Personal-Twin/hapi-fhir-jpaserver-starter
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Feat/restructuring (#422)

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* Did restructuring and made repo validation interceptor an optional bean instead as it makes it more clean

* Moved construction of FHIR servlet into a bean for better reuse of others that would like to depend directly on this library

* Disabled default validation enabled
This commit is contained in:
Jens Kristian Villadsen
2022-09-10 21:14:01 +02:00
committed by GitHub
parent c5e460dab0
commit d660d5f76d
25 changed files with 553 additions and 726 deletions
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6
src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java
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@@ -81,7 +81,7 @@ public class AppProperties {
private Integer bundle_batch_pool_size = 20; private Integer bundle_batch_pool_size = 20;
private Integer bundle_batch_pool_max_size = 100; private Integer bundle_batch_pool_max_size = 100;
private List<String> local_base_urls = new ArrayList<>(); private final List<String> local_base_urls = new ArrayList<>();
public Boolean getOpenapi_enabled() { public Boolean getOpenapi_enabled() {
return openapi_enabled; return openapi_enabled;
@@ -203,10 +203,6 @@ public class AppProperties {
this.supported_resource_types = supported_resource_types; this.supported_resource_types = supported_resource_types;
} }
public List<String> getSupported_resource_types(List<String> supported_resource_types) {
return this.supported_resource_types;
}
public Logger getLogger() { public Logger getLogger() {
return logger; return logger;
} }

12
src/main/java/ca/uhn/fhir/jpa/starter/Application.java
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@@ -3,11 +3,13 @@ package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.batch2.jobs.config.Batch2JobsConfig; import ca.uhn.fhir.batch2.jobs.config.Batch2JobsConfig;
import ca.uhn.fhir.jpa.batch2.JpaBatch2Config; import ca.uhn.fhir.jpa.batch2.JpaBatch2Config;
import ca.uhn.fhir.jpa.starter.annotations.OnEitherVersion; import ca.uhn.fhir.jpa.starter.annotations.OnEitherVersion;
import ca.uhn.fhir.jpa.starter.common.FhirTesterConfig;
import ca.uhn.fhir.jpa.starter.mdm.MdmConfig; import ca.uhn.fhir.jpa.starter.mdm.MdmConfig;
import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig; 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.SubscriptionProcessorConfig;
import ca.uhn.fhir.jpa.subscription.match.config.WebsocketDispatcherConfig; import ca.uhn.fhir.jpa.subscription.match.config.WebsocketDispatcherConfig;
import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig; import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
import ca.uhn.fhir.rest.server.RestfulServer;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.AutowireCapableBeanFactory; import org.springframework.beans.factory.config.AutowireCapableBeanFactory;
import org.springframework.boot.SpringApplication; import org.springframework.boot.SpringApplication;
@@ -23,8 +25,7 @@ import org.springframework.context.annotation.Import;
import org.springframework.web.context.support.AnnotationConfigWebApplicationContext; import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
import org.springframework.web.servlet.DispatcherServlet; import org.springframework.web.servlet.DispatcherServlet;
@ServletComponentScan(basePackageClasses = { @ServletComponentScan(basePackageClasses = {RestfulServer.class})
JpaRestfulServer.class})
@SpringBootApplication(exclude = {ElasticsearchRestClientAutoConfiguration.class}) @SpringBootApplication(exclude = {ElasticsearchRestClientAutoConfiguration.class})
@Import({ @Import({
SubscriptionSubmitterConfig.class, SubscriptionSubmitterConfig.class,
@@ -56,11 +57,10 @@ public class Application extends SpringBootServletInitializer {
@Bean @Bean
@Conditional(OnEitherVersion.class) @Conditional(OnEitherVersion.class)
public ServletRegistrationBean hapiServletRegistration() { public ServletRegistrationBean hapiServletRegistration(RestfulServer restfulServer) {
ServletRegistrationBean servletRegistrationBean = new ServletRegistrationBean(); ServletRegistrationBean servletRegistrationBean = new ServletRegistrationBean();
JpaRestfulServer jpaRestfulServer = new JpaRestfulServer(); beanFactory.autowireBean(restfulServer);
beanFactory.autowireBean(jpaRestfulServer); servletRegistrationBean.setServlet(restfulServer);
servletRegistrationBean.setServlet(jpaRestfulServer);
servletRegistrationBean.addUrlMappings("/fhir/*"); servletRegistrationBean.addUrlMappings("/fhir/*");
servletRegistrationBean.setLoadOnStartup(1); servletRegistrationBean.setLoadOnStartup(1);

