JPAStarter uplift (cqframework#721)

* remove snakeyaml CVE-2022-1471 * update jpastarter dependencies and deprecated hapi references * upgrade jpa WIP * HAPI uplift WIP * add in capability statements * Use a server config bean * update to 6.7 snapshot * update plugins WIP * update ruler dependencies WIP * add additional config for hapi-fhir based ops * update missing dependencies * Fix some beans * update external * update external jar * update jpastarter dependencies * update tests * update IT tests WIP * config updates * adding factories and loaders for plugins * updat jpastarter * latest jpa edits * update jpastarter * wip jpa updates * WIP config * Load providers eagerly * Fixing tests * jpa cqltranslator config * update core testing with measureeval * update cql config jpastarter * add missing jackson-deps pom * WIP * fix IT tests in plugins WIP * update IT tests WIP * cds hooks test wip * fix tests wip * Fix cds hooks * fix cr module tests * last updates to IT tests --------- Co-authored-by: justin.mckelvy <[email protected]> Co-authored-by: Jonathan Percival <[email protected]> Co-authored-by: Brenin Rhodes <[email protected]>
PublicHealthInformationTechnology · Jun 22, 2023 · 0dff91e · 0dff91e
1 parent 0bd8c03
commit 0dff91e
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Showing 183 changed files with 21,264 additions and 22,748 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +1,4 @@
 [submodule "external/hapi-fhir-jpaserver-starter"]
 	path = external/hapi-fhir-jpaserver-starter
 	url = https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git
+	branch = 6.7.6-snapshot-server
diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -4,6 +4,8 @@
 	// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
 	"version": "0.2.0",
 	"configurations": [
+
+
 		{
 			"type": "java",
 			"name": "Launch Application",
@@ -15,7 +17,8 @@
 				"-Ddebug=true",
 				"-Dloader.debug=true",
 				"-Dhapi.fhir.bulk_export_enabled=false",
-				"-Dspring.batch.job.enabled=false"
+				"-Dspring.batch.job.enabled=false",
+				"-Dspring.main.allow-bean-definition-overriding=true"
 			],
 		},
 		{
@@ -29,7 +32,9 @@
 				"-Ddebug=true",
 				"-Dloader.debug=true",
 				"-Dhapi.fhir.bulk_export_enabled=false",
-				"-Dspring.batch.job.enabled=false"
+				"-Dspring.batch.job.enabled=false",
+				"-Dhapi.fhir.cr_enabled=true",
+				"-Dspring.main.allow-bean-definition-overriding=true"
 			],
 			"classPaths": [
 				"$Auto",

diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -10,7 +10,9 @@
 		{
 			"name": "test-config",
 			"vmArgs": [
-				"-XX:TieredStopAtLevel=1"
+				"-XX:TieredStopAtLevel=1",
+				"-Ddebug=true",
+				"-Dloader.debug=true"
 			]
 		},
 	],
@@ -87,4 +89,4 @@
 	"thunder-client.saveToWorkspace": true,
 	"java.jdt.ls.vmargs": "-Xmx2G -XX:+UseG1GC -XX:+UseStringDeduplication",
 	"java.compile.nullAnalysis.mode": "disabled"
-}
+}
diff --git a/config/checkstyle/checkstyle.xml b/config/checkstyle/checkstyle.xml
@@ -40,4 +40,6 @@
 		<property name="message" value="Line has trailing spaces."/>
 	</module>
 
+	<suppress checks=".*" files="org[\\/]opencds[\\/]cqf[\\/]external[\\/]"/>
+
 </module>
diff --git a/core/pom.xml b/core/pom.xml
@@ -21,12 +21,78 @@
 			<artifactId>hapi-fhir-storage</artifactId>
 			<version>${hapi_version}</version>
 		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-server</artifactId>
+			<version>${hapi_version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-jpaserver-subscription</artifactId>
+			<version>${hapi_version}</version>
+		</dependency>
+
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-validation-resources-r5</artifactId>
+			<version>${hapi_version}</version>
+		</dependency>
 
