Examples with FhirVersionEnum ca.uhn.fhir.context.FhirVersionEnum used on opensource projects

Example 6 with FhirVersionEnum

use of ca.uhn.fhir.context.FhirVersionEnum 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()) {
        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();
        }
    }
    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(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);
    }
    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());
}

Example 7 with FhirVersionEnum

use of ca.uhn.fhir.context.FhirVersionEnum in project bunsen by cerner.

the class SparkRowConverter method forResource.

/**
 * Returns a row converter for the given resource type. The resource type can
 * either be a relative URL for a base resource (e.g. "Condition" or "Observation"),
 * or a URL identifying the structure definition for a given profile, such as
 * "http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient".
 * <p>
 * Resources that would be contained must be statically declared through this method
 * via similar URLs.
 * </p>
 * @param context the FHIR context
 * @param resourceTypeUrl the URL of the resource type
 * @param containedResourceTypeUrls the list of URLs of contained resource types
 * @return an Avro converter instance.
 */
public static synchronized SparkRowConverter forResource(FhirContext context, String resourceTypeUrl, List<String> containedResourceTypeUrls) {
    StructureDefinitions structureDefinitions = StructureDefinitions.create(context);
    Map<String, HapiConverter<DataType>> converters = new HashMap<>();
    String basePackage;
    FhirVersionEnum fhirVersion = context.getVersion().getVersion();
    if (FhirVersionEnum.DSTU3.equals(fhirVersion)) {
        basePackage = "com.cerner.bunsen.stu3.spark";
    } else if (FhirVersionEnum.R4.equals(fhirVersion)) {
        basePackage = "com.cerner.bunsen.r4.spark";
    } else {
        throw new IllegalArgumentException("Unsupported FHIR version " + fhirVersion.toString());
    }
    DefinitionToSparkVisitor visitor = new DefinitionToSparkVisitor(structureDefinitions.conversionSupport(), basePackage, converters);
    HapiConverter<DataType> converter = structureDefinitions.transform(visitor, resourceTypeUrl, containedResourceTypeUrls);
    RuntimeResourceDefinition[] resources = new RuntimeResourceDefinition[1 + containedResourceTypeUrls.size()];
    resources[0] = context.getResourceDefinition(converter.getElementType());
    for (int i = 0; i < containedResourceTypeUrls.size(); i++) {
        StructType parentType = (StructType) converter.getDataType();
        ArrayType containerArrayType = (ArrayType) parentType.apply("contained").dataType();
        StructType containerType = (StructType) containerArrayType.elementType();
        resources[i + 1] = context.getResourceDefinition(containerType.apply(i).name());
    }
    return new SparkRowConverter(converter, resources);
}

Example 8 with FhirVersionEnum

use of ca.uhn.fhir.context.FhirVersionEnum in project cqf-ruler by DBCG.

the class Server method initialize.

