnable() {
-    return HapiProperties.getBooleanProperty("email.starttls.enable", false);
-  }
-
-  public static Boolean getEmailStartTlsRequired() {
-    return HapiProperties.getBooleanProperty("email.starttls.required", false);
-  }
-
-  public static Boolean getEmailQuitWait() {
-    return HapiProperties.getBooleanProperty("email.quitwait", true);
-  }
-
-  public static Long getReuseCachedSearchResultsMillis() {
-    String value = HapiProperties.getProperty(REUSE_CACHED_SEARCH_RESULTS_MILLIS, "60000");
-    return Long.valueOf(value);
-  }
-
-  public static Long getExpireSearchResultsAfterMins() {
-    String value = HapiProperties.getProperty(EXPIRE_SEARCH_RESULTS_AFTER_MINS, "60");
-    return Long.valueOf(value);
-  }
-
-  public static Boolean getCorsAllowedCredentials() {
-    return HapiProperties.getBooleanProperty(CORS_ALLOW_CREDENTIALS, false);
-  }
-
-  public static boolean getValidateRequestsEnabled() {
-    return HapiProperties.getBooleanProperty(VALIDATE_REQUESTS_ENABLED, false);
-  }
-
-  public static boolean getValidateResponsesEnabled() {
-    return HapiProperties.getBooleanProperty(VALIDATE_RESPONSES_ENABLED, false);
-  }
-
-  public static boolean getFilterSearchEnabled() {
-    return HapiProperties.getBooleanProperty(FILTER_SEARCH_ENABLED, true);
-  }
-
-  public static boolean getGraphqlEnabled() {
-    return HapiProperties.getBooleanProperty(GRAPHQL_ENABLED, true);
-  }
-
-  public static boolean getEnforceReferentialIntegrityOnDelete() {
-    return HapiProperties.getBooleanProperty(ENFORCE_REFERENTIAL_INTEGRITY_ON_DELETE, true);
-  }
-
-  public static boolean getEnforceReferentialIntegrityOnWrite() {
-    return HapiProperties.getBooleanProperty(ENFORCE_REFERENTIAL_INTEGRITY_ON_WRITE, true);
-  }
-
-  public static boolean getAutoCreatePlaceholderReferenceTargets() {
-    return HapiProperties.getBooleanProperty(AUTO_CREATE_PLACEHOLDER_REFERENCE_TARGETS, true);
-  }
-
-  public static boolean getEnableIndexMissingFields() {
-    return HapiProperties.getBooleanProperty(ENABLE_INDEX_MISSING_FIELDS, false);
-  }
-
-  public static Integer getMaxBinarySize() {
-    return getIntegerProperty(MAX_BINARY_SIZE, null);
-  }
-
-  private static boolean getPropertyBoolean(String thePropertyName, boolean theDefaultValue) {
-    String value = getProperty(thePropertyName, Boolean.toString(theDefaultValue));
-    return Boolean.parseBoolean(value);
-  }
-
-  private static <T extends Enum> T getPropertyEnum(String thePropertyName, Class<T> theEnumType, T theDefaultValue) {
-    String value = getProperty(thePropertyName, theDefaultValue.name());
-    return (T) Enum.valueOf(theEnumType, value);
-  }
-
-  public static boolean getBulkExportEnabled() {
-    return HapiProperties.getBooleanProperty(BULK_EXPORT_ENABLED, true);
-  }
-
-  public static boolean isFhirPathFilterInterceptorEnabled() {
-    return HapiProperties.getBooleanProperty("fhirpath_interceptor.enabled", false);
-  }
-
-  public static boolean getPartitioningMultitenancyEnabled() {
-    return HapiProperties.getBooleanProperty(PARTITIONING_MULTITENANCY_ENABLED, false);
-  }
-
-
-}
-

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

@@ -1,11 +1,22 @@
 package ca.uhn.fhir.jpa.starter;
 
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Import;
+
 import javax.servlet.ServletException;
 
+@Import(AppProperties.class)
 public class JpaRestfulServer extends BaseJpaRestfulServer {
 
+  @Autowired
+  AppProperties appProperties;
+
   private static final long serialVersionUID = 1L;
 
+  public JpaRestfulServer() {
+    super();
+  }
+
   @Override
   protected void initialize() throws ServletException {
     super.initialize();