429
src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java
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@@ -1,429 +0,0 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.batch2.jobs.imprt.BulkDataImportProvider;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexProvider;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.cql.common.provider.CqlProviderLoader;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.binary.interceptor.BinaryStorageInterceptor;
import ca.uhn.fhir.jpa.binary.provider.BinaryAccessProvider;
import ca.uhn.fhir.jpa.bulk.export.provider.BulkDataExportProvider;
import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
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.*;
import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
import ca.uhn.fhir.mdm.provider.MdmProviderLoader;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.narrative.INarrativeGenerator;
import ca.uhn.fhir.narrative2.NullNarrativeGenerator;
import ca.uhn.fhir.rest.openapi.OpenApiInterceptor;
import ca.uhn.fhir.rest.server.*;
import ca.uhn.fhir.rest.server.interceptor.*;
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.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import com.google.common.base.Strings;
import com.google.common.collect.ImmutableList;
import org.hl7.fhir.r4.model.Bundle.BundleType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.http.HttpHeaders;
import org.springframework.web.cors.CorsConfiguration;
import javax.servlet.ServletException;
import java.util.*;
import java.util.stream.Collectors;
public class BaseJpaRestfulServer extends RestfulServer {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaRestfulServer.class);
private static final long serialVersionUID = 1L;
@Autowired
DaoRegistry daoRegistry;
@Autowired
DaoConfig daoConfig;
@Autowired
ISearchParamRegistry searchParamRegistry;
@Autowired
IFhirSystemDao fhirSystemDao;
@Autowired
ResourceProviderFactory resourceProviderFactory;
@Autowired
IJpaSystemProvider jpaSystemProvider;
@Autowired
ValueSetOperationProvider myValueSetOperationProvider;
@Autowired
IInterceptorBroadcaster interceptorBroadcaster;
@Autowired
DatabaseBackedPagingProvider databaseBackedPagingProvider;
@Autowired
IInterceptorService interceptorService;
@Autowired
IValidatorModule validatorModule;
@Autowired
Optional<GraphQLProvider> graphQLProvider;
@Autowired
BulkDataExportProvider bulkDataExportProvider;
@Autowired
BulkDataImportProvider bulkDataImportProvider;
@Autowired
PartitionManagementProvider partitionManagementProvider;
@Autowired
ValueSetOperationProvider valueSetOperationProvider;
@Autowired
ReindexProvider reindexProvider;
@Autowired
BinaryStorageInterceptor binaryStorageInterceptor;
@Autowired
Optional<BinaryAccessProvider> binaryAccessProvider;
@Autowired
IPackageInstallerSvc packageInstallerSvc;
@Autowired
AppProperties appProperties;
@Autowired
ApplicationContext myApplicationContext;
@Autowired(required = false)
IRepositoryValidationInterceptorFactory factory;
// These are set only if the features are enabled
@Autowired
Optional<CqlProviderLoader> cqlProviderLoader;
@Autowired
Optional<MdmProviderLoader> mdmProviderProvider;
@Autowired
private IValidationSupport myValidationSupport;
public BaseJpaRestfulServer() {
}
@SuppressWarnings("unchecked")
@Override
protected void initialize() throws ServletException {
super.initialize();
/*
* Create a FhirContext object that uses the version of FHIR
* specified in the properties file.
*/
// Customize supported resource types
List<String> supportedResourceTypes = appProperties.getSupported_resource_types();
if (!supportedResourceTypes.isEmpty()) {
if (!supportedResourceTypes.contains("SearchParameter")) {
supportedResourceTypes.add("SearchParameter");
}
daoRegistry.setSupportedResourceTypes(supportedResourceTypes);
}
setFhirContext(fhirSystemDao.getContext());
/*
* Order matters - the MDM provider registers itself on the resourceProviderFactory - hence the loading must be done
* ahead of provider registration
*/
if(appProperties.getMdm_enabled())
mdmProviderProvider.get().loadProvider();
registerProviders(resourceProviderFactory.createProviders());
registerProvider(jpaSystemProvider);
/*
* 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
* is a nice addition.
*
* You can also create your own subclass of the conformance provider if you need to
* provide further customization of your server's CapabilityStatement
*/
FhirVersionEnum fhirVersion = fhirSystemDao.getContext().getVersion().getVersion();
if (fhirVersion == FhirVersionEnum.DSTU2) {
JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, fhirSystemDao,
daoConfig);
confProvider.setImplementationDescription("HAPI FHIR DSTU2 Server");
setServerConformanceProvider(confProvider);
} else {
if (fhirVersion == FhirVersionEnum.DSTU3) {
JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, fhirSystemDao,
daoConfig, searchParamRegistry);
confProvider.setImplementationDescription("HAPI FHIR DSTU3 Server");
setServerConformanceProvider(confProvider);
} else if (fhirVersion == FhirVersionEnum.R4) {
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(this, fhirSystemDao,
daoConfig, searchParamRegistry, myValidationSupport);
confProvider.setImplementationDescription("HAPI FHIR R4 Server");
setServerConformanceProvider(confProvider);
} else if (fhirVersion == FhirVersionEnum.R5) {
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(this, fhirSystemDao,
daoConfig, searchParamRegistry, myValidationSupport);
confProvider.setImplementationDescription("HAPI FHIR R5 Server");
setServerConformanceProvider(confProvider);
} else {
throw new IllegalStateException();
}
}
/*
* ETag Support
*/
if (appProperties.getEtag_support_enabled() == false)
setETagSupport(ETagSupportEnum.DISABLED);
/*
* This server tries to dynamically generate narratives
*/
FhirContext ctx = getFhirContext();
INarrativeGenerator theNarrativeGenerator =
appProperties.getNarrative_enabled() ?
new DefaultThymeleafNarrativeGenerator() :
new NullNarrativeGenerator();
ctx.setNarrativeGenerator(theNarrativeGenerator);
/*
* Default to JSON and pretty printing
*/
setDefaultPrettyPrint(appProperties.getDefault_pretty_print());
/*
* Default encoding
*/
setDefaultResponseEncoding(appProperties.getDefault_encoding());
/*
* This configures the server to page search results to and from
* the database, instead of only paging them to memory. This may mean
* a performance hit when performing searches that return lots of results,
* but makes the server much more scalable.
*/
setPagingProvider(databaseBackedPagingProvider);
/*
* This interceptor formats the output using nice colourful
* HTML output when the request is detected to come from a
* browser.
*/
ResponseHighlighterInterceptor responseHighlighterInterceptor = new ResponseHighlighterInterceptor();
this.registerInterceptor(responseHighlighterInterceptor);
if (appProperties.getFhirpath_interceptor_enabled()) {
registerInterceptor(new FhirPathFilterInterceptor());
}
/*
* Add some logging for each request
*/
LoggingInterceptor loggingInterceptor = new LoggingInterceptor();
loggingInterceptor.setLoggerName(appProperties.getLogger().getName());
loggingInterceptor.setMessageFormat(appProperties.getLogger().getFormat());
loggingInterceptor.setErrorMessageFormat(appProperties.getLogger().getError_format());
loggingInterceptor.setLogExceptions(appProperties.getLogger().getLog_exceptions());
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
* 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 = appProperties.getServer_address();
if (!Strings.isNullOrEmpty(serverAddress)) {
setServerAddressStrategy(new HardcodedServerAddressStrategy(serverAddress));
} else if (appProperties.getUse_apache_address_strategy()) {
boolean useHttps = appProperties.getUse_apache_address_strategy_https();
setServerAddressStrategy(useHttps ? ApacheProxyAddressStrategy.forHttps() :
ApacheProxyAddressStrategy.forHttp());
} else {
setServerAddressStrategy(new IncomingRequestAddressStrategy());
}
/*
* If you are using DSTU3+, you may want to add a terminology uploader, which allows
* uploading of external terminologies such as Snomed CT. Note that this uploader
* does not have any security attached (any anonymous user may use it by default)
* so it is a potential security vulnerability. Consider using an AuthorizationInterceptor
* with this feature.
*/
if (ctx.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) { // <-- ENABLED RIGHT NOW
registerProvider(myApplicationContext.getBean(TerminologyUploaderProvider.class));
}
// If you want to enable the $trigger-subscription operation to allow
// manual triggering of a subscription delivery, enable this provider
if (true) { // <-- ENABLED RIGHT NOW
registerProvider(myApplicationContext.getBean(SubscriptionTriggeringProvider.class));
}
// Define your CORS configuration. This is an example
// showing a typical setup. You should customize this
// to your specific needs
if (appProperties.getCors() != null) {
ourLog.info("CORS is enabled on this server");
CorsConfiguration config = new CorsConfiguration();
config.addAllowedHeader(HttpHeaders.ORIGIN);
config.addAllowedHeader(HttpHeaders.ACCEPT);
config.addAllowedHeader(HttpHeaders.CONTENT_TYPE);
config.addAllowedHeader(HttpHeaders.AUTHORIZATION);
config.addAllowedHeader(HttpHeaders.CACHE_CONTROL);
config.addAllowedHeader("x-fhir-starter");
config.addAllowedHeader("X-Requested-With");
config.addAllowedHeader("Prefer");
List<String> allAllowedCORSOrigins = appProperties.getCors().getAllowed_origin();
allAllowedCORSOrigins.forEach(config::addAllowedOriginPattern);
ourLog.info("CORS allows the following origins: " + String.join(", ", allAllowedCORSOrigins));
config.addExposedHeader("Location");
config.addExposedHeader("Content-Location");
config.setAllowedMethods(
Arrays.asList("GET", "POST", "PUT", "DELETE", "OPTIONS", "PATCH", "HEAD"));
config.setAllowCredentials(appProperties.getCors().getAllow_Credentials());
// Create the interceptor and register it
CorsInterceptor interceptor = new CorsInterceptor(config);
registerInterceptor(interceptor);
} else {
ourLog.info("CORS is disabled on this server");
}
// If subscriptions are enabled, we want to register the interceptor that
// will activate them and match results against them
if (appProperties.getSubscription() != null) {
// Subscription debug logging
interceptorService.registerInterceptor(new SubscriptionDebugLogInterceptor());
}
// Cascading deletes
if (appProperties.getAllow_cascading_deletes()) {
CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(ctx,
daoRegistry, interceptorBroadcaster);
getInterceptorService().registerInterceptor(cascadingDeleteInterceptor);
}
// Binary Storage
if (appProperties.getBinary_storage_enabled() && binaryAccessProvider.isPresent()) {
registerProvider(binaryAccessProvider.get());
getInterceptorService().registerInterceptor(binaryStorageInterceptor);
}
// Validation
if (validatorModule != null) {
if (appProperties.getValidation().getRequests_enabled()) {
RequestValidatingInterceptor interceptor = new RequestValidatingInterceptor();
interceptor.setFailOnSeverity(ResultSeverityEnum.ERROR);
interceptor.setValidatorModules(Collections.singletonList(validatorModule));
registerInterceptor(interceptor);
}
if (appProperties.getValidation().getResponses_enabled()) {
ResponseValidatingInterceptor interceptor = new ResponseValidatingInterceptor();
interceptor.setFailOnSeverity(ResultSeverityEnum.ERROR);
interceptor.setValidatorModules(Collections.singletonList(validatorModule));
registerInterceptor(interceptor);
}
}
// GraphQL
if (appProperties.getGraphql_enabled()) {
if (fhirVersion.isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
registerProvider(graphQLProvider.get());
}
}
if (appProperties.getAllowed_bundle_types() != null) {
daoConfig.setBundleTypesAllowedForStorage(appProperties.getAllowed_bundle_types().stream().map(BundleType::toCode).collect(Collectors.toSet()));
}
daoConfig.setDeferIndexingForCodesystemsOfSize(appProperties.getDefer_indexing_for_codesystems_of_size());
if (appProperties.getOpenapi_enabled()) {
registerInterceptor(new OpenApiInterceptor());
}
// Bulk Export
if (appProperties.getBulk_export_enabled()) {
registerProvider(bulkDataExportProvider);
}
//Bulk Import
if (appProperties.getBulk_import_enabled()) {
registerProvider(bulkDataImportProvider);
}
// valueSet Operations i.e $expand
registerProvider(myValueSetOperationProvider);
//reindex Provider $reindex
registerProvider(reindexProvider);
// Partitioning
if (appProperties.getPartitioning() != null) {
registerInterceptor(new RequestTenantPartitionInterceptor());
setTenantIdentificationStrategy(new UrlBaseTenantIdentificationStrategy());
registerProviders(partitionManagementProvider);
}
if (appProperties.getClient_id_strategy() == DaoConfig.ClientIdStrategyEnum.ANY) {
daoConfig.setResourceServerIdStrategy(DaoConfig.IdStrategyEnum.UUID);
daoConfig.setResourceClientIdStrategy(appProperties.getClient_id_strategy());
}
//Parallel Batch GET execution settings
daoConfig.setBundleBatchPoolSize(appProperties.getBundle_batch_pool_size());
daoConfig.setBundleBatchPoolSize(appProperties.getBundle_batch_pool_max_size());
if (appProperties.getImplementationGuides() != null) {
Map<String, AppProperties.ImplementationGuide> guides = appProperties.getImplementationGuides();
for (Map.Entry<String, AppProperties.ImplementationGuide> guide : guides.entrySet()) {
PackageInstallationSpec packageInstallationSpec = new PackageInstallationSpec()
.setPackageUrl(guide.getValue().getUrl())
.setName(guide.getValue().getName())
.setVersion(guide.getValue().getVersion())
.setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
if(appProperties.getInstall_transitive_ig_dependencies()) {
packageInstallationSpec.setFetchDependencies(true);
packageInstallationSpec.setDependencyExcludes(ImmutableList.of("hl7.fhir.r2.core", "hl7.fhir.r3.core", "hl7.fhir.r4.core", "hl7.fhir.r5.core"));
}
packageInstallerSvc.install(packageInstallationSpec);
}
}
if(factory != null) {
interceptorService.registerInterceptor(factory.buildUsingStoredStructureDefinitions());
}
if (appProperties.getLastn_enabled()) {
daoConfig.setLastNEnabled(true);
}
if(appProperties.getInline_resource_storage_below_size() != 0){
daoConfig.setInlineResourceTextBelowSize(appProperties.getInline_resource_storage_below_size());
}
daoConfig.setStoreResourceInHSearchIndex(appProperties.getStore_resource_in_lucene_index_enabled());
daoConfig.getModelConfig().setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
daoConfig.getModelConfig().setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
}
}

