Examples with XmlParser org.hl7.fhir.r4b.formats.XmlParser used on opensource projects

Example 71 with XmlParser

use of org.hl7.fhir.r4b.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class SimpleWorkerContext method loadFromFile.

private void loadFromFile(InputStream stream, String name) throws IOException, FHIRException {
    XmlParser xml = new XmlParser();
    Bundle f;
    try {
        f = (Bundle) xml.parse(stream);
    } catch (FHIRFormatError e1) {
        throw new org.hl7.fhir.exceptions.FHIRFormatError(e1.getMessage(), e1);
    }
    for (BundleEntryComponent e : f.getEntry()) {
        if (e.getFullUrl() == null) {
            System.out.println("unidentified resource in " + name + " (no fullUrl)");
        }
        seeResource(e.getFullUrl(), e.getResource());
    }
}

Example 72 with XmlParser

use of org.hl7.fhir.r4b.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class NarrativeGeneratorTests method process.

private void process(String path) throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
    XmlParser p = new XmlParser();
    DomainResource r = (DomainResource) p.parse(new FileInputStream(path));
    gen.generate(r);
    FileOutputStream s = new FileOutputStream(Utilities.path("[tmp]", "gen.xml"));
    new XmlParser().compose(s, r, true);
    s.close();
}

Example 73 with XmlParser

use of org.hl7.fhir.r4b.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class ClientUtils method getFeedAsByteArray.

public byte[] getFeedAsByteArray(Bundle feed, 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 ? OutputStyle.PRETTY : OutputStyle.NORMAL);
        parser.compose(baos, feed);
        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 74 with XmlParser

use of org.hl7.fhir.r4b.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class ProfileUtilitiesTests method execute.

public void execute(String[] args) throws FileNotFoundException, IOException, FHIRException {
    System.out.println("loading context");
    context = SimpleWorkerContext.fromPack(Utilities.path(root, "validation.zip"));
    comp = new ProfileComparer(context);
    compare("patient-daf-dafpatient.profile.xml", "patient-qicore-qicore-patient.profile.xml");
    compare("encounter-daf-dafencounter.profile.xml", "encounter-qicore-qicore-encounter.profile.xml");
    compare("substance-daf-dafsubstance.profile.xml", "substance-qicore-qicore-substance.profile.xml");
    compare("medication-daf-dafmedication.profile.xml", "medication-qicore-qicore-medication.profile.xml");
    compare("procedure-daf-dafprocedure.profile.xml", "procedure-qicore-qicore-procedure.profile.xml");
    compare("familymemberhistory-daf-daffamilymemberhistory.profile.xml", "familymemberhistory-qicore-qicore-familymemberhistory.profile.xml");
    compare("immunization-daf-dafimmunization.profile.xml", "immunization-qicore-qicore-immunization.profile.xml");
    compare("condition-daf-dafcondition.profile.xml", "condition-qicore-qicore-condition.profile.xml");
    compare("allergyintolerance-daf-dafallergyintolerance.profile.xml", "allergyintolerance-qicore-qicore-allergyintolerance.profile.xml");
    compare("medicationadministration-daf-dafmedicationadministration.profile.xml", "medicationadministration-qicore-qicore-medicationadministration.profile.xml");
    compare("medicationdispense-daf-dafmedicationdispense.profile.xml", "medicationdispense-qicore-qicore-medicationdispense.profile.xml");
    compare("medicationprescription-daf-dafmedicationprescription.profile.xml", "medicationprescription-qicore-qicore-medicationprescription.profile.xml");
    compare("medicationstatement-daf-dafmedicationstatement.profile.xml", "medicationstatement-qicore-qicore-medicationstatement.profile.xml");
    compare("observation-daf-smokingstatus-dafsmokingstatus.profile.xml", "observation-qicore-qicore-observation.profile.xml");
    compare("observation-daf-vitalsigns-dafvitalsigns.profile.xml", "observation-qicore-qicore-observation.profile.xml");
    // compare("observation-daf-results-dafresultobs.profile.xml", "observation-qicore-qicore-observation.profile.xml");
    // compare("diagnosticorder-daf-dafdiagnosticorder.profile.xml", "diagnosticorder-qicore-qicore-diagnosticorder.profile.xml");
    // compare("diagnosticreport-daf-dafdiagnosticreport.profile.xml", "diagnosticreport-qicore-qicore-diagnosticreport.profile.xml");
    System.out.println("processing output");
    for (ProfileComparison outcome : comp.getComparisons()) {
        if (outcome.getSubset() != null)
            new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "intersection-" + outcome.getId() + ".xml")), outcome.getSubset());
        if (outcome.getSuperset() != null)
            new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "union-" + outcome.getId() + ".xml")), outcome.getSuperset());
        System.out.println("\r\n" + outcome.getId() + ": Comparison of " + outcome.getLeft().getUrl() + " and " + outcome.getRight().getUrl());
        for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.INFORMATION)
            System.out.println(vm.summary());
        for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.WARNING)
            System.out.println(vm.summary());
        for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.ERROR)
            System.out.println(vm.summary());
        for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.FATAL)
            System.out.println(vm.summary());
        System.out.println("done. " + Integer.toString(outcome.getMessages().size()) + " messages");
        System.out.println("=================================================================");
    }
}

Example 75 with XmlParser

use of org.hl7.fhir.r4b.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class ToolsHelper method executeRoundTrip.

public void executeRoundTrip(String[] args) throws IOException, FHIRException {
    FileInputStream in;
    File source = new CSFile(args[1]);
    File dest = new CSFile(args[2]);
    if (args.length >= 4) {
        Utilities.copyFile(args[1], args[3]);
    }
    if (!source.exists())
        throw new FHIRException("Source File \"" + source.getAbsolutePath() + "\" not found");
    in = new CSFileInputStream(source);
    XmlParser p = new XmlParser();
    JsonParser parser = new JsonParser();
    JsonParser pj = parser;
    Resource rf = p.parse(in);
    ByteArrayOutputStream json = new ByteArrayOutputStream();
    parser.setOutputStyle(OutputStyle.PRETTY);
    parser.compose(json, rf);
    json.close();
    TextFile.stringToFile(new String(json.toByteArray()), Utilities.changeFileExt(dest.getAbsolutePath(), ".json"));
    rf = pj.parse(new ByteArrayInputStream(json.toByteArray()));
    FileOutputStream s = new FileOutputStream(dest);
    new XmlParser().compose(s, rf, true);
    s.close();
}