Examples with IParser org.hl7.fhir.r5.formats.IParser used on opensource projects

Example 41 with IParser

use of org.hl7.fhir.r5.formats.IParser in project org.hl7.fhir.core by hapifhir.

the class BatchLoader method main.

public static void main(String[] args) throws IOException, Exception {
    if (args.length < 4) {
        System.out.println("Batch uploader takes 4 parameters in order: server base url, file/folder to upload, xml/json, and batch size");
    } else {
        String server = args[0];
        String file = args[1];
        // args[2].equals("json") ? new JsonParser() : new XmlParser();
        IParser p = new JsonParser();
        int size = Integer.parseInt(args[3]);
        size = 500;
        if (file.endsWith(".xml")) {
            throw new FHIRException("Unimplemented file type " + file);
        } else if (file.endsWith(".json")) {
            throw new FHIRException("Unimplemented file type " + file);
        } else if (file.endsWith(".zip")) {
            LoadZipFile(server, file, p, size, 0, -1);
        } else if (new File(file).isDirectory()) {
            LoadDirectory(server, file, p, size);
        } else
            throw new FHIRException("Unknown file type " + file);
    }
}

Example 42 with IParser

use of org.hl7.fhir.r5.formats.IParser in project org.hl7.fhir.core by hapifhir.

the class ByteUtils method resourceToByteArray.

public static <T extends Resource> byte[] resourceToByteArray(T resource, boolean pretty, boolean isJson) {
    ByteArrayOutputStream baos = null;
    byte[] byteArray = null;
    try {
        baos = new ByteArrayOutputStream();
        IParser parser = null;
        if (isJson) {
            parser = new JsonParser();
        } else {
            parser = new XmlParser();
        }
        parser.setOutputStyle(pretty ? IParser.OutputStyle.PRETTY : IParser.OutputStyle.NORMAL);
        parser.compose(baos, resource);
        baos.close();
        byteArray = baos.toByteArray();
        baos.close();
    } catch (Exception e) {
        try {
            baos.close();
        } catch (Exception ex) {
            throw new EFhirClientException("Error closing output stream", ex);
        }
        throw new EFhirClientException("Error converting output stream to byte array", e);
    }
    return byteArray;
}

Example 43 with IParser

use of org.hl7.fhir.r5.formats.IParser in project fhir-bridge by ehrbase.

the class FhirValidationConfiguration method validationSupport.

public IValidationSupport validationSupport() {
    ValidationSupportChain validationSupportChain = new ValidationSupportChain();
    // Validates core structure definitions
    DefaultProfileValidationSupport defaultProfileValidationSupport = new DefaultProfileValidationSupport(fhirContext);
    defaultProfileValidationSupport.fetchAllStructureDefinitions();
    defaultProfileValidationSupport.fetchCodeSystem("");
    validationSupportChain.addValidationSupport(defaultProfileValidationSupport);
    // Validates custom profiles (loaded from classpath)
    PrePopulatedValidationSupport prePopulatedValidationSupport = new PrePopulatedValidationSupport(fhirContext);
    IParser parser = fhirContext.newXmlParser();
    try {
        for (Resource resource : applicationContext.getResources("classpath:/profiles/*")) {
            StructureDefinition profile = parser.parseResource(StructureDefinition.class, resource.getInputStream());
            if (properties.isOptionalIdentifier()) {
                modifyProfile(profile);
            }
            prePopulatedValidationSupport.addStructureDefinition(profile);
        }
    } catch (IOException e) {
        throw new FhirBridgeException("An I/O exception occurred while loading custom profiles");
    }
    validationSupportChain.fetchAllStructureDefinitions();
    defaultProfileValidationSupport.fetchCodeSystem("");
    validationSupportChain.addValidationSupport(prePopulatedValidationSupport);
    // Validates terminology: CodeSystems and ValueSets (using the internal and/or remote terminology service)
    if (isTerminologyValidationEnabled()) {
        TerminologyValidationMode mode = properties.getTerminology().getMode();
        if (mode == TerminologyValidationMode.REMOTE || mode == TerminologyValidationMode.MIXED) {
            RemoteTerminologyServiceValidationSupport remoteTerminologyServerValidationSupport = new RemoteTerminologyServiceValidationSupport(fhirContext);
            remoteTerminologyServerValidationSupport.setBaseUrl(properties.getTerminology().getServerBaseUrl());
            validationSupportChain.addValidationSupport(remoteTerminologyServerValidationSupport);
        }
        if (mode == TerminologyValidationMode.INTERNAL || mode == TerminologyValidationMode.MIXED) {
            validationSupportChain.addValidationSupport(new InMemoryTerminologyServerValidationSupport(fhirContext));
            validationSupportChain.addValidationSupport(new CommonCodeSystemsTerminologyService(fhirContext));
        }
    }
    return new CachingValidationSupport(validationSupportChain);
}

Example 44 with IParser

use of org.hl7.fhir.r5.formats.IParser in project geoprism-registry by terraframe.

the class FhirBulkDataImporter method synchronize.

public void synchronize() {
    PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
    HttpClientBuilder builder = HttpClientBuilder.create();
    builder.setConnectionManager(connectionManager);
    CloseableHttpClient myClient = builder.build();
    FhirContext ctx = FhirContext.forR4();
    String statusUrl = initiateBulkExport(myClient, ctx);
    if (statusUrl != null) {
        final List<String> outputs = getExportResults(myClient, statusUrl);
        IGenericClient client = ctx.newRestfulGenericClient(this.system.getUrl());
        for (String binaryUrl : outputs) {
            Binary binary = client.fetchResourceFromUrl(Binary.class, binaryUrl);
            String base64 = binary.getContentAsBase64();
            byte[] result = Base64.getDecoder().decode(base64);
            IParser parser = ctx.newJsonParser();
            String message = new String(result);
            try (BufferedReader reader = new BufferedReader(new StringReader(message))) {
                String line = null;
                while ((line = reader.readLine()) != null) {
                    IBaseResource resource = parser.parseResource(line);
                    IIdType id = resource.getIdElement();
                    String resourceType = id.getResourceType();
                    if (resourceType.equals(ResourceTypes.LOCATION.toCode())) {
                        Location location = (Location) resource;
                        this.processor.process(location);
                    } else if (resourceType.equals(ResourceTypes.ORGANIZATION.toCode())) {
                        Organization organization = (Organization) resource;
                        this.processor.process(organization);
                    }
                }
            } catch (IOException e) {
                throw new ProgrammingErrorException(e);
            }
        }
    }
}

Example 45 with IParser

use of org.hl7.fhir.r5.formats.IParser in project geoprism-registry by terraframe.

the class FhirExportSynchronizationManager method writeToFile.

public File writeToFile() throws IOException {
    final FhirExternalSystem system = (FhirExternalSystem) this.config.getSystem();
    try (FhirConnection connection = FhirConnectionFactory.get(system)) {
        String name = SessionPredicate.generateId();
        File root = new File(new File(VaultProperties.getPath("vault.default"), "files"), name);
        root.mkdirs();
        Bundle bundle = this.generateBundle(connection);
        FhirContext ctx = FhirContext.forR4();
        IParser parser = ctx.newJsonParser();
        try {
            parser.encodeResourceToWriter(bundle, new FileWriter(new File(root, "bundle.json")));
        } catch (DataFormatException | IOException e) {
            throw new ProgrammingErrorException(e);
        }
        return root;
    } catch (Exception e) {
        throw new HttpError(e);
    }
}