use of ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator in project hapi-fhir-jpaserver-starter by hapifhir.
the class BaseJpaRestfulServer method initialize.
@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() && !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();
}
}
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));
}
// manual triggering of a subscription delivery, enable this provider
if (true) {
// <-- ENABLED RIGHT NOW
registerProvider(myApplicationContext.getBean(SubscriptionTriggeringProvider.class));
}
// 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");
}
// will activate them and match results against them
if (appProperties.getSubscription() != null) {
// Subscription debug logging
interceptorService.registerInterceptor(new SubscriptionDebugLogInterceptor());
}
if (appProperties.getAllow_cascading_deletes()) {
CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(ctx, daoRegistry, interceptorBroadcaster);
getInterceptorService().registerInterceptor(cascadingDeleteInterceptor);
}
// Binary Storage
if (appProperties.getBinary_storage_enabled()) {
getInterceptorService().registerInterceptor(binaryStorageInterceptor);
}
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);
}
// valueSet Operations i.e $expand
registerProvider(valueSetOperationProvider);
// 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);
}
daoConfig.setStoreResourceInLuceneIndex(appProperties.getStore_resource_in_lucene_index_enabled());
daoConfig.getModelConfig().setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
daoConfig.getModelConfig().setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
}
use of ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator in project drug-formulary-ri by HL7-DaVinci.
the class JpaRestfulServer method initialize.
@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.
*/
ApplicationContext appCtx = (ApplicationContext) getServletContext().getAttribute("org.springframework.web.context.WebApplicationContext.ROOT");
// Customize supported resource types
Set<String> supportedResourceTypes = HapiProperties.getSupportedResourceTypes();
if (!supportedResourceTypes.isEmpty() && !supportedResourceTypes.contains("SearchParameter")) {
supportedResourceTypes.add("SearchParameter");
}
if (!supportedResourceTypes.isEmpty()) {
DaoRegistry daoRegistry = appCtx.getBean(DaoRegistry.class);
daoRegistry.setSupportedResourceTypes(supportedResourceTypes);
}
/*
* ResourceProviders are fetched from the Spring context
*/
FhirVersionEnum fhirVersion = HapiProperties.getFhirVersion();
ResourceProviderFactory resourceProviders;
Object systemProvider;
if (fhirVersion == FhirVersionEnum.DSTU2) {
resourceProviders = appCtx.getBean("myResourceProvidersDstu2", ResourceProviderFactory.class);
systemProvider = appCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class);
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
resourceProviders = appCtx.getBean("myResourceProvidersDstu3", ResourceProviderFactory.class);
systemProvider = appCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class);
} else if (fhirVersion == FhirVersionEnum.R4) {
resourceProviders = appCtx.getBean("myResourceProvidersR4", ResourceProviderFactory.class);
systemProvider = appCtx.getBean("mySystemProviderR4", JpaSystemProviderR4.class);
} else if (fhirVersion == FhirVersionEnum.R5) {
resourceProviders = appCtx.getBean("myResourceProvidersR5", ResourceProviderFactory.class);
systemProvider = appCtx.getBean("mySystemProviderR5", JpaSystemProviderR5.class);
} else {
throw new IllegalStateException();
}
setFhirContext(appCtx.getBean(FhirContext.class));
registerProviders(resourceProviders.createProviders());
registerProvider(systemProvider);
/*
* 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
*/
IFhirSystemDao<org.hl7.fhir.r4.model.Bundle, org.hl7.fhir.r4.model.Meta> systemDao = appCtx.getBean("mySystemDaoR4", IFhirSystemDao.class);
MetadataProvider metadata = new MetadataProvider(this, systemDao, appCtx.getBean(DaoConfig.class));
// JpaConformanceProviderR4 confProvider = new JpaConformanceProviderR4(this,
// systemDao,
// appCtx.getBean(DaoConfig.class));
metadata.setImplementationDescription("Da Vinci Drug Formulary Reference Server");
setServerConformanceProvider(metadata);
/*
* ETag Support
*/
setETagSupport(HapiProperties.getEtagSupport());
/*
* This server tries to dynamically generate narratives
*/
FhirContext ctx = getFhirContext();
ctx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
/*
* Default to JSON and pretty printing
*/
setDefaultPrettyPrint(HapiProperties.getDefaultPrettyPrint());
/*
* Default encoding
*/
setDefaultResponseEncoding(HapiProperties.getDefaultEncoding());
/*
* 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(appCtx.getBean(DatabaseBackedPagingProvider.class));
/*
* 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);
/*
* Add Read Only Interceptor
*/
ReadOnlyInterceptor readOnlyInterceptor = new ReadOnlyInterceptor();
this.registerInterceptor(readOnlyInterceptor);
/*
* This interceptor handles the $export operation
*/
ExportInterceptor exportInterceptor = new ExportInterceptor();