@Override
@SuppressWarnings({ "rawtypes", "unchecked" })
protected void initialize() throws ServletException {
    super.initialize();
    log.info("Loading metadata extenders from plugins");
    Map<String, MetadataExtender> extenders = myApplicationContext.getBeansOfType(MetadataExtender.class);
    for (MetadataExtender o : extenders.values()) {
        log.info("Found {} extender", o.getClass().getName());
    }
    FhirVersionEnum fhirVersion = fhirSystemDao.getContext().getVersion().getVersion();
    String implementationDescription = myServerProperties.getImplementation_description();
    if (fhirVersion == FhirVersionEnum.DSTU2) {
        List<MetadataExtender<Conformance>> extenderList = extenders.values().stream().map(x -> (MetadataExtender<Conformance>) x).collect(Collectors.toList());
        ExtensibleJpaConformanceProviderDstu2 confProvider = new ExtensibleJpaConformanceProviderDstu2(this, fhirSystemDao, daoConfig, extenderList);
        confProvider.setImplementationDescription(firstNonNull(implementationDescription, "CQF RULER DSTU2 Server"));
        setServerConformanceProvider(confProvider);
    } else {
        if (fhirVersion == FhirVersionEnum.DSTU3) {
            List<MetadataExtender<CapabilityStatement>> extenderList = extenders.values().stream().map(x -> (MetadataExtender<CapabilityStatement>) x).collect(Collectors.toList());
            ExtensibleJpaConformanceProviderDstu3 confProvider = new ExtensibleJpaConformanceProviderDstu3(this, fhirSystemDao, daoConfig, searchParamRegistry, extenderList);
            confProvider.setImplementationDescription(firstNonNull(implementationDescription, "CQF RULER DSTU3 Server"));
            setServerConformanceProvider(confProvider);
        } else if (fhirVersion == FhirVersionEnum.R4) {
            List<MetadataExtender<IBaseConformance>> extenderList = extenders.values().stream().map(x -> (MetadataExtender<IBaseConformance>) x).collect(Collectors.toList());
            ExtensibleJpaCapabilityStatementProvider confProvider = new ExtensibleJpaCapabilityStatementProvider(this, fhirSystemDao, daoConfig, searchParamRegistry, myValidationSupport, extenderList);
            confProvider.setImplementationDescription(firstNonNull(implementationDescription, "CQF RULER R4 Server"));
            setServerConformanceProvider(confProvider);
        } else if (fhirVersion == FhirVersionEnum.R5) {
            List<MetadataExtender<IBaseConformance>> extenderList = extenders.values().stream().map(x -> (MetadataExtender<IBaseConformance>) x).collect(Collectors.toList());
            ExtensibleJpaCapabilityStatementProvider confProvider = new ExtensibleJpaCapabilityStatementProvider(this, fhirSystemDao, daoConfig, searchParamRegistry, myValidationSupport, extenderList);
            confProvider.setImplementationDescription(firstNonNull(implementationDescription, "CQF RULER R5 Server"));
            setServerConformanceProvider(confProvider);
        } else {
            throw new IllegalStateException();
        }
    }
    log.info("Loading operation providers from plugins");
    Map<String, OperationProvider> providers = myApplicationContext.getBeansOfType(OperationProvider.class);
    for (OperationProvider o : providers.values()) {
        log.info("Registering {}", o.getClass().getName());
        this.registerProvider(o);
    }
    log.info("Loading interceptors from plugins");
    Map<String, Interceptor> interceptors = myApplicationContext.getBeansOfType(Interceptor.class);
    for (Interceptor o : interceptors.values()) {
        log.info("Registering {} interceptor", o.getClass().getName());
        this.registerInterceptor(o);
    }
}

Example 9 with FhirVersionEnum

use of ca.uhn.fhir.context.FhirVersionEnum in project cqf-ruler by DBCG.

the class Ids method newId.

/**
 * Creates the appropriate IIdType for a given ResourceTypeClass
 *
 * @param <ResourceType>       an IBase type
 * @param <IdType>             an IIdType type
 * @param theResourceTypeClass the type of the Resource to create an Id for
 * @param theId                the String representation of the Id to generate
 * @return the id
 */
public static <ResourceType extends IBaseResource, IdType extends IIdType> IdType newId(Class<? extends ResourceType> theResourceTypeClass, String theId) {
    checkNotNull(theResourceTypeClass);
    checkNotNull(theId);
    FhirVersionEnum versionEnum = FhirVersions.forClass(theResourceTypeClass);
    return newId(versionEnum, theResourceTypeClass.getSimpleName(), theId);
}

Example 10 with FhirVersionEnum

use of ca.uhn.fhir.context.FhirVersionEnum in project cqf-ruler by DBCG.

the class Ids method newId.

/**
 * Creates the appropriate IIdType for a given BaseTypeClass
 *
 * @param <BaseType>       an IBase type
 * @param <IdType>         an IIdType type
 * @param theBaseTypeClass the BaseTypeClass to use for for determining the FHIR
 *                         Version
 * @param theResourceName  the type of the Resource to create an Id for
 * @param theId            the String representation of the Id to generate
 * @return the id
 */
public static <BaseType extends IBase, IdType extends IIdType> IdType newId(Class<? extends BaseType> theBaseTypeClass, String theResourceName, String theId) {
    checkNotNull(theBaseTypeClass);
    checkNotNull(theResourceName);
    checkNotNull(theId);
    FhirVersionEnum versionEnum = FhirVersions.forClass(theBaseTypeClass);
    return newId(versionEnum, theResourceName, theId);
}