src/main/resources/application.yaml

@@ -0,0 +1,129 @@
+spring:
+  datasource:
+    url: 'jdbc:h2:file:./target/database/h2'
+    username: sa
+    password: null
+    driverClassName: org.h2.Driver
+    max-active: 15
+  profiles:
+    ### This is the FHIR version. Choose between, dstu2, dstu3, r4 or r5
+    active: r4
+  jpa:
+    properties:
+      hibernate.dialect: org.hibernate.dialect.H2Dialect
+      hibernate.search.model_mapping: ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory
+      hibernate.format_sql: false
+      hibernate.show_sql: false
+      hibernate.hbm2ddl.auto: update
+      hibernate.jdbc.batch_size: 20
+      hibernate.cache.use_query_cache: false
+      hibernate.cache.use_second_level_cache: false
+      hibernate.cache.use_structured_entries: false
+      hibernate.cache.use_minimal_puts: false
+      hibernate.search.default.directory_provider: filesystem
+      hibernate.search.default.indexBase: target/lucenefiles
+      hibernate.search.lucene_version: LUCENE_CURRENT
+
+hapi:
+  fhir:
+    defer_indexing_for_codesystems_of_size: 101
+#    implementationguides:
+#      -
+#        url: https://build.fhir.org/ig/hl7dk/dk-medcom/branches/corrections/package.tgz
+#        name: dk.fhir.ig.medcom-core
+#        version: 0.8.0
+#      -
+#        name: hl7.fhir.uv.ips
+#        version: 0.3.0
+
+    #supported_resource_types:
+    #  - Patient
+    #  - Observation
+#    allow_cascading_deletes: true
+#    allow_contains_searches: true
+#    allow_external_references: true
+#    allow_multiple_delete: true
+#    allow_override_default_search_params: true
+#    allow_placeholder_references: true
+#    auto_create_placeholder_reference_targets: false
+#    default_encoding: JSON
+#    default_pretty_print: true
+#    default_page_size: 20
+#    enable_index_missing_fields: false
+#    enforce_referential_integrity_on_delete: false
+#    enforce_referential_integrity_on_write: false
+#    etag_support_enabled: true
+#    expunge_enabled: true
+#    daoconfig_client_id_strategy: null
+#    fhirpath_interceptor_enabled: false
+#    filter_search_enabled: true
+#    graphql_enabled: true
+    #partitioning:
+    #  cross_partition_reference_mode: true
+    #  multitenancy_enabled: true
+    #  partitioning_include_in_search_hashes: true
+    #cors:
+    #  allow_Credentials: true
+      # Supports multiple, comma separated allowed origin entries
+      # cors.allowed_origin=http://localhost:8080,https://localhost:8080,https://fhirtest.uhn.ca
+    #  allowed_origin:
+    #    - '*'
+
+#    logger:
+#      error_format: 'ERROR - ${requestVerb} ${requestUrl}'
+#      format: >-
+#        Path[${servletPath}] Source[${requestHeader.x-forwarded-for}]
+#        Operation[${operationType} ${operationName} ${idOrResourceName}]
+#        UA[${requestHeader.user-agent}] Params[${requestParameters}]
+#        ResponseEncoding[${responseEncodingNoDefault}]
+#      log_exceptions: true
+#      name: fhirtest.access
+#    max_binary_size: 104857600
+#    max_page_size: 200
+#    retain_cached_searches_mins: 60
+#    reuse_cached_search_results_millis: 60000
+    tester:
+      -
+          id: home
+          name: Local Tester
+          server_address: 'http://localhost:8080/hapi-fhir-jpaserver/fhir'
+          refuse_to_fetch_third_party_urls: false
+          fhir_version: R4
+      -
+          id: global
+          name: Global Tester
+          server_address: "http://hapi.fhir.org/baseR4"
+          refuse_to_fetch_third_party_urls: false
+          fhir_version: R4
+#    validation:
+#      requests_enabled: true
+#      responses_enabled: true
+#    binary_storage_enabled: true
+#    bulk_export_enabled: true
+#    partitioning_multitenancy_enabled:
+#    subscription:
+#      resthook_enabled: false
+#      websocket_enabled: false
+#      email:
+#        from: some@test.com
+#        host: google.com
+#        port:
+#        username:
+#        password:
+#        auth:
+#        startTlsEnable:
+#        startTlsRequired:
+#        quitWait:
+
+
+#
+#elasticsearch:
+#  debug:
+#    pretty_print_json_log: false
+#    refresh_after_write: false
+#  enabled: false
+#  password: SomePassword
+#  required_index_status: YELLOW
+#  rest_url: 'http://localhost:9200'
+#  schema_management_strategy: CREATE
+#  username: SomeUsername

