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

Example 36 with SearchParameter

use of org.hl7.fhir.r4.model.SearchParameter in project org.hl7.fhir.core by hapifhir.

the class SearchParameterRenderer method render.

public boolean render(XhtmlNode x, SearchParameter spd) throws IOException, FHIRException, EOperationOutcome {
    x.h2().addText(spd.getName());
    XhtmlNode p = x.para();
    p.tx("Parameter ");
    p.code().tx(spd.getCode());
    p.tx(":");
    p.code().tx(spd.getType().toCode());
    addMarkdown(x, spd.getDescription());
    XhtmlNode tbl = x.table("grid");
    XhtmlNode tr = tbl.tr();
    tr.td().tx(Utilities.pluralize("Resource", spd.getBase().size()));
    XhtmlNode td = tr.td();
    for (CodeType t : spd.getBase()) {
        StructureDefinition sd = context.getWorker().fetchTypeDefinition(t.toString());
        if (sd != null && sd.hasUserData("path")) {
            td.sep(", ").ah(sd.getUserString("path")).tx(t.getCode());
        } else {
            td.sep(", ").tx(t.getCode());
        }
    }
    tr = tbl.tr();
    tr.td().tx("Expression");
    if (spd.hasExpression()) {
        tr.td().code().tx(spd.getExpression());
    } else {
        tr.td().tx("(none)");
    }
    if (spd.hasXpathUsage()) {
        tr = tbl.tr();
        tr.td().tx("Usage");
        tr.td().tx(spd.getXpathUsage().getDisplay());
    }
    if (spd.hasXpath()) {
        tr = tbl.tr();
        tr.td().tx("XPath");
        tr.td().code().tx(spd.getXpath());
    }
    if (spd.hasTarget()) {
        tr = tbl.tr();
        tr.td().tx(Utilities.pluralize("Target Resources", spd.getTarget().size()));
        td = tr.td();
        for (CodeType t : spd.getTarget()) {
            StructureDefinition sd = context.getWorker().fetchTypeDefinition(t.toString());
            if (sd != null && sd.hasUserData("path")) {
                td.sep(", ").ah(sd.getUserString("path")).tx(t.getCode());
            } else {
                td.sep(", ").tx(t.getCode());
            }
        }
    }
    tr = tbl.tr();
    tr.td().tx("Multiples");
    if (spd.getMultipleAnd() && spd.getMultipleOr()) {
        tr.td().tx("The parameter can repeat (and) and can have repeating values (or)");
    } else if (spd.getMultipleOr()) {
        tr.td().tx("The parameter can repeat (and) but each repeat can only have one value");
    } else if (spd.getMultipleAnd()) {
        tr.td().tx("The parameter cannot repeat (and) but the single parameter can have multiple values (or)");
    } else {
        tr.td().tx("The parameter cannot repeat or have multiple values");
    }
    if (spd.hasComparator()) {
        tr = tbl.tr();
        tr.td().tx("Comparators");
        td = tr.td().tx("Allowed: ");
        for (Enumeration<SearchComparator> t : spd.getComparator()) {
            td.sep(", ").tx(t.asStringValue());
        }
    }
    if (spd.hasModifier()) {
        tr = tbl.tr();
        tr.td().tx("Modifiers");
        td = tr.td().tx("Allowed: ");
        for (Enumeration<SearchModifierCode> t : spd.getModifier()) {
            td.sep(", ").tx(t.asStringValue());
        }
    }
    if (spd.hasChain()) {
        tr = tbl.tr();
        tr.td().tx("Chains");
        td = tr.td().tx("Allowed: ");
        for (StringType t : spd.getChain()) {
            td.sep(", ").tx(t.asStringValue());
        }
    }
    if (spd.hasComponent()) {
        x.para().b().tx("Components");
        tbl = x.table("grid");
        for (SearchParameterComponentComponent t : spd.getComponent()) {
            tr = tbl.tr();
            SearchParameter tsp = context.getWorker().fetchResource(SearchParameter.class, t.getDefinition());
            if (tsp != null && tsp.hasUserData("path")) {
                tr.td().ah(tsp.getUserString("path")).tx(tsp.present());
            } else {
                tr.td().tx(t.getDefinition());
            }
            tr.td().code().tx(t.getExpression());
        }
    }
    return false;
}

Example 37 with SearchParameter

use of org.hl7.fhir.r4.model.SearchParameter 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 38 with SearchParameter

use of org.hl7.fhir.r4.model.SearchParameter in project kindling by HL7.

the class SpreadSheetReloader method processSearchParams.

private void processSearchParams(XSSFWorkbook excel) throws FHIRFormatError, FileNotFoundException, IOException {
    Bundle bnd = (Bundle) parseXml(fnSP());
    XSSFSheet src = getSheet(excel, SN_SEARCH);
    List<BundleEntryComponent> oldSPs = bnd.getEntry();
    bnd.setEntry(new ArrayList<>());
    XSSFRow cols = src.getRow(0);
    for (int i = 1; i <= src.getLastRowNum(); i++) {
        XSSFRow row = src.getRow(i);
        if (row != null && hasValue(row, cols, CN_NAME)) {
            String c = getValue(row, cols, CN_NAME);
            SearchParameter sp = getSp(oldSPs, c);
            bnd.addEntry().setResource(sp);
            readSearchParameter(row, cols, sp);
        }
    }
    saveXml(fnSP(), bnd);
}

Example 39 with SearchParameter

use of org.hl7.fhir.r4.model.SearchParameter in project kindling by HL7.

the class ValueSetFinder method checkSearchParams.

private static void checkSearchParams(File f) throws Exception {
    String folder = Utilities.getDirectoryForFile(f.getAbsolutePath());
    System.out.println(f.getName());
    try {
        Set<String> s = new HashSet<>();
        for (File fsp : new File(folder).listFiles()) {
            if (fsp.getName().startsWith("searchparameter-")) {
                SearchParameter sp = (SearchParameter) new XmlParser().parseAndClose(new FileInputStream(fsp));
                s.add(sp.getId());
            }
        }
        for (File fig : new File(folder).listFiles()) {
            if (fig.getName().startsWith("implementationguide-")) {
                ImplementationGuide ig = (ImplementationGuide) new XmlParser().parseAndClose(new FileInputStream(fig));
                ig.getDefinition().getResource().removeIf(res -> res.getReference().getReference().startsWith("SearchParameter/") && !s.contains(res.getReference().getReference().substring(res.getReference().getReference().indexOf("/") + 1)));
                if (ig.getDefinition().getResource().isEmpty()) {
                    fig.delete();
                } else {
                    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(fig), ig);
                }
            }
        }
    } catch (Exception e) {
        System.out.println("  " + e.getMessage());
    }
}

Example 40 with SearchParameter

use of org.hl7.fhir.r4.model.SearchParameter in project kindling by HL7.

the class PageProcessor method genAllSearchParams.

private String genAllSearchParams() throws Exception {
    List<SearchParameter> splist = new ArrayList<SearchParameter>();
    for (ResourceDefn rd : getDefinitions().getBaseResources().values()) addSearchParams(splist, rd);
    for (ResourceDefn rd : getDefinitions().getResources().values()) addSearchParams(splist, rd);
    for (Profile cp : getDefinitions().getPackList()) {
        addSearchParams(splist, cp);
    }
    StringBuilder b = new StringBuilder();
    genSearchParams(b, splist, "Resource");
    genSearchParams(b, splist, "DomainResource");
    genCommonSearchParams(b, splist);
    for (String n : definitions.sortedResourceNames()) genSearchParams(b, splist, n);
    return b.toString();
}