28
src/main/java/ca/uhn/fhir/jpa/starter/JpaRestfulServer.java
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@@ -1,28 +0,0 @@
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();
// Add your own customization here
}
}

128
src/main/java/ca/uhn/fhir/jpa/starter/StarterJpaConfig.java
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@@ -1,128 +0,0 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.IDaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.batch.config.NonPersistedBatchConfigurer;
import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
import ca.uhn.fhir.jpa.config.util.ResourceCountCacheUtil;
import ca.uhn.fhir.jpa.config.util.ValidationSupportConfigUtil;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.mdm.MdmLinkDaoJpaImpl;
import ca.uhn.fhir.jpa.dao.search.HSearchSortHelperImpl;
import ca.uhn.fhir.jpa.dao.search.IHSearchSortHelper;
import ca.uhn.fhir.jpa.provider.DaoRegistryResourceSupportedSvc;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChain;
import ca.uhn.fhir.mdm.dao.IMdmLinkDao;
import ca.uhn.fhir.rest.api.IResourceSupportedSvc;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
import org.springframework.batch.core.configuration.annotation.BatchConfigurer;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Primary;
import org.springframework.core.env.ConfigurableEnvironment;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
@Configuration
public class StarterJpaConfig {
@Bean
public IFulltextSearchSvc fullTextSearchSvc() {
return new FulltextSearchSvcImpl();
}
@Bean
public IStaleSearchDeletingSvc staleSearchDeletingSvc() {
return new StaleSearchDeletingSvcImpl();
}
@Primary
@Bean
public CachingValidationSupport validationSupportChain(JpaValidationSupportChain theJpaValidationSupportChain) {
return ValidationSupportConfigUtil.newCachingValidationSupport(theJpaValidationSupportChain);
}
@Bean
public BatchConfigurer batchConfigurer() {
return new NonPersistedBatchConfigurer();
}
@Autowired
AppProperties appProperties;
@Autowired
private DataSource myDataSource;
@Autowired
private ConfigurableEnvironment configurableEnvironment;
/**
* Customize 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.
*/
@Bean
public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
DatabaseBackedPagingProvider pagingProvider = new DatabaseBackedPagingProvider();
pagingProvider.setDefaultPageSize(appProperties.getDefault_page_size());
pagingProvider.setMaximumPageSize(appProperties.getMax_page_size());
return pagingProvider;
}
@Bean
public IResourceSupportedSvc resourceSupportedSvc(IDaoRegistry theDaoRegistry) {
return new DaoRegistryResourceSupportedSvc(theDaoRegistry);
}
@Bean(name = "myResourceCountsCache")
public ResourceCountCache resourceCountsCache(IFhirSystemDao<?, ?> theSystemDao) {
return ResourceCountCacheUtil.newResourceCountCache(theSystemDao);
}
@Primary
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory(
ConfigurableListableBeanFactory myConfigurableListableBeanFactory, FhirContext theFhirContext) {
LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(myConfigurableListableBeanFactory, theFhirContext);
retVal.setPersistenceUnitName("HAPI_PU");
try {
retVal.setDataSource(myDataSource);
} catch (Exception e) {
throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
}
retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment, myConfigurableListableBeanFactory));
return retVal;
}
@Bean
@Primary
public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
JpaTransactionManager retVal = new JpaTransactionManager();
retVal.setEntityManagerFactory(entityManagerFactory);
return retVal;
}
@Autowired
private ISearchParamRegistry mySearchParamRegistry;
@Bean
public IHSearchSortHelper hSearchSortHelper() {
return new HSearchSortHelperImpl(mySearchParamRegistry);
}
@Bean
public IMdmLinkDao<?> mdmLinkDao(){
return new MdmLinkDaoJpaImpl();
}
}

10
src/main/java/ca/uhn/fhir/jpa/starter/ElasticsearchConfig.java → src/main/java/ca/uhn/fhir/jpa/starter/common/ElasticsearchConfig.java
View File

@@ -1,7 +1,7 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter.common;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl; import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
import org.springframework.beans.factory.annotation.Autowired; import ca.uhn.fhir.jpa.starter.util.EnvironmentHelper;
import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration; import org.springframework.context.annotation.Configuration;
import org.springframework.core.env.ConfigurableEnvironment; import org.springframework.core.env.ConfigurableEnvironment;
@@ -10,12 +10,8 @@ import org.springframework.core.env.ConfigurableEnvironment;
@Configuration @Configuration
public class ElasticsearchConfig { public class ElasticsearchConfig {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ElasticsearchConfig.class); private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ElasticsearchConfig.class);
@Autowired
private ConfigurableEnvironment configurableEnvironment;
@Bean @Bean
public ElasticsearchSvcImpl elasticsearchSvc() { public ElasticsearchSvcImpl elasticsearchSvc(ConfigurableEnvironment configurableEnvironment) {
if (EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment)) { if (EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment)) {
String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment); String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment);
if (elasticsearchUrl.startsWith("http")) { if (elasticsearchUrl.startsWith("http")) {

99
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java → src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigCommon.java
View File