src/main/resources/hapi.properties

@@ -1,167 +0,0 @@
-# Adjust this to set the version of FHIR supported by this server. See
-# FhirVersionEnum for a list of available constants. Example values include
-# DSTU2, DSTU3, R4.
-fhir_version=R4
-
-# This is the address that the FHIR server will report as its own address.
-# If this server will be deployed (for example) to an internet accessible
-# server, put the DNS name of that server here.
-#
-# Note that this is also the address that the hapi-fhir-testpage-overlay
-# (the web UI similar to the one at http://hapi.fhir.org) will use to
-# connect internally to the FHIR server, so this also needs to be a name
-# accessible from the server itself.
-server_address=http://localhost:8080/hapi-fhir-jpaserver/fhir/
-
-enable_index_missing_fields=false
-auto_create_placeholder_reference_targets=false
-enforce_referential_integrity_on_write=false
-enforce_referential_integrity_on_delete=false
-default_encoding=JSON
-etag_support=ENABLED
-reuse_cached_search_results_millis=60000
-retain_cached_searches_mins=60
-default_page_size=20
-max_page_size=200
-allow_override_default_search_params=true
-allow_contains_searches=true
-allow_multiple_delete=true
-allow_external_references=true
-allow_cascading_deletes=true
-allow_placeholder_references=true
-expunge_enabled=true
-persistence_unit_name=HAPI_PU
-logger.name=fhirtest.access
-logger.format=Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]
-logger.error_format=ERROR - ${requestVerb} ${requestUrl}
-logger.log_exceptions=true
-datasource.driver=org.h2.Driver
-datasource.url=jdbc:h2:file:./target/database/h2
-datasource.username=
-datasource.password=
-server.name=Local Tester
-server.id=home
-test.port=
-
-###################################################
-# Binary Storage (104857600 = 100mb)
-###################################################
-max_binary_size=104857600
-
-###################################################
-# Validation
-###################################################
-# Should all incoming requests be validated
-validation.requests.enabled=false
-# Should outgoing responses be validated
-validation.responses.enabled=false
-
-###################################################
-# Search Features
-###################################################
-filter_search.enabled=true
-graphql.enabled=true
-# See FhirPathFilterInterceptor
-fhirpath_interceptor.enabled=false
-
-###################################################
-# Supported Resources
-###################################################
-# Enable the following property if you want to customize the
-# list of resources that is supported by the server (i.e. to
-# disable specific resources)
-#supported_resource_types=Patient,Observation,Encounter
-
-###################################################
-# Database Settings
-###################################################
-hibernate.dialect=org.hibernate.dialect.H2Dialect
-hibernate.search.model_mapping=ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory
-hibernate.format_sql=false
-hibernate.show_sql=false
-hibernate.hbm2ddl.auto=update
-hibernate.jdbc.batch_size=20
-hibernate.cache.use_query_cache=false
-hibernate.cache.use_second_level_cache=false
-hibernate.cache.use_structured_entries=false
-hibernate.cache.use_minimal_puts=false
-hibernate.search.default.directory_provider=filesystem
-hibernate.search.default.indexBase=target/lucenefiles
-hibernate.search.lucene_version=LUCENE_CURRENT
-tester.config.refuse_to_fetch_third_party_urls=false
-
-##################################################
-# ElasticSearch
-# Note that using ElasticSearch is disabled by
-# default and the server will use Lucene instead.
-##################################################
-elasticsearch.enabled=false
-elasticsearch.rest_url=http://localhost:9200
-elasticsearch.username=SomeUsername
-elasticsearch.password=SomePassword
-elasticsearch.required_index_status=YELLOW
-elasticsearch.schema_management_strategy=CREATE
-# Immediately refresh indexes after every write. This is very bad for
-# performance, but can be helpful for testing.
-elasticsearch.debug.refresh_after_write=false
-elasticsearch.debug.pretty_print_json_log=false
-
-
-##################################################
-# Binary Storage Operations
-##################################################
-binary_storage.enabled=true
-
-##################################################
-# Bulk Data Specification
-##################################################
-bulk.export.enabled=true
-
-##################################################
-# CORS Settings
-##################################################
-cors.enabled=true
-cors.allowCredentials=true
-# Supports multiple, comma separated allowed origin entries
-# cors.allowed_origin=http://localhost:8080,https://localhost:8080,https://fhirtest.uhn.ca
-cors.allowed_origin=*
-
-##################################################
-# Allowed Bundle Types for persistence (defaults are: COLLECTION,DOCUMENT,MESSAGE)
-##################################################
-#allowed_bundle_types=COLLECTION,DOCUMENT,MESSAGE,TRANSACTION,TRANSACTIONRESPONSE,BATCH,BATCHRESPONSE,HISTORY,SEARCHSET
-
-##################################################
-# Subscriptions
-##################################################
-
-# Enable REST Hook Subscription Channel
-subscription.resthook.enabled=false
-
-# Enable Email Subscription Channel
-subscription.email.enabled=false
-email.enabled=false
-email.from=some@test.com
-email.host=
-email.port=0
-email.username=
-email.password=
-
-# Enable Websocket Subscription Channel
-subscription.websocket.enabled=false
-
-###################################################
-# EMPI
-###################################################
-empi.enabled=false
-
-###################################################
-# Partitioning And Multitenancy
-###################################################
-partitioning.enabled=false
-partitioning.cross_partition_reference_mode=NOT_ALLOWED
-partitioning.partitioning_include_in_search_hashes=true
-partitioning.multitenancy.enabled=false
-
-#daoconfig.client_id_strategy=ANY
-

src/main/resources/logback.xml

@@ -9,24 +9,6 @@
 		</encoder>
 	</appender>
 
-	<appender name="EMPI_TROUBLESHOOTING" class="ch.qos.logback.core.rolling.RollingFileAppender">
-		<filter class="ch.qos.logback.classic.filter.ThresholdFilter"><level>DEBUG</level></filter>
-		<file>${smile.basedir}/log/empi-troubleshooting.log</file>
-		<rollingPolicy class="ch.qos.logback.core.rolling.FixedWindowRollingPolicy">
-			<fileNamePattern>${smile.basedir}/log/empi-troubleshooting.log.%i.gz</fileNamePattern>
-			<minIndex>1</minIndex>
-			<maxIndex>9</maxIndex>
-		</rollingPolicy>
-		<triggeringPolicy class="ch.qos.logback.core.rolling.SizeBasedTriggeringPolicy">
-			<maxFileSize>5MB</maxFileSize>
-		</triggeringPolicy>
-		<encoder>
-			<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n${log.stackfilter.pattern}</pattern>
-		</encoder>
-	</appender>
-	<logger name="ca.uhn.fhir.log.empi_troubleshooting" level="TRACE">
-		<appender-ref ref="EMPI_TROUBLESHOOTING"/>
-	</logger>
 
 	<root level="INFO">
 		<appender-ref ref="STDOUT" />

src/main/webapp/WEB-INF/web.xml

@@ -1,54 +0,0 @@
-<web-app
-		xmlns="http://xmlns.jcp.org/xml/ns/javaee"
-		xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-		xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee http://xmlns.jcp.org/xml/ns/javaee/web-app_3_1.xsd"
-		metadata-complete="false"
-		version="3.1">
-
-	<listener>
-		<listener-class>org.springframework.web.context.ContextLoaderListener</listener-class>
-	</listener>
-	<context-param>
-		<param-name>contextClass</param-name>
-		<param-value>
-			ca.uhn.fhir.jpa.starter.ApplicationContext
-		</param-value>
-	</context-param>
-	<context-param>
-		<param-name>contextConfigLocation</param-name>
-		<param-value>
-		</param-value>
-	</context-param>
-
-	<!-- Servlets -->
-	<servlet>
-		<servlet-name>spring</servlet-name>
-		<servlet-class>org.springframework.web.servlet.DispatcherServlet</servlet-class>
-		<init-param>
-			<param-name>contextClass</param-name>
-			<param-value>org.springframework.web.context.support.AnnotationConfigWebApplicationContext</param-value>
-		</init-param>
-		<init-param>
-			<param-name>contextConfigLocation</param-name>
-			<param-value>
-				ca.uhn.fhir.jpa.starter.FhirTesterConfig
-			</param-value>
-		</init-param>
-		<load-on-startup>2</load-on-startup>
-	</servlet>
-	<servlet-mapping>
-		<servlet-name>spring</servlet-name>
-		<url-pattern>/</url-pattern>
-	</servlet-mapping>
-
-	<servlet>
-		<servlet-name>fhirServlet</servlet-name>
-		<servlet-class>ca.uhn.fhir.jpa.starter.JpaRestfulServer</servlet-class>
-		<load-on-startup>1</load-on-startup>
-	</servlet>
-	<servlet-mapping>
-		<servlet-name>fhirServlet</servlet-name>
-		<url-pattern>/fhir/*</url-pattern>
-	</servlet-mapping>
-
-</web-app>

