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Fix #30 - Upgrade to HAPI FHIR 3.8.0

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This commit is contained in:
James Agnew
2019-06-10 05:25:41 -07:00
parent b3a0f84712
commit 5b90f1f1f4
3 changed files with 276 additions and 172 deletions
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287
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java
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@@ -1,26 +1,21 @@
package ca.uhn.fhir.jpa.starter;
import java.lang.reflect.InvocationTargetException;
import java.sql.Driver;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.subscription.module.cache.SubscriptionDeliveryHandlerFactory;
import ca.uhn.fhir.jpa.subscription.module.subscriber.email.IEmailSender;
import ca.uhn.fhir.jpa.subscription.module.subscriber.email.JavaMailEmailSender;
import org.apache.commons.dbcp2.BasicDataSource;
import org.hl7.fhir.instance.model.Subscription;
import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import org.thymeleaf.util.Validate;
import java.lang.reflect.InvocationTargetException;
import java.sql.Driver;
/**
* This is the primary configuration file for the example server
*/
@@ -28,173 +23,149 @@ import org.thymeleaf.util.Validate;
@EnableTransactionManagement()
public class FhirServerConfigCommon {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirServerConfigCommon.class);
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirServerConfigCommon.class);
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 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();
@Autowired
private SubscriptionDeliveryHandlerFactory mySubscriptionDeliveryHandlerFactory;
public FhirServerConfigCommon() {
ourLog.info("Server configured to " + (this.allowContainsSearches ? "allow" : "deny") + " contains searches");
ourLog.info("Server configured to " + (this.allowMultipleDelete ? "allow" : "deny") + " multiple deletes");
ourLog.info("Server configured to " + (this.allowExternalReferences ? "allow" : "deny") + " external references");
ourLog.info("Server configured to " + (this.expungeEnabled ? "enable" : "disable") + " expunges");
ourLog.info("Server configured to " + (this.allowPlaceholderReferences ? "allow" : "deny") + " placeholder references");
ourLog.info("Server configured to " + (this.allowOverrideDefaultSearchParams ? "allow" : "deny") + " overriding default search params");
public FhirServerConfigCommon() {
ourLog.info("Server configured to " + (this.allowContainsSearches ? "allow" : "deny") + " contains searches");
ourLog.info("Server configured to " + (this.allowMultipleDelete ? "allow" : "deny") + " multiple deletes");
ourLog.info("Server configured to " + (this.allowExternalReferences ? "allow" : "deny") + " external references");
ourLog.info("Server configured to " + (this.expungeEnabled ? "enable" : "disable") + " expunges");
ourLog.info("Server configured to " + (this.allowPlaceholderReferences ? "allow" : "deny") + " placeholder references");
ourLog.info("Server configured to " + (this.allowOverrideDefaultSearchParams ? "allow" : "deny") + " overriding default search params");
if (this.emailEnabled) {
ourLog.info("Server is configured to enable email with host '" + this.emailHost + "' and port " + this.emailPort.toString());
ourLog.info("Server will use '" + this.emailFrom + "' as the from email address");
if (this.emailEnabled) {
ourLog.info("Server is configured to enable email with host '" + this.emailHost + "' and port " + this.emailPort.toString());
ourLog.info("Server will use '" + this.emailFrom + "' as the from email address");
if (this.emailUsername != null && this.emailUsername.length() > 0) {
ourLog.info("Server is configured to use username '" + this.emailUsername + "' for email");
}
if (this.emailUsername != null && this.emailUsername.length() > 0) {
ourLog.info("Server is configured to use username '" + this.emailUsername + "' for email");
}
if (this.emailPassword != null && this.emailPassword.length() > 0) {
ourLog.info("Server is configured to use a password for email");
}
}
if (this.emailPassword != null && this.emailPassword.length() > 0) {
ourLog.info("Server is configured to use a password for email");
}
}
if (this.subscriptionRestHookEnabled) {
ourLog.info("REST-hook subscriptions enabled");
}
if (this.subscriptionRestHookEnabled) {
ourLog.info("REST-hook subscriptions enabled");
}
if (this.subscriptionEmailEnabled) {
ourLog.info("Email subscriptions enabled");
}
}
if (this.subscriptionEmailEnabled) {
ourLog.info("Email subscriptions enabled");
}
}
/**
* Configure FHIR properties around the the JPA server via this bean
*/
@Bean()
public DaoConfig daoConfig() {