+		<dependency>
+			<groupId>org.simplejavamail</groupId>
+			<artifactId>simple-java-mail</artifactId>
+			<exclusions>
+				<exclusion>
+					<groupId>jakarta.annotation</groupId>
+					<artifactId>jakarta.annotation-api</artifactId>
+				</exclusion>
+			</exclusions>
+		</dependency>
+
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>org.hl7.fhir.r5</artifactId>
+			<version>6.0.15</version>
+		</dependency>
+
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>org.hl7.fhir.convertors</artifactId>
+			<version>6.0.15</version>
+		</dependency>
+		<dependency>
+			<groupId>org.opencds.cqf.cql</groupId>
+			<artifactId>evaluator.jackson-deps</artifactId>
+			<type>pom</type>
+		</dependency>
 		<dependency>
 			<groupId>org.opencds.cqf.cql</groupId>
 			<artifactId>evaluator.fhir</artifactId>
 		</dependency>
-
+		<dependency>
+			<groupId>org.opencds.cqf.cql</groupId>
+			<artifactId>evaluator.library</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.opencds.cqf.cql</groupId>
+			<artifactId>evaluator.activitydefinition</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.opencds.cqf.cql</groupId>
+			<artifactId>evaluator.plandefinition</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.opencds.cqf.cql</groupId>
+			<artifactId>evaluator.questionnaire</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.opencds.cqf.cql</groupId>
+			<artifactId>evaluator.questionnaireresponse</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.opencds.cqf.cql</groupId>
+			<artifactId>evaluator.spring</artifactId>
+		</dependency>
 		<dependency>
 			<groupId>javax</groupId>
 			<artifactId>javaee-api</artifactId>

diff --git a/core/src/main/java/org/opencds/cqf/ruler/Application.java b/core/src/main/java/org/opencds/cqf/ruler/Application.java
@@ -4,33 +4,38 @@
 import org.opencds.cqf.external.mdm.MdmConfig;
 import org.opencds.cqf.ruler.config.BeanFinderConfig;
 import org.opencds.cqf.ruler.config.RulerConfig;
-import org.opencds.cqf.ruler.config.ServerProperties;
-import org.opencds.cqf.ruler.config.TesterUIConfig;
 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.autoconfigure.quartz.QuartzAutoConfiguration;
+import org.springframework.boot.autoconfigure.thymeleaf.ThymeleafAutoConfiguration;
 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.Conditional;
 import org.springframework.context.annotation.Import;
 
+import ca.uhn.fhir.batch2.jobs.config.Batch2JobsConfig;
+import ca.uhn.fhir.jpa.batch2.JpaBatch2Config;
+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 ca.uhn.fhir.rest.server.RestfulServer;
 
-@ServletComponentScan(basePackageClasses = Application.class)
-@SpringBootApplication(exclude = { ElasticsearchRestClientAutoConfiguration.class, QuartzAutoConfiguration.class })
+@SpringBootApplication(exclude = { ElasticsearchRestClientAutoConfiguration.class, ThymeleafAutoConfiguration.class })
 @Import({
-		RulerConfig.class,
-		ServerProperties.class,
+		SubscriptionSubmitterConfig.class,
+		SubscriptionProcessorConfig.class,
+		SubscriptionChannelConfig.class,
 		WebsocketDispatcherConfig.class,
 		MdmConfig.class,
-		TesterUIConfig.class,
-		BeanFinderConfig.class, })
+		JpaBatch2Config.class,
+		Batch2JobsConfig.class,
+		BeanFinderConfig.class,
+		RulerConfig.class })
 public class Application extends SpringBootServletInitializer {
 
 	public static void main(String[] args) {
@@ -49,12 +54,10 @@ protected SpringApplicationBuilder configure(SpringApplicationBuilder builder) {
 
 	@Bean
 	@Conditional(OnEitherVersion.class)
-	public ServletRegistrationBean<Server> hapiServletRegistration() {
-		ServletRegistrationBean<Server> servletRegistrationBean = new ServletRegistrationBean<>();
-		Server server = new Server();
-		beanFactory.autowireBean(server);
-		servletRegistrationBean.setName("fhir servlet");
-		servletRegistrationBean.setServlet(server);
+	public ServletRegistrationBean hapiServletRegistration(RestfulServer restfulServer) {
+		var servletRegistrationBean = new ServletRegistrationBean();
+		beanFactory.autowireBean(restfulServer);
+		servletRegistrationBean.setServlet(restfulServer);
 		servletRegistrationBean.addUrlMappings("/fhir/*");
 		servletRegistrationBean.setLoadOnStartup(1);
 

diff --git a/...in/java/org/opencds/cqf/ruler/Server.java → ...a/org/opencds/cqf/ruler/ServerConfig.java b/...in/java/org/opencds/cqf/ruler/Server.java → ...a/org/opencds/cqf/ruler/ServerConfig.java
@@ -6,100 +6,49 @@
 import java.util.Map;
 import java.util.stream.Collectors;
 