src/test/java/ca/uhn/fhir/jpa/starter/Demo.java

@@ -0,0 +1,20 @@
+package ca.uhn.fhir.jpa.starter;
+
+import org.springframework.boot.SpringApplication;
+import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.boot.autoconfigure.elasticsearch.ElasticsearchRestClientAutoConfiguration;
+import org.springframework.boot.web.servlet.ServletComponentScan;
+
+@ServletComponentScan(basePackageClasses = {JpaRestfulServer.class})
+@SpringBootApplication(exclude = ElasticsearchRestClientAutoConfiguration.class)
+public class Demo {
+
+  public static void main(String[] args) {
+
+    System.setProperty("spring.profiles.active", "r4");
+    System.setProperty("spring.batch.job.enabled", "false");
+    SpringApplication.run(Demo.class, args);
+
+    //Server is now accessible at eg. http://localhost:8080/metadata
+  }
+}

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu2IT.java

@@ -5,79 +5,53 @@ import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
-import ca.uhn.fhir.test.utilities.JettyUtil;
-import org.eclipse.jetty.server.Server;
-import org.eclipse.jetty.webapp.WebAppContext;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
-
+import org.junit.jupiter.api.extension.ExtendWith;
-import java.nio.file.Paths;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.web.server.LocalServerPort;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
+@ExtendWith(SpringExtension.class)
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties =
+  {
+    "spring.batch.job.enabled=false",
+    "spring.profiles.active=dstu2",
+    "spring.datasource.url=jdbc:h2:mem:dbr2"
+  })
 public class ExampleServerDstu2IT {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu2IT.class);
-	private static IGenericClient ourClient;
+	private IGenericClient ourClient;
-	private static FhirContext ourCtx;
+	private FhirContext ourCtx;
-	private static int ourPort;
-	private static Server ourServer;
 
-	static {
+  @LocalServerPort
-		HapiProperties.forceReload();
+  private int port;
-		HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "DSTU2");
-		HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:h2:mem:dbr2");
-		ourCtx = FhirContext.forDstu2();
-	}
 
   @Test
-	public void testCreateAndRead() {
+	void testCreateAndRead() {
-		ourLog.info("Base URL is: " +  HapiProperties.getServerAddress());
+
 		String methodName = "testCreateResourceConditional";
 
 		Patient pt = new Patient();
 		pt.addName().addFamily(methodName);
 		IIdType id = ourClient.create().resource(pt).execute().getId();
-
 		Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
 		assertEquals(methodName, pt2.getName().get(0).getFamily().get(0).getValue());
 	}
 
-	@AfterAll
-	public static void afterClass() throws Exception {
-		ourServer.stop();
-	}
 
-	@BeforeAll
+	@BeforeEach
-	public static void beforeClass() throws Exception {
+	void beforeEach() {
-		String path = Paths.get("").toAbsolutePath().toString();
-
-		ourLog.info("Project base path is: {}", path);
-
-		ourServer = new Server(0);
-
-		WebAppContext webAppContext = new WebAppContext();
-		webAppContext.setContextPath("/hapi-fhir-jpaserver");
-		webAppContext.setDescriptor(path + "/src/main/webapp/WEB-INF/web.xml");
-		webAppContext.setResourceBase(path + "/target/hapi-fhir-jpaserver-starter");
-		webAppContext.setParentLoaderPriority(true);
-
-		ourServer.setHandler(webAppContext);
-		ourServer.start();
-
-		ourPort = JettyUtil.getPortForStartedServer(ourServer);
 
+    ourCtx = FhirContext.forDstu2();
 		ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
 		ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
-		String ourServerBase = "http://localhost:" + ourPort + "/hapi-fhir-jpaserver/fhir/";
+		String ourServerBase = "http://localhost:" + port + "/hapi-fhir-jpaserver/fhir/";
 		ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
 		ourClient.registerInterceptor(new LoggingInterceptor(true));
 	}
-
-	public static void main(String[] theArgs) throws Exception {
-		ourPort = 8080;
-		beforeClass();
-	}
 }

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java

@@ -7,9 +7,6 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
-import ca.uhn.fhir.test.utilities.JettyUtil;
-import org.eclipse.jetty.server.Server;
-import org.eclipse.jetty.webapp.WebAppContext;
 import org.eclipse.jetty.websocket.api.Session;
 import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
 import org.eclipse.jetty.websocket.client.WebSocketClient;
@@ -18,39 +15,44 @@ import org.hl7.fhir.dstu3.model.Observation;
 import org.hl7.fhir.dstu3.model.Patient;
 import org.hl7.fhir.dstu3.model.Subscription;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.web.server.LocalServerPort;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
 
 import java.net.URI;
-import java.nio.file.Paths;
 import java.util.concurrent.Future;
 import java.util.concurrent.TimeUnit;
 
 import static ca.uhn.fhir.util.TestUtil.waitForSize;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
+@ExtendWith(SpringExtension.class)
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties =
+  {
+    "spring.batch.job.enabled=false",
+    "spring.profiles.active=dstu3",
+    "spring.datasource.url=jdbc:h2:mem:dbr3",
+    "hapi.fhir.subscription.websocket_enabled=true",
+    "hapi.fhir.allow_external_references=true",
+    "hapi.fhir.allow_placeholder_references=true",
+  })
+
+
 public class ExampleServerDstu3IT {
 