DaoConfig retVal = new DaoConfig();
/**
* Configure FHIR properties around the the JPA server via this bean
*/
@Bean()
public DaoConfig daoConfig() {
DaoConfig retVal = new DaoConfig();
retVal.setAllowContainsSearches(this.allowContainsSearches);
retVal.setAllowMultipleDelete(this.allowMultipleDelete);
retVal.setAllowExternalReferences(this.allowExternalReferences);
retVal.setExpungeEnabled(this.expungeEnabled);
retVal.setAutoCreatePlaceholderReferenceTargets(this.allowPlaceholderReferences);
retVal.setEmailFromAddress(this.emailFrom);
retVal.setAllowContainsSearches(this.allowContainsSearches);
retVal.setAllowMultipleDelete(this.allowMultipleDelete);
retVal.setAllowExternalReferences(this.allowExternalReferences);
retVal.setExpungeEnabled(this.expungeEnabled);
retVal.setAutoCreatePlaceholderReferenceTargets(this.allowPlaceholderReferences);
retVal.setEmailFromAddress(this.emailFrom);
Integer maxFetchSize = HapiProperties.getMaximumFetchSize();
retVal.setFetchSizeDefaultMaximum(maxFetchSize);
ourLog.info("Server configured to have a maximum fetch size of " + (maxFetchSize == Integer.MAX_VALUE? "'unlimited'": maxFetchSize));
Integer maxFetchSize = HapiProperties.getMaximumFetchSize();
retVal.setFetchSizeDefaultMaximum(maxFetchSize);
ourLog.info("Server configured to have a maximum fetch size of " + (maxFetchSize == Integer.MAX_VALUE ? "'unlimited'" : maxFetchSize));
Long reuseCachedSearchResultsMillis = HapiProperties.getReuseCachedSearchResultsMillis();
retVal.setReuseCachedSearchResultsForMillis(reuseCachedSearchResultsMillis );
ourLog.info("Server configured to cache search results for {} milliseconds", reuseCachedSearchResultsMillis);
// Subscriptions are enabled by channel type
if (HapiProperties.getSubscriptionRestHookEnabled()) {
ourLog.info("Enabling REST-hook subscriptions");
retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.RESTHOOK);
}
if (HapiProperties.getSubscriptionEmailEnabled()) {
ourLog.info("Enabling email subscriptions");
retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.EMAIL);
}
if (HapiProperties.getSubscriptionWebsocketEnabled()) {
ourLog.info("Enabling websocket subscriptions");
retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.WEBSOCKET);
}
Long reuseCachedSearchResultsMillis = HapiProperties.getReuseCachedSearchResultsMillis();
retVal.setReuseCachedSearchResultsForMillis(reuseCachedSearchResultsMillis);
ourLog.info("Server configured to cache search results for {} milliseconds", reuseCachedSearchResultsMillis);
return retVal;
}
// Subscriptions are enabled by channel type
if (HapiProperties.getSubscriptionRestHookEnabled()) {
ourLog.info("Enabling REST-hook subscriptions");
retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.RESTHOOK);
}
if (HapiProperties.getSubscriptionEmailEnabled()) {
ourLog.info("Enabling email subscriptions");
retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.EMAIL);
}
if (HapiProperties.getSubscriptionWebsocketEnabled()) {
ourLog.info("Enabling websocket subscriptions");
retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.WEBSOCKET);
}
@Bean
public ModelConfig modelConfig() {
ModelConfig modelConfig = new ModelConfig();
modelConfig.setAllowContainsSearches(this.allowContainsSearches);
modelConfig.setAllowExternalReferences(this.allowExternalReferences);
modelConfig.setDefaultSearchParamsCanBeOverridden(this.allowOverrideDefaultSearchParams);
modelConfig.setEmailFromAddress(this.emailFrom);
return retVal;
}
// You can enable these if you want to support Subscriptions from your server
if (this.subscriptionRestHookEnabled) {
modelConfig.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.RESTHOOK);
}
@Bean
public ModelConfig modelConfig() {
ModelConfig modelConfig = new ModelConfig();
modelConfig.setAllowContainsSearches(this.allowContainsSearches);
modelConfig.setAllowExternalReferences(this.allowExternalReferences);
modelConfig.setDefaultSearchParamsCanBeOverridden(this.allowOverrideDefaultSearchParams);
modelConfig.setEmailFromAddress(this.emailFrom);
if (this.subscriptionEmailEnabled) {
modelConfig.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.EMAIL);
}
// You can enable these if you want to support Subscriptions from your server
if (this.subscriptionRestHookEnabled) {
modelConfig.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.RESTHOOK);
}
return modelConfig;
}
if (this.subscriptionEmailEnabled) {
modelConfig.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.EMAIL);
}
/**
* The following bean configures the database connection. The 'url' property value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates that the server should save resources in a
* directory called "jpaserver_derby_files".
