Examples with FHIRVersion org.hl7.fhir.r5.model.Enumerations.FHIRVersion used on opensource projects

Example 1 with FHIRVersion

use of org.hl7.fhir.r5.model.Enumerations.FHIRVersion in project kindling by HL7.

the class SpecNPMPackageGenerator method determineVersion.

private FHIRVersion determineVersion(Map<String, byte[]> files) throws FHIRException {
    byte[] b = files.get("version.info");
    if (b == null)
        return FHIRVersion.NULL;
    String s = new String(b);
    s = Utilities.stripBOM(s).trim();
    while (s.charAt(0) != '[') s = s.substring(1);
    byte[] bytes = {};
    try {
        bytes = s.getBytes("UTF-8");
    } catch (UnsupportedEncodingException e) {
    }
    ByteArrayInputStream bs = new ByteArrayInputStream(bytes);
    IniFile ini = new IniFile(bs);
    String v = ini.getStringProperty("FHIR", "version");
    if (v == null)
        throw new Error("unable to determine version from " + new String(bytes));
    if ("3.0.0".equals(v))
        v = "3.0.1";
    return FHIRVersion.fromCode(v);
}

Example 2 with FHIRVersion

use of org.hl7.fhir.r5.model.Enumerations.FHIRVersion in project kindling by HL7.

the class JsonLDDefinitionsGenerator method generate.

// private String genDate;
// private String version;
// private BuildWorkerContext workerContext;
public void generate(Definitions definitions, IniFile ini, String tmpResDir, String dstDir, String srcDir, FHIRVersion version, String genDate, BuildWorkerContext workerContext) throws Exception {
    // this.genDate = genDate;
    // this.version = version;
    // this.workerContext = workerContext;
    JsonObject defn = new JsonObject();
    JsonObject context = new JsonObject();
    defn.add("@context", context);
    defn.addProperty("@id", "http://hl7.org/fhir/");
    context.addProperty("fhir", "http://hl7.org/fhir/");
    context.addProperty("xsd", "http://www.w3.org/2001/XMLSchema#");
    // properties for primitives, helpers, format features
    addProperty(context, "value", "fhir:value", "xsd:string");
    addProperty(context, "decimal", "fhir:value", "xsd:decimal");
    addProperty(context, "integer", "fhir:value", "xsd:integer");
    if (!version.isR4B()) {
        addProperty(context, "integer64", "fhir:value", "xsd:string");
    }
    addProperty(context, "boolean", "fhir:value", "xsd:boolean");
    addProperty(context, "binary", "fhir:value", "xsd:base64Binary");
    addProperty(context, "date", "fhir:value", "xsd:date");
    addProperty(context, "dateTime", "fhir:value", "xsd:dateTime");
    addProperty(context, "gYearMonth", "fhir:value", "xsd:gYearMonth");
    addProperty(context, "gYear", "fhir:value", "xsd:gYear");
    addProperty(context, "link", "fhir:link", "@id");
    addProperty(context, "concept", "fhir:concept", "@id");
    addProperty(context, "index", "fhir:index", "xsd:integer");
    addProperty(context, "role", "fhir:nodeRole", "@id");
    // elements defined in FHIR:
    for (TypeRef tr : definitions.getKnownTypes()) {
        if (!definitions.hasPrimitiveType(tr.getName()) && !tr.getName().equals("SimpleQuantity") && !tr.getName().equals("MoneyQuantity")) {
            TypeDefn root = definitions.getElementDefn(tr.getName());
            new JsonLDGenerator(definitions, workerContext, definitions.getKnownTypes()).generate(context, root, version, genDate);
        }
    }
    List<String> names = new ArrayList<String>();
    names.addAll(definitions.getResources().keySet());
    names.addAll(definitions.getBaseResources().keySet());
    names.add("Parameters");
    Collections.sort(names);
    for (String name : names) {
        ResourceDefn root = definitions.getResourceByName(name);
        new JsonLDGenerator(definitions, workerContext, definitions.getKnownTypes()).generate(context, root.getRoot(), version, genDate);
    }
    save(defn, dstDir + "fhir.jsonld");
}

Example 3 with FHIRVersion

use of org.hl7.fhir.r5.model.Enumerations.FHIRVersion in project cqf-ruler by DBCG.

the class ExpressionEvaluation method setupContext.