-  private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu3IT.class);
+  private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu2IT.class);
-  private static IGenericClient ourClient;
+  private IGenericClient ourClient;
-  private static FhirContext ourCtx;
+  private FhirContext ourCtx;
-  private static int ourPort;
-  private static Server ourServer;
 
-  static {
+  @LocalServerPort
-    HapiProperties.forceReload();
+  private int port;
-    HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "DSTU3");
-    HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:h2:mem:dbr3");
-    HapiProperties.setProperty(HapiProperties.SUBSCRIPTION_WEBSOCKET_ENABLED, "true");
-    HapiProperties.setProperty(HapiProperties.ALLOW_EXTERNAL_REFERENCES, "true");
-    HapiProperties.setProperty(HapiProperties.ALLOW_PLACEHOLDER_REFERENCES, "true");
-    ourCtx = FhirContext.forDstu3();
-  }
 
   @Test
   public void testCreateAndRead() {
-    ourLog.info("Base URL is: " + HapiProperties.getServerAddress());
+
     String methodName = "testCreateResourceConditional";
 
     Patient pt = new Patient();
@@ -90,7 +92,7 @@ public class ExampleServerDstu3IT {
     SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON);
 
     myWebSocketClient.start();
-    URI echoUri = new URI("ws://localhost:" + ourPort + "/hapi-fhir-jpaserver/websocket");
+    URI echoUri = new URI("ws://localhost:" + port + "/hapi-fhir-jpaserver/websocket");
     ClientUpgradeRequest request = new ClientUpgradeRequest();
     ourLog.info("Connecting to : {}", echoUri);
     Future<Session> connection = myWebSocketClient.connect(mySocketImplementation, echoUri, request);
@@ -119,39 +121,15 @@ public class ExampleServerDstu3IT {
     ourClient.delete().resourceById(mySubscriptionId).execute();
   }
 
-  @AfterAll
+  @BeforeEach
-  public static void afterClass() throws Exception {
+  void beforeEach() {
-    ourServer.stop();
-  }
-
-  @BeforeAll
-  public static void beforeClass() throws Exception {
-    String path = Paths.get("").toAbsolutePath().toString();
-
-    ourLog.info("Project base path is: {}", path);
-
-    ourServer = new Server(0);
-
-    WebAppContext webAppContext = new WebAppContext();
-    webAppContext.setContextPath("/hapi-fhir-jpaserver");
-    webAppContext.setDescriptor(path + "/src/main/webapp/WEB-INF/web.xml");
-    webAppContext.setResourceBase(path + "/target/hapi-fhir-jpaserver-starter");
-    webAppContext.setParentLoaderPriority(true);
-
-    ourServer.setHandler(webAppContext);
-    ourServer.start();
-
-    ourPort = JettyUtil.getPortForStartedServer(ourServer);
 
+    ourCtx = FhirContext.forDstu3();
     ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
     ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
-    String ourServerBase = "http://localhost:" + ourPort + "/hapi-fhir-jpaserver/fhir/";
+    String ourServerBase = "http://localhost:" + port + "/hapi-fhir-jpaserver/fhir/";
     ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
     ourClient.registerInterceptor(new LoggingInterceptor(true));
   }
 
-  public static void main(String[] theArgs) throws Exception {
-    ourPort = 8080;
-    beforeClass();
-  }
 }

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java

@@ -7,26 +7,20 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
-import ca.uhn.fhir.test.utilities.JettyUtil;
 import ca.uhn.fhir.util.BundleUtil;
-import org.eclipse.jetty.server.Server;
-import org.eclipse.jetty.webapp.WebAppContext;
 import org.eclipse.jetty.websocket.api.Session;
 import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
 import org.eclipse.jetty.websocket.client.WebSocketClient;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.*;
-import org.hl7.fhir.r4.model.Observation;
+import org.junit.jupiter.api.BeforeEach;
-import org.hl7.fhir.r4.model.Patient;
-import org.hl7.fhir.r4.model.Person;
-import org.hl7.fhir.r4.model.Reference;
-import org.hl7.fhir.r4.model.Subscription;
-import org.junit.jupiter.api.AfterAll;
-import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.web.server.LocalServerPort;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
 
 import java.net.URI;
-import java.nio.file.Paths;
 import java.util.Collection;
 import java.util.List;
 import java.util.Optional;
@@ -38,26 +32,30 @@ import static org.awaitility.Awaitility.await;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
+@ExtendWith(SpringExtension.class)
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties =
+  {
+    "spring.batch.job.enabled=false",
+    "spring.profiles.active=r4",
+    "spring.datasource.url=jdbc:h2:mem:dbr4",
+    "hapi.fhir.subscription.websocket_enabled=true",
+    "hapi.fhir.empi_enabled=true",
+    //Override is currently required when using Empi as the construction of the Empi beans are ambiguous as they are constructed multiple places. This is evident when running in a spring boot environment
+    "spring.main.allow-bean-definition-overriding=true"
+  })
 public class ExampleServerR4IT {
 
-    private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerR4IT.class);
+  private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu2IT.class);
-    private static IGenericClient ourClient;
+  private IGenericClient ourClient;
-    private static FhirContext ourCtx;
+  private FhirContext ourCtx;
-    private static int ourPort;
+
-    private static Server ourServer;
+  @LocalServerPort
+  private int port;
 