-import javax.servlet.ServletException;
-
 import org.hl7.fhir.dstu3.model.CapabilityStatement;
 import org.hl7.fhir.instance.model.api.IBaseConformance;
-import org.opencds.cqf.external.AppProperties;
-import org.opencds.cqf.external.BaseJpaRestfulServer;
-import org.opencds.cqf.external.mdm.MdmConfig;
 import org.opencds.cqf.ruler.api.Interceptor;
 import org.opencds.cqf.ruler.api.MetadataExtender;
 import org.opencds.cqf.ruler.api.OperationProvider;
 import org.opencds.cqf.ruler.capability.ExtensibleJpaCapabilityStatementProvider;
 import org.opencds.cqf.ruler.capability.ExtensibleJpaConformanceProviderDstu2;
 import org.opencds.cqf.ruler.capability.ExtensibleJpaConformanceProviderDstu3;
-import org.opencds.cqf.ruler.config.BeanFinderConfig;
 import org.opencds.cqf.ruler.config.ServerProperties;
-import org.opencds.cqf.ruler.config.TesterUIConfig;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationContext;
-import org.springframework.context.annotation.Import;
 
-import ca.uhn.fhir.batch2.jobs.config.Batch2JobsConfig;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.support.IValidationSupport;
-import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
-import ca.uhn.fhir.jpa.batch2.JpaBatch2Config;
-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 ca.uhn.fhir.model.dstu2.resource.Conformance;
+import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 
-@Import({
-		ServerProperties.class,
-		SubscriptionSubmitterConfig.class,
-		SubscriptionProcessorConfig.class,
-		SubscriptionChannelConfig.class,
-		WebsocketDispatcherConfig.class,
-		MdmConfig.class,
-		JpaBatch2Config.class,
-		Batch2JobsConfig.class,
-		TesterUIConfig.class,
-		BeanFinderConfig.class })
-public class Server extends BaseJpaRestfulServer {
-	private static final long serialVersionUID = 1L;
-
-	private static Logger log = LoggerFactory.getLogger(Server.class);
-
-	@Autowired
-	DaoConfig myDaoConfig;
-
-	@Autowired
-	ISearchParamRegistry mySearchParamRegistry;
-
-	@SuppressWarnings("rawtypes")
-	@Autowired
-	IFhirSystemDao myFhirSystemDao;
+public class ServerConfig {
 
-	@Autowired
-	private IValidationSupport myValidationSupport;
-
-	@Autowired
-	ApplicationContext applicationContext;
-
-	@Autowired
-	AppProperties myAppProperties;
-
-	@Autowired
-	ServerProperties myServerProperties;
-
-	public Server() {
-		super();
-	}
+	private static Logger log = LoggerFactory.getLogger(ServerConfig.class);
 
-	@Override
-	@SuppressWarnings({ "rawtypes", "unchecked" })
-	protected void initialize() throws ServletException {
-		super.initialize();
+	@SuppressWarnings({ "unchecked", "rawtypes" })
+	public ServerConfig(RestfulServer server, ApplicationContext applicationContext,
+							  JpaStorageSettings myJpaStorageSettings, ISearchParamRegistry mySearchParamRegistry,
+							  IFhirSystemDao myFhirSystemDao, IValidationSupport myValidationSupport,
+							  ServerProperties myServerProperties) {
 
 		log.info("Loading operation providers from plugins");
 		Map<String, OperationProvider> providers = applicationContext.getBeansOfType(OperationProvider.class);
 		for (OperationProvider o : providers.values()) {
 			log.info("Registering {}", o.getClass().getName());
-			this.registerProvider(o);
+			server.registerProvider(o);
 		}
 
 		log.info("Loading interceptors from plugins");
 		Map<String, Interceptor> interceptors = applicationContext.getBeansOfType(Interceptor.class);
 		for (Interceptor o : interceptors.values()) {
 			log.info("Registering {} interceptor", o.getClass().getName());
-			this.registerInterceptor(o);
+			server.registerInterceptor(o);
 		}
 