private Context setupContext(DomainResource instance, String cql, String patientId, Boolean aliasedExpression, RequestDetails theRequest) {
    JpaFhirDal jpaFhirDal = jpaFhirDalFactory.create(theRequest);
    List<CanonicalType> libraries = getLibraryReferences(instance, theRequest);
    String fhirVersion = this.fhirContext.getVersion().getVersion().getFhirVersionString();
    // Remove LocalLibrary from cache first...
    VersionedIdentifier localLibraryIdentifier = new VersionedIdentifier().withId("LocalLibrary");
    globalLibraryCache.remove(localLibraryIdentifier);
    // temporary LibraryLoader to resolve library dependencies when building
    // includes
    LibraryLoader tempLibraryLoader = libraryLoaderFactory.create(new ArrayList<LibraryContentProvider>(Arrays.asList(jpaLibraryContentProviderFactory.create(theRequest))));
    String source = "";
    if (aliasedExpression) {
        if (libraries.size() != 1) {
            throw new RuntimeException("If an aliased expression is provided, there must be exactly one primary Library");
        }
        VersionedIdentifier vi = getVersionedIdentifierFromCanonical(libraries.get(0));
        // Still not the best way to build include, but at least checks dal for an
        // existing library
        // Check if id works for LibraryRetrieval
        org.cqframework.cql.elm.execution.Library executionLibrary = null;
        try {
            executionLibrary = tempLibraryLoader.load(vi);
        } catch (Exception e) {
        // log error
        }
        if (executionLibrary == null) {
            Library library = (Library) jpaFhirDal.read(new IdType("Library", Canonicals.getIdPart(libraries.get(0))));
            vi.setId(library.getName());
            if (library.getVersion() != null) {
                vi.setVersion(library.getVersion());
            }
        }
        source = String.format("library LocalLibrary using FHIR version '" + fhirVersion + "' include FHIRHelpers version '" + fhirVersion + "' called FHIRHelpers %s parameter %s %s parameter \"%%context\" %s define Expression: %s", buildIncludes(tempLibraryLoader, jpaFhirDal, libraries, theRequest), instance.fhirType(), instance.fhirType(), instance.fhirType(), vi.getId() + ".\"" + cql + "\"");
    } else {
        source = String.format("library LocalLibrary using FHIR version '" + fhirVersion + "' include FHIRHelpers version '" + fhirVersion + "' called FHIRHelpers %s parameter %s %s parameter \"%%context\" %s define Expression: %s", buildIncludes(tempLibraryLoader, jpaFhirDal, libraries, theRequest), instance.fhirType(), instance.fhirType(), instance.fhirType(), cql);
    }
    LibraryLoader libraryLoader = libraryLoaderFactory.create(new ArrayList<LibraryContentProvider>(Arrays.asList(jpaLibraryContentProviderFactory.create(theRequest), new InMemoryLibraryContentProvider(Arrays.asList(source)))));
    // resolve execution context
    return setupContext(instance, patientId, libraryLoader, theRequest);
}

Example 4 with FHIRVersion

use of org.hl7.fhir.r5.model.Enumerations.FHIRVersion 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));
    }
}

Example 5 with FHIRVersion

use of org.hl7.fhir.r5.model.Enumerations.FHIRVersion in project ab2d by CMSgov.

the class ErrorHandler method generateFHIRError.

private ResponseEntity<JsonNode> generateFHIRError(Exception e, HttpHeaders httpHeaders, HttpServletRequest request) throws IOException {
    String msg = getRootCause(e);
    HttpStatus httpStatus = getErrorResponse(e.getClass());
    FhirVersion version = FhirVersion.fromAB2DUrl(request.getRequestURI());
    IBaseResource operationOutcome = version.getErrorOutcome(msg);
    String encoded = version.outcomePrettyToJSON(operationOutcome);
    // Log so that Splunk can pick this up and alert
    log.warn("{} {}", ExceptionUtils.getRootCause(e).getClass(), msg);
    eventLogger.log(new ApiResponseEvent(MDC.get(ORGANIZATION), null, ErrorHandler.getErrorResponse(e.getClass()), "FHIR Error", msg, (String) request.getAttribute(REQUEST_ID)));
    return new ResponseEntity<>(new ObjectMapper().readTree(encoded), httpHeaders, httpStatus);
}