@@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter.common;
import ca.uhn.fhir.jpa.api.config.DaoConfig; import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.binary.api.IBinaryStorageSvc; import ca.uhn.fhir.jpa.binary.api.IBinaryStorageSvc;
@@ -7,6 +7,8 @@ import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider;
import ca.uhn.fhir.jpa.model.config.PartitionSettings; import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.config.PartitionSettings.CrossPartitionReferenceMode; import ca.uhn.fhir.jpa.model.config.PartitionSettings.CrossPartitionReferenceMode;
import ca.uhn.fhir.jpa.model.entity.ModelConfig; import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.starter.AppProperties;
import ca.uhn.fhir.jpa.starter.util.JpaHibernatePropertiesProvider;
import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory; import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory;
import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailSenderImpl; import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailSenderImpl;
import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender; import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
@@ -14,6 +16,7 @@ import ca.uhn.fhir.rest.server.mail.IMailSvc;
import ca.uhn.fhir.rest.server.mail.MailConfig; import ca.uhn.fhir.rest.server.mail.MailConfig;
import ca.uhn.fhir.rest.server.mail.MailSvc; import ca.uhn.fhir.rest.server.mail.MailSvc;
import com.google.common.base.Strings; import com.google.common.base.Strings;
import org.hl7.fhir.r4.model.Bundle.BundleType;
import org.hl7.fhir.dstu2.model.Subscription; import org.hl7.fhir.dstu2.model.Subscription;
import org.springframework.boot.env.YamlPropertySourceLoader; import org.springframework.boot.env.YamlPropertySourceLoader;
import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Bean;
@@ -25,6 +28,7 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
import java.util.HashSet; import java.util.HashSet;
import java.util.Optional; import java.util.Optional;
import java.util.stream.Collectors;
/** /**
* This is the primary configuration file for the example server * This is the primary configuration file for the example server
@@ -78,54 +82,85 @@ public class FhirServerConfigCommon {
*/ */
@Bean @Bean
public DaoConfig daoConfig(AppProperties appProperties) { public DaoConfig daoConfig(AppProperties appProperties) {
DaoConfig retVal = new DaoConfig(); DaoConfig daoConfig = new DaoConfig();
retVal.setIndexMissingFields(appProperties.getEnable_index_missing_fields() ? DaoConfig.IndexEnabledEnum.ENABLED : DaoConfig.IndexEnabledEnum.DISABLED); daoConfig.setIndexMissingFields(appProperties.getEnable_index_missing_fields() ? DaoConfig.IndexEnabledEnum.ENABLED : DaoConfig.IndexEnabledEnum.DISABLED);
retVal.setAutoCreatePlaceholderReferenceTargets(appProperties.getAuto_create_placeholder_reference_targets()); daoConfig.setAutoCreatePlaceholderReferenceTargets(appProperties.getAuto_create_placeholder_reference_targets());
retVal.setEnforceReferentialIntegrityOnWrite(appProperties.getEnforce_referential_integrity_on_write()); daoConfig.setEnforceReferentialIntegrityOnWrite(appProperties.getEnforce_referential_integrity_on_write());
retVal.setEnforceReferentialIntegrityOnDelete(appProperties.getEnforce_referential_integrity_on_delete()); daoConfig.setEnforceReferentialIntegrityOnDelete(appProperties.getEnforce_referential_integrity_on_delete());
retVal.setAllowContainsSearches(appProperties.getAllow_contains_searches()); daoConfig.setAllowContainsSearches(appProperties.getAllow_contains_searches());
retVal.setAllowMultipleDelete(appProperties.getAllow_multiple_delete()); daoConfig.setAllowMultipleDelete(appProperties.getAllow_multiple_delete());
retVal.setAllowExternalReferences(appProperties.getAllow_external_references()); daoConfig.setAllowExternalReferences(appProperties.getAllow_external_references());
retVal.setSchedulingDisabled(!appProperties.getDao_scheduling_enabled()); daoConfig.setSchedulingDisabled(!appProperties.getDao_scheduling_enabled());
retVal.setDeleteExpungeEnabled(appProperties.getDelete_expunge_enabled()); daoConfig.setDeleteExpungeEnabled(appProperties.getDelete_expunge_enabled());
retVal.setExpungeEnabled(appProperties.getExpunge_enabled()); daoConfig.setExpungeEnabled(appProperties.getExpunge_enabled());
if(appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null) if(appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null)
retVal.setEmailFromAddress(appProperties.getSubscription().getEmail().getFrom()); daoConfig.setEmailFromAddress(appProperties.getSubscription().getEmail().getFrom());
Integer maxFetchSize = appProperties.getMax_page_size(); Integer maxFetchSize = appProperties.getMax_page_size();
retVal.setFetchSizeDefaultMaximum(maxFetchSize); daoConfig.setFetchSizeDefaultMaximum(maxFetchSize);
ourLog.info("Server configured to have a maximum fetch size of " + (maxFetchSize == Integer.MAX_VALUE ? "'unlimited'" : maxFetchSize)); ourLog.info("Server configured to have a maximum fetch size of " + (maxFetchSize == Integer.MAX_VALUE ? "'unlimited'" : maxFetchSize));
Long reuseCachedSearchResultsMillis = appProperties.getReuse_cached_search_results_millis(); Long reuseCachedSearchResultsMillis = appProperties.getReuse_cached_search_results_millis();
retVal.setReuseCachedSearchResultsForMillis(reuseCachedSearchResultsMillis); daoConfig.setReuseCachedSearchResultsForMillis(reuseCachedSearchResultsMillis);
ourLog.info("Server configured to cache search results for {} milliseconds", reuseCachedSearchResultsMillis); ourLog.info("Server configured to cache search results for {} milliseconds", reuseCachedSearchResultsMillis);
Long retainCachedSearchesMinutes = appProperties.getRetain_cached_searches_mins(); Long retainCachedSearchesMinutes = appProperties.getRetain_cached_searches_mins();
retVal.setExpireSearchResultsAfterMillis(retainCachedSearchesMinutes * 60 * 1000); daoConfig.setExpireSearchResultsAfterMillis(retainCachedSearchesMinutes * 60 * 1000);
if(appProperties.getSubscription() != null) { if(appProperties.getSubscription() != null) {
// Subscriptions are enabled by channel type // Subscriptions are enabled by channel type
if (appProperties.getSubscription().getResthook_enabled()) { if (appProperties.getSubscription().getResthook_enabled()) {
ourLog.info("Enabling REST-hook subscriptions"); ourLog.info("Enabling REST-hook subscriptions");
retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.RESTHOOK); daoConfig.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.RESTHOOK);
} }
if (appProperties.getSubscription().getEmail() != null) { if (appProperties.getSubscription().getEmail() != null) {
ourLog.info("Enabling email subscriptions"); ourLog.info("Enabling email subscriptions");
retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.EMAIL); daoConfig.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.EMAIL);
} }
if (appProperties.getSubscription().getWebsocket_enabled()) { if (appProperties.getSubscription().getWebsocket_enabled()) {
ourLog.info("Enabling websocket subscriptions"); ourLog.info("Enabling websocket subscriptions");
retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.WEBSOCKET); daoConfig.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.WEBSOCKET);
} }
} }
retVal.setFilterParameterEnabled(appProperties.getFilter_search_enabled()); daoConfig.setFilterParameterEnabled(appProperties.getFilter_search_enabled());
retVal.setAdvancedHSearchIndexing(appProperties.getAdvanced_lucene_indexing()); daoConfig.setAdvancedHSearchIndexing(appProperties.getAdvanced_lucene_indexing());
retVal.setTreatBaseUrlsAsLocal(new HashSet<>(appProperties.getLocal_base_urls())); daoConfig.setTreatBaseUrlsAsLocal(new HashSet<>(appProperties.getLocal_base_urls()));
return retVal; if (appProperties.getLastn_enabled()) {
daoConfig.setLastNEnabled(true);
}
if(appProperties.getInline_resource_storage_below_size() != 0){
daoConfig.setInlineResourceTextBelowSize(appProperties.getInline_resource_storage_below_size());
}
daoConfig.setStoreResourceInHSearchIndex(appProperties.getStore_resource_in_lucene_index_enabled());
daoConfig.getModelConfig().setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
daoConfig.getModelConfig().setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
if (appProperties.getAllowed_bundle_types() != null) {
daoConfig.setBundleTypesAllowedForStorage(appProperties.getAllowed_bundle_types().stream().map(BundleType::toCode).collect(Collectors.toSet()));
}
daoConfig.setDeferIndexingForCodesystemsOfSize(appProperties.getDefer_indexing_for_codesystems_of_size());
if (appProperties.getClient_id_strategy() == DaoConfig.ClientIdStrategyEnum.ANY) {
daoConfig.setResourceServerIdStrategy(DaoConfig.IdStrategyEnum.UUID);
daoConfig.setResourceClientIdStrategy(appProperties.getClient_id_strategy());
}
//Parallel Batch GET execution settings
daoConfig.setBundleBatchPoolSize(appProperties.getBundle_batch_pool_size());
daoConfig.setBundleBatchPoolSize(appProperties.getBundle_batch_pool_max_size());
return daoConfig;
} }
@Bean @Bean
@@ -183,24 +218,6 @@ public class FhirServerConfigCommon {
return modelConfig; 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;
}*/
@Lazy @Lazy
@Bean @Bean
public IBinaryStorageSvc binaryStorageSvc(AppProperties appProperties) { public IBinaryStorageSvc binaryStorageSvc(AppProperties appProperties) {

2
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java → src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigDstu2.java
View File

@@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter.common;
import ca.uhn.fhir.jpa.config.JpaDstu2Config; import ca.uhn.fhir.jpa.config.JpaDstu2Config;
import ca.uhn.fhir.jpa.starter.annotations.OnDSTU2Condition; import ca.uhn.fhir.jpa.starter.annotations.OnDSTU2Condition;

3
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java → src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigDstu3.java
View File

@@ -1,9 +1,8 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter.common;
import ca.uhn.fhir.jpa.config.dstu3.JpaDstu3Config; import ca.uhn.fhir.jpa.config.dstu3.JpaDstu3Config;
import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition; import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition;
import ca.uhn.fhir.jpa.starter.cql.StarterCqlDstu3Config; import ca.uhn.fhir.jpa.starter.cql.StarterCqlDstu3Config;
import ca.uhn.fhir.jpa.starter.mdm.MdmConfig;
import org.springframework.context.annotation.Conditional; import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration; import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import; import org.springframework.context.annotation.Import;

3
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java → src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigR4.java
View File

@@ -1,9 +1,8 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter.common;
import ca.uhn.fhir.jpa.config.r4.JpaR4Config; import ca.uhn.fhir.jpa.config.r4.JpaR4Config;
import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition; import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
import ca.uhn.fhir.jpa.starter.cql.StarterCqlR4Config; import ca.uhn.fhir.jpa.starter.cql.StarterCqlR4Config;
import ca.uhn.fhir.jpa.starter.mdm.MdmConfig;
import org.springframework.context.annotation.Conditional; import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration; import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import; import org.springframework.context.annotation.Import;