 		log.info("Loading metadata extenders from plugins");
@@ -114,34 +63,34 @@ protected void initialize() throws ServletException {
 		if (fhirVersion == FhirVersionEnum.DSTU2) {
 			List<MetadataExtender<Conformance>> extenderList = extenders.values().stream()
 					.map(x -> (MetadataExtender<Conformance>) x).collect(Collectors.toList());
-			ExtensibleJpaConformanceProviderDstu2 confProvider = new ExtensibleJpaConformanceProviderDstu2(this,
+			ExtensibleJpaConformanceProviderDstu2 confProvider = new ExtensibleJpaConformanceProviderDstu2(server,
 					myFhirSystemDao,
-					myDaoConfig, extenderList);
+					myJpaStorageSettings, extenderList);
 			confProvider.setImplementationDescription(firstNonNull(implementationDescription, "CQF RULER DSTU2 Server"));
-			setServerConformanceProvider(confProvider);
+			server.setServerConformanceProvider(confProvider);
 		} else {
 			if (fhirVersion == FhirVersionEnum.DSTU3) {
 				List<MetadataExtender<CapabilityStatement>> extenderList = extenders.values().stream()
 						.map(x -> (MetadataExtender<CapabilityStatement>) x).collect(Collectors.toList());
-				ExtensibleJpaConformanceProviderDstu3 confProvider = new ExtensibleJpaConformanceProviderDstu3(this,
-						myFhirSystemDao, myDaoConfig, mySearchParamRegistry, extenderList);
+				ExtensibleJpaConformanceProviderDstu3 confProvider = new ExtensibleJpaConformanceProviderDstu3(server,
+						myFhirSystemDao, myJpaStorageSettings, mySearchParamRegistry, extenderList);
 				confProvider
 						.setImplementationDescription(firstNonNull(implementationDescription, "CQF RULER DSTU3 Server"));
-				setServerConformanceProvider(confProvider);
+				server.setServerConformanceProvider(confProvider);
 			} else if (fhirVersion == FhirVersionEnum.R4) {
 				List<MetadataExtender<IBaseConformance>> extenderList = extenders.values().stream()
 						.map(x -> (MetadataExtender<IBaseConformance>) x).collect(Collectors.toList());
-				ExtensibleJpaCapabilityStatementProvider confProvider = new ExtensibleJpaCapabilityStatementProvider(this,
-						myFhirSystemDao, myDaoConfig, mySearchParamRegistry, myValidationSupport, extenderList);
+				ExtensibleJpaCapabilityStatementProvider confProvider = new ExtensibleJpaCapabilityStatementProvider(server,
+						myFhirSystemDao, myJpaStorageSettings, mySearchParamRegistry, myValidationSupport, extenderList);
 				confProvider.setImplementationDescription(firstNonNull(implementationDescription, "CQF RULER R4 Server"));
-				setServerConformanceProvider(confProvider);
+				server.setServerConformanceProvider(confProvider);
 			} else if (fhirVersion == FhirVersionEnum.R5) {
 				List<MetadataExtender<IBaseConformance>> extenderList = extenders.values().stream()
 						.map(x -> (MetadataExtender<IBaseConformance>) x).collect(Collectors.toList());
-				ExtensibleJpaCapabilityStatementProvider confProvider = new ExtensibleJpaCapabilityStatementProvider(this,
-						myFhirSystemDao, myDaoConfig, mySearchParamRegistry, myValidationSupport, extenderList);
+				ExtensibleJpaCapabilityStatementProvider confProvider = new ExtensibleJpaCapabilityStatementProvider(server,
+						myFhirSystemDao, myJpaStorageSettings, mySearchParamRegistry, myValidationSupport, extenderList);
 				confProvider.setImplementationDescription(firstNonNull(implementationDescription, "CQF RULER R5 Server"));
-				setServerConformanceProvider(confProvider);
+				server.setServerConformanceProvider(confProvider);
 			} else {
 				throw new IllegalStateException();
 			}

diff --git a/core/src/main/java/org/opencds/cqf/ruler/builder/CompositionBuilder.java b/core/src/main/java/org/opencds/cqf/ruler/builder/CompositionBuilder.java
@@ -4,6 +4,7 @@
 import static com.google.common.base.Preconditions.checkNotNull;
 
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.Date;
 import java.util.List;
 
@@ -231,10 +232,11 @@ protected void initializeR5(T theResource) {
 
 		composition
 				.setDate(myDate)
-				.setIdentifier(new org.hl7.fhir.r5.model.Identifier().setSystem(getIdentifier().getKey())
-						.setValue(getIdentifier().getValue()))
+				.setIdentifier(
+						Collections.singletonList(new org.hl7.fhir.r5.model.Identifier().setSystem(getIdentifier().getKey())
+								.setValue(getIdentifier().getValue())))
 				.setStatus(CompositionStatus.valueOf(myStatus))
-				.setSubject(new org.hl7.fhir.r5.model.Reference(mySubject))
+				.setSubject(Collections.singletonList(new org.hl7.fhir.r5.model.Reference(mySubject)))
 				.setTitle(myTitle)
 				.setType(new org.hl7.fhir.r5.model.CodeableConcept()
 						.addCoding(new org.hl7.fhir.r5.model.Coding()