this.registerInterceptor(exportInterceptor);
/*
* 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);
/*
* Add Authorization interceptor
*/
PatientAuthorizationInterceptor authorizationInterceptor = new PatientAuthorizationInterceptor();
this.registerInterceptor(authorizationInterceptor);
/*
* 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 = HapiProperties.getServerAddress();
if (serverAddress != null && serverAddress.length() > 0) {
setServerAddressStrategy(new HardcodedServerAddressStrategy(serverAddress));
}
/*
* 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 (false) {
// <-- DISABLED RIGHT NOW
registerProvider(appCtx.getBean(TerminologyUploaderProvider.class));
}
// manual triggering of a subscription delivery, enable this provider
if (false) {
// <-- DISABLED RIGHT NOW
SubscriptionTriggeringProvider retriggeringProvider = appCtx.getBean(SubscriptionTriggeringProvider.class);
registerProvider(retriggeringProvider);
}
// to your specific needs
if (HapiProperties.getCorsEnabled()) {
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");
String allAllowedCORSOrigins = HapiProperties.getCorsAllowedOrigin();
Arrays.stream(allAllowedCORSOrigins.split(",")).forEach(o -> {
config.addAllowedOrigin(o);
});
config.addAllowedOrigin(HapiProperties.getCorsAllowedOrigin());
config.addExposedHeader("Location");
config.addExposedHeader("Content-Location");
config.setAllowedMethods(Arrays.asList("GET", "POST", "PUT", "DELETE", "OPTIONS", "PATCH", "HEAD"));
config.setAllowCredentials(HapiProperties.getCorsAllowedCredentials());
// Create the interceptor and register it
CorsInterceptor interceptor = new CorsInterceptor(config);
registerInterceptor(interceptor);
}
// will activate them and match results against them
if (HapiProperties.getSubscriptionWebsocketEnabled() || HapiProperties.getSubscriptionEmailEnabled() || HapiProperties.getSubscriptionRestHookEnabled()) {
// Loads subscription interceptors (SubscriptionActivatingInterceptor,
// SubscriptionMatcherInterceptor)
// with activation of scheduled subscription
SubscriptionInterceptorLoader subscriptionInterceptorLoader = appCtx.getBean(SubscriptionInterceptorLoader.class);
subscriptionInterceptorLoader.registerInterceptors();
// Subscription debug logging
IInterceptorService interceptorService = appCtx.getBean(IInterceptorService.class);
interceptorService.registerInterceptor(new SubscriptionDebugLogInterceptor());
}
// Cascading deletes
DaoRegistry daoRegistry = appCtx.getBean(DaoRegistry.class);
IInterceptorBroadcaster interceptorBroadcaster = appCtx.getBean(IInterceptorBroadcaster.class);
if (HapiProperties.getAllowCascadingDeletes()) {
CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(daoRegistry, interceptorBroadcaster);
getInterceptorService().registerInterceptor(cascadingDeleteInterceptor);
}
// Binary Storage
if (HapiProperties.isBinaryStorageEnabled()) {
BinaryStorageInterceptor binaryStorageInterceptor = appCtx.getBean(BinaryStorageInterceptor.class);
getInterceptorService().registerInterceptor(binaryStorageInterceptor);
}
// Validation
IValidatorModule validatorModule;
switch(fhirVersion) {
case DSTU2:
validatorModule = appCtx.getBean("myInstanceValidatorDstu2", IValidatorModule.class);
break;
case DSTU3:
validatorModule = appCtx.getBean("myInstanceValidatorDstu3", IValidatorModule.class);
break;
case R4:
validatorModule = appCtx.getBean("myInstanceValidatorR4", IValidatorModule.class);
break;
case R5:
validatorModule = appCtx.getBean("myInstanceValidatorR5", IValidatorModule.class);
break;
// These versions are not supported by HAPI FHIR JPA
case DSTU2_HL7ORG:
case DSTU2_1:
default:
validatorModule = null;
break;
}
if (validatorModule != null) {
if (HapiProperties.getValidateRequestsEnabled()) {
RequestValidatingInterceptor interceptor = new RequestValidatingInterceptor();
interceptor.setFailOnSeverity(ResultSeverityEnum.ERROR);
interceptor.setValidatorModules(Collections.singletonList(validatorModule));
registerInterceptor(interceptor);
}
if (HapiProperties.getValidateResponsesEnabled()) {
ResponseValidatingInterceptor interceptor = new ResponseValidatingInterceptor();
interceptor.setFailOnSeverity(ResultSeverityEnum.ERROR);
interceptor.setValidatorModules(Collections.singletonList(validatorModule));
registerInterceptor(interceptor);
}
}
// GraphQL
if (HapiProperties.getGraphqlEnabled()) {
if (fhirVersion.isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
registerProvider(appCtx.getBean(GraphQLProvider.class));
}
}
if (!HapiProperties.getAllowedBundleTypes().isEmpty()) {
String allowedBundleTypesString = HapiProperties.getAllowedBundleTypes();
Set<String> allowedBundleTypes = new HashSet<>();
Arrays.stream(allowedBundleTypesString.split(",")).forEach(o -> {
BundleType type = BundleType.valueOf(o);
allowedBundleTypes.add(type.toCode());
});
DaoConfig config = appCtx.getBean(DaoConfig.class);
config.setBundleTypesAllowedForStorage(Collections.unmodifiableSet(new TreeSet<>(allowedBundleTypes)));
}
// Bulk Export
if (HapiProperties.getBulkExportEnabled()) {
registerProvider(appCtx.getBean(BulkDataExportProvider.class));
}
}
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