-    static {
-        HapiProperties.forceReload();
-        HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:h2:mem:dbr4");
-        HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "R4");
-        HapiProperties.setProperty(HapiProperties.SUBSCRIPTION_WEBSOCKET_ENABLED, "true");
-        HapiProperties.setProperty(HapiProperties.EMPI_ENABLED, "true");
-        ourCtx = FhirContext.forR4();
-    }
 
   @Test
-    public void testCreateAndRead() {
+  void testCreateAndRead() {
-        ourLog.info("Base URL is: " + HapiProperties.getServerAddress());
+
     String methodName = "testCreateResourceConditional";
 
     Patient pt = new Patient();
@@ -121,7 +119,7 @@ public class ExampleServerR4IT {
     SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON);
 
     myWebSocketClient.start();
-        URI echoUri = new URI("ws://localhost:" + ourPort + "/hapi-fhir-jpaserver/websocket");
+    URI echoUri = new URI("ws://localhost:" + port + "/hapi-fhir-jpaserver/websocket");
     ClientUpgradeRequest request = new ClientUpgradeRequest();
     ourLog.info("Connecting to : {}", echoUri);
     Future<Session> connection = myWebSocketClient.connect(mySocketImplementation, echoUri, request);
@@ -154,42 +152,15 @@ public class ExampleServerR4IT {
     return ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size();
   }
 
-  @AfterAll
-    public static void afterClass() throws Exception {
-        ourServer.stop();
-    }
 
-    @BeforeAll
+  @BeforeEach
-    public static void beforeClass() throws Exception {
+  void beforeEach() {
-        String path = Paths.get("").toAbsolutePath().toString();
-
-        ourLog.info("Project base path is: {}", path);
-
-        ourServer = new Server(0);
-
-        WebAppContext webAppContext = new WebAppContext();
-        webAppContext.setContextPath("/hapi-fhir-jpaserver");
-        webAppContext.setDisplayName("HAPI FHIR");
-        webAppContext.setDescriptor(path + "/src/main/webapp/WEB-INF/web.xml");
-        webAppContext.setResourceBase(path + "/target/hapi-fhir-jpaserver-starter");
-        webAppContext.setParentLoaderPriority(true);
-
-        ourServer.setHandler(webAppContext);
-        ourServer.start();
-
-        ourPort = JettyUtil.getPortForStartedServer(ourServer);
 
+    ourCtx = FhirContext.forR4();
     ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
     ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
-        String ourServerBase = HapiProperties.getServerAddress();
+    String ourServerBase = "http://localhost:" + port + "/hapi-fhir-jpaserver/fhir/";
-        ourServerBase = "http://localhost:" + ourPort + "/hapi-fhir-jpaserver/fhir/";
-
     ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
     ourClient.registerInterceptor(new LoggingInterceptor(true));
   }
-
-    public static void main(String[] theArgs) throws Exception {
-        ourPort = 8080;
-        beforeClass();
-    }
 }

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java

@@ -1,5 +1,9 @@
 package ca.uhn.fhir.jpa.starter;
 
+import static ca.uhn.fhir.util.TestUtil.waitForSize;
+import static org.awaitility.Awaitility.await;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.api.CacheControlDirective;
 import ca.uhn.fhir.rest.api.EncodingEnum;
@@ -7,9 +11,9 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
-import ca.uhn.fhir.test.utilities.JettyUtil;
+import java.net.URI;
-import org.eclipse.jetty.server.Server;
+import java.util.concurrent.Future;
-import org.eclipse.jetty.webapp.WebAppContext;
+import java.util.concurrent.TimeUnit;
 import org.eclipse.jetty.websocket.api.Session;
 import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
 import org.eclipse.jetty.websocket.client.WebSocketClient;
@@ -20,38 +24,34 @@ import org.hl7.fhir.r5.model.Observation;
 import org.hl7.fhir.r5.model.Patient;
 import org.hl7.fhir.r5.model.Subscription;
 import org.hl7.fhir.r5.model.SubscriptionTopic;
-import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.web.server.LocalServerPort;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
 
-import java.net.URI;
+@ExtendWith(SpringExtension.class)
-import java.nio.file.Paths;
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties =
-import java.util.concurrent.Future;
+  {
-import java.util.concurrent.TimeUnit;
+    "spring.batch.job.enabled=false",
-
+    "spring.profiles.active=r5",
-import static ca.uhn.fhir.util.TestUtil.waitForSize;
+    "spring.datasource.url=jdbc:h2:mem:dbr5",
-import static org.awaitility.Awaitility.await;
+    "hapi.fhir.subscription.websocket_enabled=true"
-import static org.junit.jupiter.api.Assertions.assertEquals;
+  })
-
 public class ExampleServerR5IT {
 
-  private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerR5IT.class);
+  private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu2IT.class);
-  private static IGenericClient ourClient;
+  private IGenericClient ourClient;
-  private static FhirContext ourCtx;
+  private FhirContext ourCtx;
-  private static int ourPort;
+
-  private static Server ourServer;
+  @LocalServerPort
+  private int port;
 
-  static {
-    HapiProperties.forceReload();
-    HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:h2:mem:dbr5");
-    HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "R5");
-    HapiProperties.setProperty(HapiProperties.SUBSCRIPTION_WEBSOCKET_ENABLED, "true");
-    ourCtx = FhirContext.forR5();
-  }
 
   @Test
   public void testCreateAndRead() {
-    ourLog.info("Base URL is: " + HapiProperties.getServerAddress());
+
     String methodName = "testCreateResourceConditional";
 