2
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java → src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigR5.java
View File

@@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter.common;
import ca.uhn.fhir.jpa.config.r5.JpaR5Config; import ca.uhn.fhir.jpa.config.r5.JpaR5Config;
import ca.uhn.fhir.jpa.starter.annotations.OnR5Condition; import ca.uhn.fhir.jpa.starter.annotations.OnR5Condition;

15
src/main/java/ca/uhn/fhir/jpa/starter/FhirTesterConfig.java → src/main/java/ca/uhn/fhir/jpa/starter/common/FhirTesterConfig.java
View File

@@ -1,5 +1,6 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter.common;
import ca.uhn.fhir.jpa.starter.AppProperties;
import ca.uhn.fhir.to.FhirTesterMvcConfig; import ca.uhn.fhir.to.FhirTesterMvcConfig;
import ca.uhn.fhir.to.TesterConfig; import ca.uhn.fhir.to.TesterConfig;
import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Bean;
@@ -36,15 +37,15 @@ public class FhirTesterConfig {
@Bean @Bean
public TesterConfig testerConfig(AppProperties appProperties) { public TesterConfig testerConfig(AppProperties appProperties) {
TesterConfig retVal = new TesterConfig(); TesterConfig retVal = new TesterConfig();
appProperties.getTester().entrySet().stream().forEach(t -> { appProperties.getTester().forEach((key, value) -> {
retVal retVal
.addServer() .addServer()
.withId(t.getKey()) .withId(key)
.withFhirVersion(t.getValue().getFhir_version()) .withFhirVersion(value.getFhir_version())
.withBaseUrl(t.getValue().getServer_address()) .withBaseUrl(value.getServer_address())
.withName(t.getValue().getName()); .withName(value.getName());
retVal.setRefuseToFetchThirdPartyUrls( retVal.setRefuseToFetchThirdPartyUrls(
t.getValue().getRefuse_to_fetch_third_party_urls()); value.getRefuse_to_fetch_third_party_urls());
}); });
return retVal; return retVal;

433
src/main/java/ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.java Normal file
View File