*
* A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
*/
@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();
retVal.setDriver(driver);
retVal.setUrl(HapiProperties.getDataSourceUrl());
retVal.setUsername(HapiProperties.getDataSourceUsername());
retVal.setPassword(HapiProperties.getDataSourcePassword());
retVal.setMaxTotal(HapiProperties.getDataSourceMaxPoolSize());
return retVal;
}
return modelConfig;
}
/**
* The following bean configures the database connection. The 'url' property value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates that the server should save resources in a
* directory called "jpaserver_derby_files".
* <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")
public BasicDataSource dataSource() throws ClassNotFoundException, NoSuchMethodException, IllegalAccessException, InvocationTargetException, InstantiationException {
BasicDataSource retVal = new BasicDataSource();
Driver driver = (Driver) Class.forName(HapiProperties.getDataSourceDriver()).getConstructor().newInstance();
retVal.setDriver(driver);
retVal.setUrl(HapiProperties.getDataSourceUrl());
retVal.setUsername(HapiProperties.getDataSourceUsername());
retVal.setPassword(HapiProperties.getDataSourcePassword());
retVal.setMaxTotal(HapiProperties.getDataSourceMaxPoolSize());
return retVal;
}
@Bean()
public IEmailSender emailSender() {
if (this.emailEnabled) {
JavaMailEmailSender retVal = new JavaMailEmailSender();
retVal.setSmtpServerHostname(this.emailHost);
retVal.setSmtpServerPort(this.emailPort);
retVal.setSmtpServerUsername(this.emailUsername);
retVal.setSmtpServerPassword(this.emailPassword);
Validate.notNull(mySubscriptionDeliveryHandlerFactory, "No subscription delivery handler");
mySubscriptionDeliveryHandlerFactory.setEmailSender(retVal);
/**
* Do some fancy logging to create a nice access log that has details about each incoming request.
*/
public IServerInterceptor loggingInterceptor() {
LoggingInterceptor retVal = new LoggingInterceptor();
retVal.setLoggerName(HapiProperties.getLoggerName());
retVal.setMessageFormat(HapiProperties.getLoggerFormat());
retVal.setErrorMessageFormat(HapiProperties.getLoggerErrorFormat());
retVal.setLogExceptions(HapiProperties.getLoggerLogExceptions());
return retVal;
}
return retVal;
}
/**
* This interceptor adds some pretty syntax highlighting in responses when a browser is detected
*/
@Bean(autowire = Autowire.BY_TYPE)
public IServerInterceptor responseHighlighterInterceptor() {
ResponseHighlighterInterceptor retVal = new ResponseHighlighterInterceptor();
return retVal;
}
@Autowired
private SubscriptionDeliveryHandlerFactory mySubscriptionDeliveryHandlerFactory;
@Bean()
public IEmailSender emailSender() {
if (this.emailEnabled) {
JavaMailEmailSender retVal = new JavaMailEmailSender();
retVal.setSmtpServerHostname(this.emailHost);
retVal.setSmtpServerPort(this.emailPort);
retVal.setSmtpServerUsername(this.emailUsername);
retVal.setSmtpServerPassword(this.emailPassword);
Validate.notNull(mySubscriptionDeliveryHandlerFactory, "No subscription delivery handler");
mySubscriptionDeliveryHandlerFactory.setEmailSender(retVal);
return retVal;
}
return null;
}
return null;
}
}

35
src/main/java/ca/uhn/fhir/jpa/starter/JpaRestfulServer.java
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@@ -2,9 +2,9 @@ package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.model.interceptor.executor.InterceptorService;
import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
@@ -17,21 +17,21 @@ import ca.uhn.fhir.jpa.provider.r4.TerminologyUploaderProviderR4;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.subscription.SubscriptionInterceptorLoader;
import ca.uhn.fhir.jpa.subscription.module.interceptor.SubscriptionDebugLogInterceptor;
