Examples with Use org.hl7.fhir.r4.model.ExplanationOfBenefit.Use used on opensource projects

Example 81 with Use

use of org.hl7.fhir.r4.model.ExplanationOfBenefit.Use in project openmrs-module-fhir2 by openmrs.

the class ObservationFhirResourceProviderIntegrationTest method shouldSupportMultiplePagesAsXML.

@Test
public void shouldSupportMultiplePagesAsXML() throws Exception {
    MockHttpServletResponse response = get("/Observation?subject.name=Chebaskwony&_sort=-date").accept(FhirMediaTypes.XML).go();
    assertThat(response, isOk());
    assertThat(response.getContentType(), is(FhirMediaTypes.XML.toString()));
    assertThat(response.getContentAsString(), notNullValue());
    Bundle results = readBundleResponse(response);
    assertThat(results, notNullValue());
    assertThat(results.getType(), equalTo(Bundle.BundleType.SEARCHSET));
    assertThat(results.hasEntry(), is(true));
    List<Observation> observations = results.getEntry().stream().map(Bundle.BundleEntryComponent::getResource).filter(it -> it instanceof Observation).map(it -> (Observation) it).collect(Collectors.toList());
    Bundle.BundleLinkComponent link = results.getLink("next");
    while (link != null) {
        String nextUrl = link.getUrl();
        URL url = new URL(nextUrl);
        // NB Because we cannot use the *full* URL, we use the relevant portion, which in this case, is just the query
        // string
        response = get("?" + url.getQuery()).accept(FhirMediaTypes.XML).go();
        assertThat(response, isOk());
        assertThat(response.getContentType(), is(FhirMediaTypes.XML.toString()));
        assertThat(response.getContentAsString(), notNullValue());
        results = readBundleResponse(response);
        assertThat(results, notNullValue());
        assertThat(results.getType(), equalTo(Bundle.BundleType.SEARCHSET));
        assertThat(results.hasEntry(), is(true));
        observations.addAll(results.getEntry().stream().map(Bundle.BundleEntryComponent::getResource).filter(it -> it instanceof Observation).map(it -> (Observation) it).collect(Collectors.toList()));
        link = results.getLink("next");
    }
    assertThat(observations, hasSize(equalTo(results.getTotal())));
    for (int i = 1; i < observations.size(); i++) {
        assertThat(observations.get(i - 1).getEffectiveDateTimeType().getValue(), sameOrAfter(observations.get(i).getEffectiveDateTimeType().getValue()));
    }
}

Example 82 with Use

use of org.hl7.fhir.r4.model.ExplanationOfBenefit.Use in project Gravity-SDOH-Exchange-RI by FHIR.

the class TaskPollingService method demoRunQRThroughStructureMap.

/*
  A TEST polling service, implemented during January 2022 Connectathon, that automatically runs questionnaireResponse
  resources through a StructureMap. If any exception occurs - just ignore it.
   */
public void demoRunQRThroughStructureMap() {
    log.info("Looking for TOP 3 Patient QuestionnaireResponse resources without derived Observations...");
    // TODO use repository instead
    Bundle tasksBundle = openEhrClient.search().forResource(QuestionnaireResponse.class).where(new StringClientParam(Constants.PARAM_PROFILE).matches().value(SDOHProfiles.QUESTIONNAIRE_RESPONSE)).revInclude(Observation.INCLUDE_DERIVED_FROM.setRecurse(false)).sort().descending(QuestionnaireResponse.AUTHORED).count(3).returnBundle(Bundle.class).execute();
    List<QuestionnaireResponse> responses = FhirUtil.getFromBundle(tasksBundle, QuestionnaireResponse.class, Bundle.SearchEntryMode.MATCH);
    Set<String> derivedFrom = FhirUtil.getFromBundle(tasksBundle, Observation.class, Bundle.SearchEntryMode.INCLUDE).stream().map(o -> o.getDerivedFromFirstRep().getReferenceElement().getIdPart()).collect(Collectors.toSet());
    if (responses.size() != derivedFrom.size()) {
        log.info("Found " + (responses.size() - derivedFrom.size()) + " QuestionnaireResponse resources without observations.");
        List<QuestionnaireResponse> newResponses = responses.stream().filter(qr -> !derivedFrom.contains(qr.getIdElement().getIdPart())).collect(Collectors.toList());
        for (QuestionnaireResponse nr : newResponses) {
            log.info("Converting QuestionnaireResponse with id: " + nr.getIdElement().getIdPart());
            try {
                // TODO move parser logic within the convert service. Use resources instead
                JSONParser parser = new JSONParser(JSONParser.MODE_JSON_SIMPLE);
                Map<String, Object> result = convertService.convert((JSONObject) parser.parse(fhirContext.newJsonParser().encodeResourceToString(nr)));
                Bundle bundle = (Bundle) fhirContext.newJsonParser().parseResource(new JSONObject(result).toJSONString());
                bundle.getEntry().forEach(e -> e.setRequest(new Bundle.BundleEntryRequestComponent().setMethod(Bundle.HTTPVerb.POST).setUrl(e.getResource().getClass().getSimpleName())));
                openEhrClient.transaction().withBundle(bundle).execute();
            } catch (Exception exc) {
                // Just ignore this specific resource and go to the next one
                log.warn(exc.getMessage(), exc);
            }
        }
    }
    log.info("QuestionnaireResponse update process finished.");
}

Example 83 with Use

use of org.hl7.fhir.r4.model.ExplanationOfBenefit.Use in project Gravity-SDOH-Exchange-RI by FHIR.

the class TaskReferenceResolver method getRequester.

public Organization getRequester() {
    if (localRequester == null) {
        Organization requester = externalRequester.copy();
        // Remove SDOH profile, Logica does not support this.
        // TODO Use SDOH Profiles.
        requester.setMeta(null);
        requester.addIdentifier().setSystem(identifierSystem).setValue(requester.getIdElement().getIdPart());
        requester.setId(IdType.newRandomUuid());
        return requester;
    }
    return localRequester;
}

Example 84 with Use

use of org.hl7.fhir.r4.model.ExplanationOfBenefit.Use in project Gravity-SDOH-Exchange-RI by FHIR.

the class ServiceRequestReferenceResolver method getGoal.

public Goal getGoal(IIdType iIdType) {
    Goal goal = localGoals.get(iIdType.getIdPart());
    if (goal == null) {
        goal = externalGoals.get(iIdType.getIdPart()).copy();
        // Remove SDOH profile, Logica does not support this.
        // TODO Use SDOH Profiles.
        goal.setMeta(null);
        // Set identifier to link resource from EHR
        goal.addIdentifier().setSystem(identifierSystem).setValue(goal.getIdElement().getIdPart());
        goal.setId(IdType.newRandomUuid());
    }
    return goal;
}

Example 85 with Use

use of org.hl7.fhir.r4.model.ExplanationOfBenefit.Use 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));
    }
}