@@ -0,0 +1,433 @@
package ca.uhn.fhir.jpa.starter.common;
import ca.uhn.fhir.batch2.jobs.imprt.BulkDataImportProvider;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexProvider;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.jpa.api.IDaoRegistry;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.batch.config.NonPersistedBatchConfigurer;
import ca.uhn.fhir.jpa.binary.interceptor.BinaryStorageInterceptor;
import ca.uhn.fhir.jpa.binary.provider.BinaryAccessProvider;
import ca.uhn.fhir.jpa.bulk.export.provider.BulkDataExportProvider;
import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
import ca.uhn.fhir.jpa.config.util.ResourceCountCacheUtil;
import ca.uhn.fhir.jpa.config.util.ValidationSupportConfigUtil;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.mdm.MdmLinkDaoJpaImpl;
import ca.uhn.fhir.jpa.dao.search.HSearchSortHelperImpl;
import ca.uhn.fhir.jpa.dao.search.IHSearchSortHelper;
import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingInterceptor;
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.*;
import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
import ca.uhn.fhir.jpa.starter.AppProperties;
import ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory;
import ca.uhn.fhir.jpa.starter.util.EnvironmentHelper;
import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChain;
import ca.uhn.fhir.mdm.dao.IMdmLinkDao;
import ca.uhn.fhir.mdm.provider.MdmProviderLoader;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.narrative2.NullNarrativeGenerator;
import ca.uhn.fhir.rest.api.IResourceSupportedSvc;
import ca.uhn.fhir.rest.openapi.OpenApiInterceptor;
import ca.uhn.fhir.rest.server.*;
import ca.uhn.fhir.rest.server.interceptor.*;
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.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import com.google.common.base.Strings;
import com.google.common.collect.ImmutableList;
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
import org.springframework.batch.core.configuration.annotation.BatchConfigurer;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Primary;
import org.springframework.core.env.ConfigurableEnvironment;
import org.springframework.http.HttpHeaders;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.web.cors.CorsConfiguration;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import java.util.*;
import static ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory.ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR;
@Configuration
public class StarterJpaConfig {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(StarterJpaConfig.class);
@Bean
public IFulltextSearchSvc fullTextSearchSvc() {
return new FulltextSearchSvcImpl();
}
@Bean
public IStaleSearchDeletingSvc staleSearchDeletingSvc() {
return new StaleSearchDeletingSvcImpl();
}
@Primary
@Bean
public CachingValidationSupport validationSupportChain(JpaValidationSupportChain theJpaValidationSupportChain) {
return ValidationSupportConfigUtil.newCachingValidationSupport(theJpaValidationSupportChain);
}
@Bean
public BatchConfigurer batchConfigurer() {
return new NonPersistedBatchConfigurer();
}
@Autowired
private ConfigurableEnvironment configurableEnvironment;
/**
* Customize 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.
*/
@Bean
public DatabaseBackedPagingProvider databaseBackedPagingProvider(AppProperties appProperties) {
DatabaseBackedPagingProvider pagingProvider = new DatabaseBackedPagingProvider();
pagingProvider.setDefaultPageSize(appProperties.getDefault_page_size());
pagingProvider.setMaximumPageSize(appProperties.getMax_page_size());
return pagingProvider;
}
@Bean
public IResourceSupportedSvc resourceSupportedSvc(IDaoRegistry theDaoRegistry) {
return new DaoRegistryResourceSupportedSvc(theDaoRegistry);
}
@Bean(name = "myResourceCountsCache")
public ResourceCountCache resourceCountsCache(IFhirSystemDao<?, ?> theSystemDao) {
return ResourceCountCacheUtil.newResourceCountCache(theSystemDao);
}
@Primary
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory(DataSource myDataSource, ConfigurableListableBeanFactory myConfigurableListableBeanFactory, FhirContext theFhirContext) {
LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(myConfigurableListableBeanFactory, theFhirContext);
retVal.setPersistenceUnitName("HAPI_PU");
try {
retVal.setDataSource(myDataSource);
} catch (Exception e) {
throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
}
retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment, myConfigurableListableBeanFactory));
return retVal;
}
@Bean
@Primary
public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
JpaTransactionManager retVal = new JpaTransactionManager();
retVal.setEntityManagerFactory(entityManagerFactory);
return retVal;
}
@Bean
public IHSearchSortHelper hSearchSortHelper(ISearchParamRegistry mySearchParamRegistry) {
return new HSearchSortHelperImpl(mySearchParamRegistry);
}
@Bean
@ConditionalOnProperty(prefix = "hapi.fhir", name = ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR, havingValue = "true")
public RepositoryValidatingInterceptor repositoryValidatingInterceptor(IRepositoryValidationInterceptorFactory factory) {
return factory.buildUsingStoredStructureDefinitions();
}
@Bean
public LoggingInterceptor loggingInterceptor(AppProperties appProperties) {
/*
* Add some logging for each request
*/
LoggingInterceptor loggingInterceptor = new LoggingInterceptor();
loggingInterceptor.setLoggerName(appProperties.getLogger().getName());
loggingInterceptor.setMessageFormat(appProperties.getLogger().getFormat());
loggingInterceptor.setErrorMessageFormat(appProperties.getLogger().getError_format());
loggingInterceptor.setLogExceptions(appProperties.getLogger().getLog_exceptions());
return loggingInterceptor;
}
@Bean
@Primary
/*
This bean is currently necessary to override from MDM settings
*/
IMdmLinkDao mdmLinkDao() {
return new MdmLinkDaoJpaImpl();
}
@Bean
@ConditionalOnProperty(prefix = "hapi.fhir", name = "cors")
public CorsInterceptor corsInterceptor(AppProperties appProperties) {
// Define your CORS configuration. This is an example
// showing a typical setup. You should customize this
// to your specific needs
ourLog.info("CORS is enabled on this server");
CorsConfiguration config = new CorsConfiguration();
config.addAllowedHeader(HttpHeaders.ORIGIN);
config.addAllowedHeader(HttpHeaders.ACCEPT);
config.addAllowedHeader(HttpHeaders.CONTENT_TYPE);
config.addAllowedHeader(HttpHeaders.AUTHORIZATION);
config.addAllowedHeader(HttpHeaders.CACHE_CONTROL);
config.addAllowedHeader("x-fhir-starter");
config.addAllowedHeader("X-Requested-With");
config.addAllowedHeader("Prefer");
List<String> allAllowedCORSOrigins = appProperties.getCors().getAllowed_origin();
allAllowedCORSOrigins.forEach(config::addAllowedOriginPattern);
ourLog.info("CORS allows the following origins: " + String.join(", ", allAllowedCORSOrigins));
config.addExposedHeader("Location");
config.addExposedHeader("Content-Location");
config.setAllowedMethods(Arrays.asList("GET", "POST", "PUT", "DELETE", "OPTIONS", "PATCH", "HEAD"));
config.setAllowCredentials(appProperties.getCors().getAllow_Credentials());
// Create the interceptor and register it
return new CorsInterceptor(config);
}
@Bean
public RestfulServer restfulServer(IFhirSystemDao<?, ?> fhirSystemDao, AppProperties appProperties, DaoRegistry daoRegistry, Optional<MdmProviderLoader> mdmProviderProvider, IJpaSystemProvider jpaSystemProvider, ResourceProviderFactory resourceProviderFactory, DaoConfig daoConfig, ISearchParamRegistry searchParamRegistry, IValidationSupport theValidationSupport, DatabaseBackedPagingProvider databaseBackedPagingProvider, LoggingInterceptor loggingInterceptor, Optional<TerminologyUploaderProvider> terminologyUploaderProvider, Optional<SubscriptionTriggeringProvider> subscriptionTriggeringProvider, Optional<CorsInterceptor> corsInterceptor, IInterceptorBroadcaster interceptorBroadcaster, Optional<BinaryAccessProvider> binaryAccessProvider, BinaryStorageInterceptor binaryStorageInterceptor, IValidatorModule validatorModule, Optional<GraphQLProvider> graphQLProvider, BulkDataExportProvider bulkDataExportProvider, BulkDataImportProvider bulkDataImportProvider, ValueSetOperationProvider theValueSetOperationProvider, ReindexProvider reindexProvider, PartitionManagementProvider partitionManagementProvider, Optional<RepositoryValidatingInterceptor> repositoryValidatingInterceptor, IPackageInstallerSvc packageInstallerSvc) {
RestfulServer fhirServer = new RestfulServer(fhirSystemDao.getContext());
List<String> supportedResourceTypes = appProperties.getSupported_resource_types();
if (!supportedResourceTypes.isEmpty()) {
if (!supportedResourceTypes.contains("SearchParameter")) {
supportedResourceTypes.add("SearchParameter");
}
daoRegistry.setSupportedResourceTypes(supportedResourceTypes);
}
if (appProperties.getNarrative_enabled()) {
fhirSystemDao.getContext().setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
} else {
fhirSystemDao.getContext().setNarrativeGenerator(new NullNarrativeGenerator());
}
if (appProperties.getMdm_enabled()) mdmProviderProvider.get().loadProvider();
fhirServer.registerProviders(resourceProviderFactory.createProviders());
fhirServer.registerProvider(jpaSystemProvider);
fhirServer.setServerConformanceProvider(calculateConformanceProvider(fhirSystemDao, fhirServer, daoConfig, searchParamRegistry, theValidationSupport));
/*
* ETag Support
*/
if (!appProperties.getEtag_support_enabled()) fhirServer.setETagSupport(ETagSupportEnum.DISABLED);
/*
* Default to JSON and pretty printing
*/
fhirServer.setDefaultPrettyPrint(appProperties.getDefault_pretty_print());
/*
* Default encoding
*/
fhirServer.setDefaultResponseEncoding(appProperties.getDefault_encoding());
/*
* This configures the server to page search results to and from
* the database, instead of only paging them to memory. This may mean
* a performance hit when performing searches that return lots of results,
* but makes the server much more scalable.
*/
fhirServer.setPagingProvider(databaseBackedPagingProvider);
/*
* This interceptor formats the output using nice colourful
* HTML output when the request is detected to come from a
* browser.
*/
fhirServer.registerInterceptor(new ResponseHighlighterInterceptor());
if (appProperties.getFhirpath_interceptor_enabled()) {
fhirServer.registerInterceptor(new FhirPathFilterInterceptor());
}
fhirServer.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
* 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 = appProperties.getServer_address();
if (!Strings.isNullOrEmpty(serverAddress)) {
fhirServer.setServerAddressStrategy(new HardcodedServerAddressStrategy(serverAddress));
} else if (appProperties.getUse_apache_address_strategy()) {
boolean useHttps = appProperties.getUse_apache_address_strategy_https();
fhirServer.setServerAddressStrategy(useHttps ? ApacheProxyAddressStrategy.forHttps() : ApacheProxyAddressStrategy.forHttp());
} else {
fhirServer.setServerAddressStrategy(new IncomingRequestAddressStrategy());
}
/*
* If you are using DSTU3+, you may want to add a terminology uploader, which allows
* uploading of external terminologies such as Snomed CT. Note that this uploader
* does not have any security attached (any anonymous user may use it by default)
* so it is a potential security vulnerability. Consider using an AuthorizationInterceptor
* with this feature.
*/
if (fhirSystemDao.getContext().getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) { // <-- ENABLED RIGHT NOW
fhirServer.registerProvider(terminologyUploaderProvider.get());
}
// If you want to enable the $trigger-subscription operation to allow
// manual triggering of a subscription delivery, enable this provider
if (true) { // <-- ENABLED RIGHT NOW
fhirServer.registerProvider(subscriptionTriggeringProvider.get());
}
corsInterceptor.ifPresent(fhirServer::registerInterceptor);
if (appProperties.getSubscription() != null) {
// Subscription debug logging
fhirServer.registerInterceptor(new SubscriptionDebugLogInterceptor());
}
if (appProperties.getAllow_cascading_deletes()) {
CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(fhirSystemDao.getContext(), daoRegistry, interceptorBroadcaster);
fhirServer.registerInterceptor(cascadingDeleteInterceptor);
}
// Binary Storage
if (appProperties.getBinary_storage_enabled() && binaryAccessProvider.isPresent()) {
fhirServer.registerProvider(binaryAccessProvider.get());
fhirServer.registerInterceptor(binaryStorageInterceptor);
}
// Validation
if (validatorModule != null) {
if (appProperties.getValidation().getRequests_enabled()) {
RequestValidatingInterceptor interceptor = new RequestValidatingInterceptor();
interceptor.setFailOnSeverity(ResultSeverityEnum.ERROR);
interceptor.setValidatorModules(Collections.singletonList(validatorModule));
fhirServer.registerInterceptor(interceptor);
}
if (appProperties.getValidation().getResponses_enabled()) {
ResponseValidatingInterceptor interceptor = new ResponseValidatingInterceptor();
interceptor.setFailOnSeverity(ResultSeverityEnum.ERROR);
interceptor.setValidatorModules(Collections.singletonList(validatorModule));
fhirServer.registerInterceptor(interceptor);
}
}
// GraphQL
if (appProperties.getGraphql_enabled()) {
if (fhirSystemDao.getContext().getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
fhirServer.registerProvider(graphQLProvider.get());
}
}
if (appProperties.getOpenapi_enabled()) {
fhirServer.registerInterceptor(new OpenApiInterceptor());
}
// Bulk Export
if (appProperties.getBulk_export_enabled()) {
fhirServer.registerProvider(bulkDataExportProvider);
}
//Bulk Import
if (appProperties.getBulk_import_enabled()) {
fhirServer.registerProvider(bulkDataImportProvider);
}
// valueSet Operations i.e $expand
fhirServer.registerProvider(theValueSetOperationProvider);
//reindex Provider $reindex
fhirServer.registerProvider(reindexProvider);
// Partitioning
if (appProperties.getPartitioning() != null) {
fhirServer.registerInterceptor(new RequestTenantPartitionInterceptor());
fhirServer.setTenantIdentificationStrategy(new UrlBaseTenantIdentificationStrategy());
fhirServer.registerProviders(partitionManagementProvider);
}
repositoryValidatingInterceptor.ifPresent(fhirServer::registerInterceptor);
if (appProperties.getImplementationGuides() != null) {
Map<String, AppProperties.ImplementationGuide> guides = appProperties.getImplementationGuides();
for (Map.Entry<String, AppProperties.ImplementationGuide> guide : guides.entrySet()) {
PackageInstallationSpec packageInstallationSpec = new PackageInstallationSpec().setPackageUrl(guide.getValue().getUrl()).setName(guide.getValue().getName()).setVersion(guide.getValue().getVersion()).setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
if (appProperties.getInstall_transitive_ig_dependencies()) {
packageInstallationSpec.setFetchDependencies(true);
packageInstallationSpec.setDependencyExcludes(ImmutableList.of("hl7.fhir.r2.core", "hl7.fhir.r3.core", "hl7.fhir.r4.core", "hl7.fhir.r5.core"));
}
packageInstallerSvc.install(packageInstallationSpec);
}
}
return fhirServer;
}
public static IServerConformanceProvider<?> calculateConformanceProvider(IFhirSystemDao fhirSystemDao, RestfulServer fhirServer, DaoConfig daoConfig, ISearchParamRegistry searchParamRegistry, IValidationSupport theValidationSupport) {
FhirVersionEnum fhirVersion = fhirSystemDao.getContext().getVersion().getVersion();
if (fhirVersion == FhirVersionEnum.DSTU2) {
JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(fhirServer, fhirSystemDao, daoConfig);
confProvider.setImplementationDescription("HAPI FHIR DSTU2 Server");
return confProvider;
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(fhirServer, fhirSystemDao, daoConfig, searchParamRegistry);
confProvider.setImplementationDescription("HAPI FHIR DSTU3 Server");
return confProvider;
} else if (fhirVersion == FhirVersionEnum.R4) {
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, daoConfig, searchParamRegistry, theValidationSupport);
confProvider.setImplementationDescription("HAPI FHIR R4 Server");
return confProvider;
} else if (fhirVersion == FhirVersionEnum.R5) {
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, daoConfig, searchParamRegistry, theValidationSupport);
confProvider.setImplementationDescription("HAPI FHIR R5 Server");
return confProvider;
} else {
throw new IllegalStateException();
}
}
}