import ca.uhn.fhir.jpa.util.ResourceProviderFactory;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Meta;
import org.springframework.web.cors.CorsConfiguration;
import org.springframework.context.ApplicationContext;
import org.springframework.web.cors.CorsConfiguration;
import javax.servlet.ServletException;
import java.util.Arrays;
import java.util.List;
public class JpaRestfulServer extends RestfulServer {
@@ -52,16 +52,16 @@ public class JpaRestfulServer extends RestfulServer {
* ResourceProviders are fetched from the Spring context
*/
FhirVersionEnum fhirVersion = HapiProperties.getFhirVersion();
List<IResourceProvider> resourceProviders;
ResourceProviderFactory resourceProviders;
Object systemProvider;
if (fhirVersion == FhirVersionEnum.DSTU2) {
resourceProviders = appCtx.getBean("myResourceProvidersDstu2", List.class);
resourceProviders = appCtx.getBean("myResourceProvidersDstu2", ResourceProviderFactory.class);
systemProvider = appCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class);
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
resourceProviders = appCtx.getBean("myResourceProvidersDstu3", List.class);
resourceProviders = appCtx.getBean("myResourceProvidersDstu3", ResourceProviderFactory.class);
systemProvider = appCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class);
} else if (fhirVersion == FhirVersionEnum.R4) {
resourceProviders = appCtx.getBean("myResourceProvidersR4", List.class);
resourceProviders = appCtx.getBean("myResourceProvidersR4", ResourceProviderFactory.class);
systemProvider = appCtx.getBean("mySystemProviderR4", JpaSystemProviderR4.class);
} else {
throw new IllegalStateException();
@@ -69,7 +69,7 @@ public class JpaRestfulServer extends RestfulServer {
setFhirContext(appCtx.getBean(FhirContext.class));
registerProviders(resourceProviders);
registerProviders(resourceProviders.createProviders());
registerProvider(systemProvider);
/*
@@ -133,9 +133,20 @@ public class JpaRestfulServer extends RestfulServer {
* HTML output when the request is detected to come from a
* browser.
*/
ResponseHighlighterInterceptor responseHighlighterInterceptor = appCtx.getBean(ResponseHighlighterInterceptor.class);
ResponseHighlighterInterceptor responseHighlighterInterceptor = new ResponseHighlighterInterceptor();
;
this.registerInterceptor(responseHighlighterInterceptor);
/*
* Add some logging for each request
*/
LoggingInterceptor loggingInterceptor = new LoggingInterceptor();
loggingInterceptor.setLoggerName(HapiProperties.getLoggerName());
loggingInterceptor.setMessageFormat(HapiProperties.getLoggerFormat());
loggingInterceptor.setErrorMessageFormat(HapiProperties.getLoggerErrorFormat());
loggingInterceptor.setLogExceptions(HapiProperties.getLoggerLogExceptions());
this.registerInterceptor(loggingInterceptor);
/*
* If you are hosting this server at a specific DNS name, the server will try to
* figure out the FHIR base URL based on what the web container tells it, but
@@ -172,7 +183,7 @@ public class JpaRestfulServer extends RestfulServer {
// Define your CORS configuration. This is an example
// showing a typical setup. You should customize this
// to your specific needs
if(HapiProperties.getCorsEnabled()) {
if (HapiProperties.getCorsEnabled()) {
CorsConfiguration config = new CorsConfiguration();
config.addAllowedHeader("x-fhir-starter");
config.addAllowedHeader("Origin");
@@ -202,7 +213,7 @@ public class JpaRestfulServer extends RestfulServer {
subscriptionInterceptorLoader.registerInterceptors();
// Subscription debug logging
InterceptorService interceptorService = (InterceptorService) appCtx.getBean("interceptorService");
IInterceptorService interceptorService = appCtx.getBean(IInterceptorService.class);
interceptorService.registerInterceptor(new SubscriptionDebugLogInterceptor());
}