     Patient pt = new Patient();
@@ -97,7 +97,7 @@ public class ExampleServerR5IT {
     SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON);
 
     myWebSocketClient.start();
-    URI echoUri = new URI("ws://localhost:" + ourPort + "/hapi-fhir-jpaserver/websocket");
+    URI echoUri = new URI("ws://localhost:" + port + "/hapi-fhir-jpaserver/websocket");
     ClientUpgradeRequest request = new ClientUpgradeRequest();
     ourLog.info("Connecting to : {}", echoUri);
     Future<Session> connection = myWebSocketClient.connect(mySocketImplementation, echoUri, request);
@@ -123,41 +123,14 @@ public class ExampleServerR5IT {
     ourClient.delete().resourceById(mySubscriptionId).execute();
   }
 
-  @AfterAll
+  @BeforeEach
-  public static void afterClass() throws Exception {
+  void beforeEach() {
-    ourServer.stop();
-  }
-
-  @BeforeAll
-  public static void beforeClass() throws Exception {
-    String path = Paths.get("").toAbsolutePath().toString();
-
-    ourLog.info("Project base path is: {}", path);
-
-    ourServer = new Server(0);
-
-    WebAppContext webAppContext = new WebAppContext();
-    webAppContext.setContextPath("/hapi-fhir-jpaserver");
-    webAppContext.setDisplayName("HAPI FHIR");
-    webAppContext.setDescriptor(path + "/src/main/webapp/WEB-INF/web.xml");
-    webAppContext.setResourceBase(path + "/target/hapi-fhir-jpaserver-starter");
-    webAppContext.setParentLoaderPriority(true);
-
-    ourServer.setHandler(webAppContext);
-    ourServer.start();
-
-    ourPort = JettyUtil.getPortForStartedServer(ourServer);
 
+    ourCtx = FhirContext.forR5();
     ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
     ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
-    String ourServerBase = "http://localhost:" + ourPort + "/hapi-fhir-jpaserver/fhir/";
+    String ourServerBase = "http://localhost:" + port + "/hapi-fhir-jpaserver/fhir/";
-
     ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
     ourClient.registerInterceptor(new LoggingInterceptor(true));
   }
-
-  public static void main(String[] theArgs) throws Exception {
-    ourPort = 8080;
-    beforeClass();
-  }
 }

src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java

@@ -7,44 +7,42 @@ import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
 import ca.uhn.fhir.rest.client.interceptor.UrlTenantSelectionInterceptor;
 import ca.uhn.fhir.rest.server.provider.ProviderConstants;
-import ca.uhn.fhir.test.utilities.JettyUtil;
+import org.hl7.fhir.r4.model.*;
-import org.eclipse.jetty.server.Server;
+import org.junit.jupiter.api.BeforeEach;
-import org.eclipse.jetty.webapp.WebAppContext;
-import org.hl7.fhir.r4.model.Bundle;
-import org.hl7.fhir.r4.model.CodeType;
-import org.hl7.fhir.r4.model.IntegerType;
-import org.hl7.fhir.r4.model.Parameters;
-import org.hl7.fhir.r4.model.Patient;
-import org.junit.jupiter.api.AfterAll;
-import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
-
+import org.junit.jupiter.api.extension.ExtendWith;
-import java.nio.file.Paths;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.web.server.LocalServerPort;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
+@ExtendWith(SpringExtension.class)
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties =
+  {
+    "spring.batch.job.enabled=false",
+    "spring.profiles.active=r4",
+    "spring.datasource.url=jdbc:h2:mem:dbr4-mt",
+    "hapi.fhir.subscription.websocket_enabled=true",
+    "hapi.fhir.partitioning.partitioning_include_in_search_hashes=false"
+
+  })
 public class MultitenantServerR4IT {
 
-  private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(MultitenantServerR4IT.class);
+
-  private static IGenericClient ourClient;
+  private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu2IT.class);
-  private static FhirContext ourCtx;
+  private IGenericClient ourClient;
-  private static int ourPort;
+  private FhirContext ourCtx;
-  private static Server ourServer;
+
+  @LocalServerPort
+  private int port;
+
   private static UrlTenantSelectionInterceptor ourClientTenantInterceptor;
 
-  static {
-    HapiProperties.forceReload();
-    HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:h2:mem:dbr4-mt");
-    HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "R4");
-    HapiProperties.setProperty(HapiProperties.SUBSCRIPTION_WEBSOCKET_ENABLED, "true");
-    HapiProperties.setProperty(HapiProperties.PARTITIONING_ENABLED, "true");
-    HapiProperties.setProperty(HapiProperties.PARTITIONING_MULTITENANCY_ENABLED, "true");
-    ourCtx = FhirContext.forR4();
-  }
 
   @Test
   public void testCreateAndReadInTenantA() {
-    ourLog.info("Base URL is: " + HapiProperties.getServerAddress());
+
 
     // Create tenant A
     ourClientTenantInterceptor.setTenantId("DEFAULT");
@@ -70,7 +68,7 @@ public class MultitenantServerR4IT {
 
   @Test
   public void testCreateAndReadInTenantB() {
-    ourLog.info("Base URL is: " + HapiProperties.getServerAddress());
+
 
     // Create tenant A
     ourClientTenantInterceptor.setTenantId("DEFAULT");
@@ -94,45 +92,16 @@ public class MultitenantServerR4IT {
     assertEquals("Family B", pt2.getName().get(0).getFamily());
   }
 