4
src/main/java/ca/uhn/fhir/jpa/starter/IRepositoryValidationInterceptorFactory.java → src/main/java/ca/uhn/fhir/jpa/starter/common/validation/IRepositoryValidationInterceptorFactory.java
View File

@@ -1,8 +1,10 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter.common.validation;
import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingInterceptor; import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingInterceptor;
public interface IRepositoryValidationInterceptorFactory { public interface IRepositoryValidationInterceptorFactory {
String ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR = "enable_repository_validating_interceptor";
RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions(); RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions();
RepositoryValidatingInterceptor build(); RepositoryValidatingInterceptor build();

13
src/main/java/ca/uhn/fhir/jpa/starter/RepositoryValidationInterceptorFactoryDstu3.java → src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryDstu3.java
View File

@@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter.common.validation;
import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry; import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
@@ -19,6 +19,8 @@ import java.util.List;
import java.util.Map; import java.util.Map;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory.ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR;
/** /**
* This class can be customized to enable the {@link RepositoryValidatingInterceptor} * This class can be customized to enable the {@link RepositoryValidatingInterceptor}
* on this server. * on this server.
@@ -26,7 +28,7 @@ import java.util.stream.Collectors;
* The <code>enable_repository_validating_interceptor</code> property must be enabled in <code>application.yaml</code> * The <code>enable_repository_validating_interceptor</code> property must be enabled in <code>application.yaml</code>
* in order to use this class. * in order to use this class.
*/ */
@ConditionalOnProperty(prefix = "hapi.fhir", name = "enable_repository_validating_interceptor", havingValue = "true") @ConditionalOnProperty(prefix = "hapi.fhir", name = ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR, havingValue = "true")
@Configuration @Configuration
@Conditional(OnDSTU3Condition.class) @Conditional(OnDSTU3Condition.class)
public class RepositoryValidationInterceptorFactoryDstu3 implements IRepositoryValidationInterceptorFactory { public class RepositoryValidationInterceptorFactoryDstu3 implements IRepositoryValidationInterceptorFactory {
@@ -50,10 +52,9 @@ public class RepositoryValidationInterceptorFactoryDstu3 implements IRepositoryV
.map(StructureDefinition.class::cast) .map(StructureDefinition.class::cast)
.collect(Collectors.groupingBy(StructureDefinition::getType)); .collect(Collectors.groupingBy(StructureDefinition::getType));
structureDefintions.entrySet().forEach(structureDefinitionListEntry -> structureDefintions.forEach((key, value) -> {
{ String[] urls = value.stream().map(StructureDefinition::getUrl).toArray(String[]::new);
String[] urls = structureDefinitionListEntry.getValue().stream().map(StructureDefinition::getUrl).toArray(String[]::new); repositoryValidatingRuleBuilder.forResourcesOfType(key).requireAtLeastOneProfileOf(urls).and().requireValidationToDeclaredProfiles();
repositoryValidatingRuleBuilder.forResourcesOfType(structureDefinitionListEntry.getKey()).requireAtLeastOneProfileOf(urls).and().requireValidationToDeclaredProfiles();
}); });
List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build(); List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();

13
src/main/java/ca/uhn/fhir/jpa/starter/RepositoryValidationInterceptorFactoryR4.java → src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryR4.java
View File

@@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter.common.validation;
import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry; import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
@@ -19,6 +19,8 @@ import java.util.List;
import java.util.Map; import java.util.Map;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory.ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR;
/** /**
* This class can be customized to enable the {@link ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingInterceptor} * This class can be customized to enable the {@link ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingInterceptor}
* on this server. * on this server.
@@ -26,7 +28,7 @@ import java.util.stream.Collectors;
* The <code>enable_repository_validating_interceptor</code> property must be enabled in <code>application.yaml</code> * The <code>enable_repository_validating_interceptor</code> property must be enabled in <code>application.yaml</code>
* in order to use this class. * in order to use this class.
*/ */
@ConditionalOnProperty(prefix = "hapi.fhir", name = "enable_repository_validating_interceptor", havingValue = "true") @ConditionalOnProperty(prefix = "hapi.fhir", name = ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR, havingValue = "true")
@Configuration @Configuration
@Conditional(OnR4Condition.class) @Conditional(OnR4Condition.class)
public class RepositoryValidationInterceptorFactoryR4 implements IRepositoryValidationInterceptorFactory { public class RepositoryValidationInterceptorFactoryR4 implements IRepositoryValidationInterceptorFactory {
@@ -51,10 +53,9 @@ public class RepositoryValidationInterceptorFactoryR4 implements IRepositoryVali
.map(StructureDefinition.class::cast) .map(StructureDefinition.class::cast)
.collect(Collectors.groupingBy(StructureDefinition::getType)); .collect(Collectors.groupingBy(StructureDefinition::getType));
structureDefintions.entrySet().forEach(structureDefinitionListEntry -> structureDefintions.forEach((key, value) -> {
{ String[] urls = value.stream().map(StructureDefinition::getUrl).toArray(String[]::new);
String[] urls = structureDefinitionListEntry.getValue().stream().map(StructureDefinition::getUrl).toArray(String[]::new); repositoryValidatingRuleBuilder.forResourcesOfType(key).requireAtLeastOneProfileOf(urls).and().requireValidationToDeclaredProfiles();
repositoryValidatingRuleBuilder.forResourcesOfType(structureDefinitionListEntry.getKey()).requireAtLeastOneProfileOf(urls).and().requireValidationToDeclaredProfiles();
}); });
List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build(); List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();

13
src/main/java/ca/uhn/fhir/jpa/starter/RepositoryValidationInterceptorFactoryR5.java → src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryR5.java
View File

@@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter.common.validation;
import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry; import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
@@ -19,6 +19,8 @@ import java.util.List;
import java.util.Map; import java.util.Map;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory.ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR;
/** /**
* This class can be customized to enable the {@link RepositoryValidatingInterceptor} * This class can be customized to enable the {@link RepositoryValidatingInterceptor}
* on this server. * on this server.
@@ -26,7 +28,7 @@ import java.util.stream.Collectors;
* The <code>enable_repository_validating_interceptor</code> property must be enabled in <code>application.yaml</code> * The <code>enable_repository_validating_interceptor</code> property must be enabled in <code>application.yaml</code>
* in order to use this class. * in order to use this class.
*/ */
@ConditionalOnProperty(prefix = "hapi.fhir", name = "enable_repository_validating_interceptor", havingValue = "true") @ConditionalOnProperty(prefix = "hapi.fhir", name = ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR, havingValue = "true")
@Configuration @Configuration
@Conditional(OnR5Condition.class) @Conditional(OnR5Condition.class)
public class RepositoryValidationInterceptorFactoryR5 implements IRepositoryValidationInterceptorFactory { public class RepositoryValidationInterceptorFactoryR5 implements IRepositoryValidationInterceptorFactory {
@@ -50,10 +52,9 @@ public class RepositoryValidationInterceptorFactoryR5 implements IRepositoryVali
.map(StructureDefinition.class::cast) .map(StructureDefinition.class::cast)
.collect(Collectors.groupingBy(StructureDefinition::getType)); .collect(Collectors.groupingBy(StructureDefinition::getType));
structureDefintions.entrySet().forEach(structureDefinitionListEntry -> structureDefintions.forEach((key, value) -> {
{ String[] urls = value.stream().map(StructureDefinition::getUrl).toArray(String[]::new);
String[] urls = structureDefinitionListEntry.getValue().stream().map(StructureDefinition::getUrl).toArray(String[]::new); repositoryValidatingRuleBuilder.forResourcesOfType(key).requireAtLeastOneProfileOf(urls).and().requireValidationToDeclaredProfiles();
repositoryValidatingRuleBuilder.forResourcesOfType(structureDefinitionListEntry.getKey()).requireAtLeastOneProfileOf(urls).and().requireValidationToDeclaredProfiles();
}); });
List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build(); List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();

