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

Example 46 with IParser

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

the class FhirImportTest method testBasicImport.

@Request
@Test
public void testBasicImport() throws InterruptedException {
    try {
        FhirExternalSystem system = createExternalSystem();
        SynchronizationConfig config = createSyncConfig(system);
        FhirSyncImportConfig iConfig = (FhirSyncImportConfig) config.buildConfiguration();
        FhirResourceProcessor processor = FhirFactory.getProcessor(iConfig.getImplementation());
        IParser parser = FhirContext.forR4().newJsonParser();
        Bundle bundle = new Bundle();
        bundle.addEntry(new BundleEntryComponent().setResource((Resource) parser.parseResource(this.getClass().getResourceAsStream("/fhir/organization.json"))));
        bundle.addEntry(new BundleEntryComponent().setResource((Resource) parser.parseResource(this.getClass().getResourceAsStream("/fhir/location.json"))));
        FhirResourceImporter importer = new FhirResourceImporter(new BasicFhirConnection(system), processor, null, null);
        importer.synchronize(bundle);
        ServerGeoObjectIF geoobject = new ServerGeoObjectService().getGeoObjectByCode("USATestDataHsTwo", "USATestDataHealthStop");
        geoobject.setDate(new Date());
        LocalizedValue displayLabel = geoobject.getDisplayLabel();
        Assert.assertEquals("USATestDataHsTwo ZZZZZZZ", displayLabel.getValue());
    } finally {
        TestDataSet.deleteExternalSystems("FHIRImportTest");
    }
}

Example 47 with IParser

use of org.hl7.fhir.r5.formats.IParser in project redmatch by aehrc.

the class RedmatchApi method save.

private void save(Map<String, List<DomainResource>> grouped, Path tgtDir, ProgressReporter progressReporter, CancelChecker cancelToken) throws IOException {
    try {
        log.info("Saving to output folder " + tgtDir);
        if (progressReporter != null) {
            progressReporter.reportProgress(Progress.reportStart("Saving files"));
        }
        IParser jsonParser = ctx.newJsonParser();
        double div = grouped.size() / 100.0;
        int i = 0;
        for (String key : grouped.keySet()) {
            File f = new File(tgtDir.toFile(), key + ".ndjson");
            try (BufferedWriter bw = new BufferedWriter(new FileWriter(f))) {
                for (DomainResource dr : grouped.get(key)) {
                    jsonParser.encodeResourceToWriter(dr, bw);
                    bw.newLine();
                }
            }
            i++;
            if (progressReporter != null) {
                progressReporter.reportProgress(Progress.reportProgress((int) Math.floor(i / div)));
            }
            if (cancelToken != null && cancelToken.isCanceled()) {
                return;
            }
        }
    } finally {
        if (progressReporter != null) {
            progressReporter.reportProgress(Progress.reportEnd());
        }
    }
}

Example 48 with IParser

use of org.hl7.fhir.r5.formats.IParser in project nia-patient-switching-standard-adaptor by NHSDigital.

the class SDSServiceTest method parseResponses.

@BeforeAll
public static void parseResponses() throws IOException {
    FhirContext context = FhirContext.forDstu3();
    context.newJsonParser();
    context.setParserErrorHandler(new StrictErrorHandler());
    IParser jsonParser = context.newJsonParser();
    readResponsesFromFile();
    ehrResponseBundle = jsonParser.parseResource(Bundle.class, sdsResponseEHRExtract);
    copcResponseBundle = jsonParser.parseResource(Bundle.class, sdsResponseCopcMessage);
    noResultsBundle = jsonParser.parseResource(Bundle.class, sdsResponseNoResults);
}

Example 49 with IParser

use of org.hl7.fhir.r5.formats.IParser in project CRD by HL7-DaVinci.

the class CdsConnectFileStore method processFhirFiles.

private void processFhirFiles(List<CdsConnectFile> files, String topic) {
    // process the fhir resource files
    // setup the proper FHIR Context for the version of FHIR we are dealing with
    FhirContext r4ctx = new org.hl7.davinci.r4.FhirComponents().getFhirContext();
    IParser r4parser = r4ctx.newJsonParser();
    // suppress the unknown element warnings
    r4parser.setParserErrorHandler(new SuppressParserErrorHandler());
    // process all of the files found within the topic/artifact
    for (CdsConnectFile file : files) {
        String path = file.getPath();
        String filename = file.getFilename();
        if (filename.endsWith(".json")) {
            logger.info("        process: FHIR Resource: " + filename);
            String[] parts = filename.split("-");
            if (parts.length > 2) {
                // String resourceType = parts[0];
                String fhirVersion = parts[1];
                String name = parts[2];
                IBaseResource baseResource = null;
                byte[] fileContents = file.getCqlBundle();
                if (fhirVersion.equalsIgnoreCase("R4")) {
                    baseResource = r4parser.parseResource(new ByteArrayInputStream(fileContents));
                }
                processFhirResource(baseResource, path, filename, fhirVersion, topic);
            }
        }
    }
}

Example 50 with IParser

use of org.hl7.fhir.r5.formats.IParser in project CRD by HL7-DaVinci.

the class GitHubFileStore method processFhirFolder.

private void processFhirFolder(String topic, String fhirVersion, String fhirPath) {
    fhirVersion = fhirVersion.toUpperCase();
    logger.info("      GitHubFileStore::processFhirFolder(): " + fhirVersion + ": " + fhirPath);
    // setup the proper FHIR Context for the version of FHIR we are dealing with
    FhirContext ctx = null;
    if (fhirVersion.equalsIgnoreCase("R4")) {
        ctx = new org.hl7.davinci.r4.FhirComponents().getFhirContext();
    } else {
        logger.warn("unsupported FHIR version: " + fhirVersion + ", skipping folder");
        return;
    }
    IParser parser = ctx.newJsonParser();
    // suppress the unknown element warnings
    parser.setParserErrorHandler(new SuppressParserErrorHandler());
    for (String folder : connection.getDirectory(fhirPath)) {
        if (folder.equalsIgnoreCase("resources")) {
            String fullFolderPath = fhirPath + "/" + folder;
            for (String resource : connection.getDirectory(fullFolderPath)) {
                String filename = resource;
                String fullFilePath = fullFolderPath + "/" + filename;
                logger.info("        process: FHIR Resource: " + filename);
                String[] parts = filename.split("-");
                if (parts.length > 2) {
                    // = parts[0];
                    String resourceType;
                    if (!parts[1].equalsIgnoreCase(fhirVersion)) {
                        logger.warn("GitHubFileStore::processFhirFolder() warning: FhirVersion doesn't match!");
                        continue;
                    }
                    InputStream inputStream = connection.getFile(fullFilePath);
                    if (inputStream != null) {
                        IBaseResource baseResource = parser.parseResource(inputStream);
                        processFhirResource(baseResource, filename, filename, fhirVersion, topic);
                    } else {
                        logger.warn("could not find file: " + fullFilePath);
                        continue;
                    }
                }
            }
        }
    }
}