-  @AfterAll
+  @BeforeEach
-  public static void afterClass() throws Exception {
+  void beforeEach() {
-    ourServer.stop();
-  }
-
-  @BeforeAll
-  public static void beforeClass() throws Exception {
-    String path = Paths.get("").toAbsolutePath().toString();
-
-    ourLog.info("Project base path is: {}", path);
-
-    ourServer = new Server(0);
-
-    WebAppContext webAppContext = new WebAppContext();
-    webAppContext.setContextPath("/hapi-fhir-jpaserver");
-    webAppContext.setDisplayName("HAPI FHIR");
-    webAppContext.setDescriptor(path + "/src/main/webapp/WEB-INF/web.xml");
-    webAppContext.setResourceBase(path + "/target/hapi-fhir-jpaserver-starter");
-    webAppContext.setParentLoaderPriority(true);
-
-    ourServer.setHandler(webAppContext);
-    ourServer.start();
-
-    ourPort = JettyUtil.getPortForStartedServer(ourServer);
-
-    ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
-    ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
-    String ourServerBase = HapiProperties.getServerAddress();
-    ourServerBase = "http://localhost:" + ourPort + "/hapi-fhir-jpaserver/fhir/";
-
-    ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
-    ourClient.registerInterceptor(new LoggingInterceptor(true));
 
     ourClientTenantInterceptor = new UrlTenantSelectionInterceptor();
+    ourCtx = FhirContext.forR4();
+    ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
+    ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
+    String ourServerBase = "http://localhost:" + port + "/hapi-fhir-jpaserver/fhir/";
+    ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
+    ourClient.registerInterceptor(new LoggingInterceptor(true));
     ourClient.registerInterceptor(ourClientTenantInterceptor);
   }
-
-  public static void main(String[] theArgs) throws Exception {
-    ourPort = 8080;
-    beforeClass();
-  }
 }

src/test/java/ca/uhn/fhir/jpa/starter/RandomServerPortProvider.java

@@ -1,36 +0,0 @@
-package ca.uhn.fhir.jpa.starter;
-
-import java.io.IOException;
-import java.net.ServerSocket;
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * Provides server ports
- */
-public class RandomServerPortProvider {
-
-	private static List<Integer> ourPorts = new ArrayList<Integer>(); 
-	
-	public static int findFreePort() {
-		ServerSocket server;
-		try {
-			server = new ServerSocket(0);
-			int port = server.getLocalPort();
-			ourPorts.add(port);
-			server.close();
-			Thread.sleep(500);
-			return port;
-		} catch (IOException e) {
-			throw new Error(e);
-		} catch (InterruptedException e) {
-			throw new Error(e);
-		}
-	}
-
-	public static List<Integer> list() {
-		return ourPorts;
-	}
-
-}
- 

src/test/resources/application-integrationtest.yaml

@@ -0,0 +1,104 @@
+spring:
+  datasource:
+    url: 'jdbc:h2:file:./target/database/h2'
+    username: sa
+    password: null
+    driverClassName: org.h2.Driver
+    max-active: 15
+  profiles:
+    ### This is the FHIR version. Choose between, dstu2, dstu3, r4 or r5
+    active: r4
+
+hapi:
+  fhir:
+    #supported_resource_types:
+    #  - Patient
+    #  - Observation
+#    allow_cascading_deletes: true
+#    allow_contains_searches: true
+#    allow_external_references: true
+#    allow_multiple_delete: true
+#    allow_override_default_search_params: true
+#    allow_placeholder_references: true
+#    auto_create_placeholder_reference_targets: false
+#    default_encoding: JSON
+#    default_pretty_print: true
+#    default_page_size: 20
+#    enable_index_missing_fields: false
+#    enforce_referential_integrity_on_delete: false
+#    enforce_referential_integrity_on_write: false
+#    etag_support_enabled: true
+#    expunge_enabled: true
+#    daoconfig_client_id_strategy: null
+#    fhirpath_interceptor_enabled: false
+#    filter_search_enabled: true
+#    graphql_enabled: true
+    #partitioning:
+    #  cross_partition_reference_mode: true
+    #  multitenancy_enabled: true
+    #  partitioning_include_in_search_hashes: true
+    #cors:
+    #  allow_Credentials: true
+      # Supports multiple, comma separated allowed origin entries
+      # cors.allowed_origin=http://localhost:8080,https://localhost:8080,https://fhirtest.uhn.ca
+    #  allowed_origin:
+    #    - '*'
+
+#    logger:
+#      error_format: 'ERROR - ${requestVerb} ${requestUrl}'
+#      format: >-
+#        Path[${servletPath}] Source[${requestHeader.x-forwarded-for}]
+#        Operation[${operationType} ${operationName} ${idOrResourceName}]
+#        UA[${requestHeader.user-agent}] Params[${requestParameters}]
+#        ResponseEncoding[${responseEncodingNoDefault}]
+#      log_exceptions: true
+#      name: fhirtest.access
+#    max_binary_size: 104857600
+#    max_page_size: 200
+#    retain_cached_searches_mins: 60
+#    reuse_cached_search_results_millis: 60000
+    tester:
+      -
+          id: home
+          name: Local Tester
+          server_address: 'http://localhost:8080/hapi-fhir-jpaserver/fhir'
+          refuse_to_fetch_third_party_urls: false
+          fhir_version: R4
+      -
+          id: global
+          name: Global Tester
+          server_address: "http://hapi.fhir.org/baseR4"
+          refuse_to_fetch_third_party_urls: false
+          fhir_version: R4
+#    validation:
+#      requests_enabled: true
+#      responses_enabled: true
+#    binary_storage_enabled: true
+#    bulk_export_enabled: true
+#    partitioning_multitenancy_enabled:
+#    subscription:
+#      resthook_enabled: false
+#      websocket_enabled: false
+#      email:
+#        from: some@test.com
+#        host: google.com
+#        port:
+#        username:
+#        password:
+#        auth:
+#        startTlsEnable:
+#        startTlsRequired:
+#        quitWait:
+
+
+#
+#elasticsearch:
+#  debug:
+#    pretty_print_json_log: false
+#    refresh_after_write: false
+#  enabled: false
+#  password: SomePassword
+#  required_index_status: YELLOW
+#  rest_url: 'http://localhost:9200'
+#  schema_management_strategy: CREATE
+#  username: SomeUsername