3
src/main/java/ca/uhn/fhir/jpa/starter/cql/CqlConfigCondition.java
View File

@@ -9,7 +9,6 @@ public class CqlConfigCondition implements Condition {
@Override @Override
public boolean matches(ConditionContext theConditionContext, AnnotatedTypeMetadata theAnnotatedTypeMetadata) { public boolean matches(ConditionContext theConditionContext, AnnotatedTypeMetadata theAnnotatedTypeMetadata) {
String property = theConditionContext.getEnvironment().getProperty("hapi.fhir.cql_enabled"); String property = theConditionContext.getEnvironment().getProperty("hapi.fhir.cql_enabled");
boolean enabled = Boolean.parseBoolean(property); return Boolean.parseBoolean(property);
return enabled;
} }
} }

19
src/main/java/ca/uhn/fhir/jpa/starter/EnvironmentHelper.java → src/main/java/ca/uhn/fhir/jpa/starter/util/EnvironmentHelper.java
View File

@@ -1,9 +1,10 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter.util;
import ca.uhn.fhir.jpa.config.HapiFhirLocalContainerEntityManagerFactoryBean; import ca.uhn.fhir.jpa.config.HapiFhirLocalContainerEntityManagerFactoryBean;
import ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers; import ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers;
import ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder; import ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder;
import org.apache.lucene.util.Version; import org.apache.lucene.util.Version;
import org.hibernate.boot.model.naming.CamelCaseToUnderscoresNamingStrategy;
import org.hibernate.cfg.AvailableSettings; import org.hibernate.cfg.AvailableSettings;
import org.hibernate.search.backend.elasticsearch.cfg.ElasticsearchBackendSettings; import org.hibernate.search.backend.elasticsearch.cfg.ElasticsearchBackendSettings;
import org.hibernate.search.backend.elasticsearch.index.IndexStatus; import org.hibernate.search.backend.elasticsearch.index.IndexStatus;
@@ -27,6 +28,8 @@ import java.util.HashMap;
import java.util.Map; import java.util.Map;
import java.util.Properties; import java.util.Properties;
import static java.util.Objects.requireNonNullElse;
public class EnvironmentHelper { public class EnvironmentHelper {
public static Properties getHibernateProperties(ConfigurableEnvironment environment, public static Properties getHibernateProperties(ConfigurableEnvironment environment,
@@ -41,7 +44,7 @@ public class EnvironmentHelper {
//Spring Boot Autoconfiguration defaults //Spring Boot Autoconfiguration defaults
properties.putIfAbsent(AvailableSettings.SCANNER, "org.hibernate.boot.archive.scan.internal.DisabledScanner"); properties.putIfAbsent(AvailableSettings.SCANNER, "org.hibernate.boot.archive.scan.internal.DisabledScanner");
properties.putIfAbsent(AvailableSettings.IMPLICIT_NAMING_STRATEGY, SpringImplicitNamingStrategy.class.getName()); properties.putIfAbsent(AvailableSettings.IMPLICIT_NAMING_STRATEGY, SpringImplicitNamingStrategy.class.getName());
properties.putIfAbsent(AvailableSettings.PHYSICAL_NAMING_STRATEGY, SpringPhysicalNamingStrategy.class.getName()); properties.putIfAbsent(AvailableSettings.PHYSICAL_NAMING_STRATEGY, CamelCaseToUnderscoresNamingStrategy.class.getName());
//TODO The bean factory should be added as parameter but that requires that it can be injected from the entityManagerFactory bean from xBaseConfig //TODO The bean factory should be added as parameter but that requires that it can be injected from the entityManagerFactory bean from xBaseConfig
//properties.putIfAbsent(AvailableSettings.BEAN_CONTAINER, new SpringBeanContainer(beanFactory)); //properties.putIfAbsent(AvailableSettings.BEAN_CONTAINER, new SpringBeanContainer(beanFactory));
@@ -102,18 +105,6 @@ public class EnvironmentHelper {
return properties; return properties;
} }
//TODO Removed when we're up on Java 11
private static <T> T requireNonNullElse(T obj, T defaultObj) {
return (obj != null) ? obj : requireNonNull(defaultObj, "defaultObj");
}
//TODO Removed when we're up on Java 11
private static <T> T requireNonNull(T obj, String message) {
if (obj == null)
throw new NullPointerException(message);
return obj;
}
public static String getElasticsearchServerUrl(ConfigurableEnvironment environment) { public static String getElasticsearchServerUrl(ConfigurableEnvironment environment) {
return environment.getProperty("elasticsearch.rest_url", String.class); return environment.getProperty("elasticsearch.rest_url", String.class);
} }

2
src/main/java/ca/uhn/fhir/jpa/starter/JpaHibernatePropertiesProvider.java → src/main/java/ca/uhn/fhir/jpa/starter/util/JpaHibernatePropertiesProvider.java
View File

@@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter.util;
import ca.uhn.fhir.context.ConfigurationException; import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider; import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider;

2
src/main/resources/application.yaml
View File

@@ -89,7 +89,7 @@ hapi:
# default_pretty_print: true # default_pretty_print: true
# default_page_size: 20 # default_page_size: 20
# delete_expunge_enabled: true # delete_expunge_enabled: true
# enable_repository_validating_interceptor: false # enable_repository_validating_interceptor: true
# enable_index_missing_fields: false # enable_index_missing_fields: false
# enable_index_of_type: true # enable_index_of_type: true
# enable_index_contained_resource: false # enable_index_contained_resource: false

20
src/test/java/ca/uhn/fhir/jpa/starter/Demo.java
View File

@@ -1,20 +0,0 @@
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/fhir/metadata
}
}

4
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java
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@@ -113,7 +113,7 @@ public class ExampleServerDstu3IT implements IServerSupport {
.execute(); .execute();
List<Parameters.ParametersParameterComponent> response = outParams.getParameter(); List<Parameters.ParametersParameterComponent> response = outParams.getParameter();
Assert.assertTrue(!response.isEmpty()); Assert.assertFalse(response.isEmpty());
Parameters.ParametersParameterComponent component = response.get(0); Parameters.ParametersParameterComponent component = response.get(0);
Assert.assertTrue(component.getResource() instanceof MeasureReport); Assert.assertTrue(component.getResource() instanceof MeasureReport);
MeasureReport report = (MeasureReport) component.getResource(); MeasureReport report = (MeasureReport) component.getResource();
@@ -149,7 +149,7 @@ public class ExampleServerDstu3IT implements IServerSupport {
private Bundle loadBundle(String theLocation, FhirContext theCtx, IGenericClient theClient) throws IOException { private Bundle loadBundle(String theLocation, FhirContext theCtx, IGenericClient theClient) throws IOException {
String json = stringFromResource(theLocation); String json = stringFromResource(theLocation);
Bundle bundle = (Bundle) theCtx.newJsonParser().parseResource(json); Bundle bundle = (Bundle) theCtx.newJsonParser().parseResource(json);
Bundle result = (Bundle) theClient.transaction().withBundle(bundle).execute(); Bundle result = theClient.transaction().withBundle(bundle).execute();
return result; return result;
} }

4
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java
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@@ -1,15 +1,11 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.CacheControlDirective; import ca.uhn.fhir.rest.api.CacheControlDirective;
import ca.uhn.fhir.rest.api.EncodingEnum; import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome; import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.client.api.IGenericClient; import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum; import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import org.eclipse.jetty.websocket.api.Session; import org.eclipse.jetty.websocket.api.Session;
import org.eclipse.jetty.websocket.client.ClientUpgradeRequest; import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
import org.eclipse.jetty.websocket.client.WebSocketClient; import org.eclipse.jetty.websocket.client.WebSocketClient;

4
src/test/java/ca/uhn/fhir/jpa/starter/SocketImplementation.java
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@@ -15,10 +15,10 @@ import java.util.List;
public class SocketImplementation { public class SocketImplementation {
private static final Logger ourLog = org.slf4j.LoggerFactory.getLogger(SocketImplementation.class); private static final Logger ourLog = org.slf4j.LoggerFactory.getLogger(SocketImplementation.class);
private String myCriteria; private final String myCriteria;
protected String myError; protected String myError;
protected boolean myGotBound; protected boolean myGotBound;
private List<String> myMessages = new ArrayList<String>(); private final List<String> myMessages = new ArrayList<String>();
protected int myPingCount; protected int myPingCount;
protected String mySubsId; protected String mySubsId;
private Session session; private Session session;