Examples with XmlParser org.hl7.fhir.r4.formats.XmlParser used on opensource projects

Example 51 with XmlParser

use of org.hl7.fhir.r4.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class R3ToR5Loader method loadBundle.

@Override
public Bundle loadBundle(InputStream stream, boolean isJson) throws FHIRException, IOException {
    Resource r3 = null;
    if (isJson)
        r3 = new JsonParser().parse(stream);
    else
        r3 = new XmlParser().parse(stream);
    org.hl7.fhir.r5.model.Resource r5 = VersionConvertorFactory_30_50.convertResource(r3, advisor);
    Bundle b;
    if (r5 instanceof Bundle)
        b = (Bundle) r5;
    else {
        b = new Bundle();
        b.setId(UUID.randomUUID().toString().toLowerCase());
        b.setType(BundleType.COLLECTION);
        b.addEntry().setResource(r5).setFullUrl(r5 instanceof CanonicalResource ? ((CanonicalResource) r5).getUrl() : null);
    }
    for (CodeSystem cs : advisor.getCslist()) {
        BundleEntryComponent be = b.addEntry();
        be.setFullUrl(cs.getUrl());
        be.setResource(cs);
    }
    if (killPrimitives) {
        List<BundleEntryComponent> remove = new ArrayList<BundleEntryComponent>();
        for (BundleEntryComponent be : b.getEntry()) {
            if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
                StructureDefinition sd = (StructureDefinition) be.getResource();
                if (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE)
                    remove.add(be);
            }
        }
        b.getEntry().removeAll(remove);
    }
    if (patchUrls) {
        for (BundleEntryComponent be : b.getEntry()) {
            if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
                StructureDefinition sd = (StructureDefinition) be.getResource();
                sd.setUrl(sd.getUrl().replace(URL_BASE, URL_DSTU3));
                sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
                for (ElementDefinition ed : sd.getSnapshot().getElement()) patchUrl(ed);
                for (ElementDefinition ed : sd.getDifferential().getElement()) patchUrl(ed);
            }
        }
    }
    return b;
}

Example 52 with XmlParser

use of org.hl7.fhir.r4.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class GenValueSetExpansionConvertor method main.

public static void main(String[] args) throws FHIRFormatError, IOException {
    String src = args[0];
    String tgt = args[1];
    Bundle bundle = (Bundle) new XmlParser().parse(new FileInputStream(src));
    for (BundleEntryComponent be : bundle.getEntry()) {
        Resource res = be.getResource();
        if (res != null) {
            String id = res.getId();
            if (Utilities.noString(id))
                id = tail(((ValueSet) res).getUrl());
            String dst = Utilities.path(tgt, res.fhirType() + "-" + id + ".json");
            System.out.println(dst);
            new JsonParser().setOutputStyle(OutputStyle.NORMAL).compose(new FileOutputStream(dst), res);
        }
    }
}

Example 53 with XmlParser

use of org.hl7.fhir.r4.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class R2ToR3Loader method loadBundle.

@Override
public Bundle loadBundle(InputStream stream, boolean isJson) throws FHIRException, IOException {
    Resource r2;
    if (isJson)
        r2 = new JsonParser().parse(stream);
    else
        r2 = new XmlParser().parse(stream);
    org.hl7.fhir.dstu3.model.Resource r3 = VersionConvertorFactory_10_30.convertResource(r2, advisor_10_30);
    Bundle b;
    if (r3 instanceof Bundle) {
        b = (Bundle) r3;
    } else {
        b = new Bundle();
        b.setId(UUID.randomUUID().toString().toLowerCase());
        b.setType(BundleType.COLLECTION);
        b.addEntry().setResource(r3).setFullUrl(r3 instanceof MetadataResource ? ((MetadataResource) r3).getUrl() : null);
    }
    advisor_10_30.getCslist().forEach(cs -> {
        BundleEntryComponent be = b.addEntry();
        be.setFullUrl(cs.getUrl());
        be.setResource(cs);
    });
    advisor_10_30.getCslist().clear();
    if (killPrimitives) {
        List<BundleEntryComponent> remove = new ArrayList<BundleEntryComponent>();
        for (BundleEntryComponent be : b.getEntry()) {
            if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
                StructureDefinition sd = (StructureDefinition) be.getResource();
                if (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE)
                    remove.add(be);
            }
        }
        b.getEntry().removeAll(remove);
    }
    if (patchUrls) {
        b.getEntry().stream().filter(be -> be.hasResource() && be.getResource() instanceof StructureDefinition).map(be -> (StructureDefinition) be.getResource()).forEach(sd -> {
            sd.setUrl(sd.getUrl().replace(URL_BASE, URL_DSTU2));
            sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
        });
    }
    return b;
}

Example 54 with XmlParser

use of org.hl7.fhir.r4.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class ProfileUtilitiesTests method compareXml.

private void compareXml(StructureDefinition base, StructureDefinition focus) throws FileNotFoundException, IOException {
    base.setText(null);
    focus.setText(null);
    base.setDifferential(null);
    // focus.setDifferential(null);
    String f1 = Utilities.path("c:", "temp", "base.xml");
    String f2 = Utilities.path("c:", "temp", "derived.xml");
    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f1), base);
    ;
    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f2), focus);
    ;
    String diff = Utilities.path(System.getenv("ProgramFiles(X86)"), "WinMerge", "WinMergeU.exe");
    List<String> command = new ArrayList<String>();
    command.add("\"" + diff + "\" \"" + f1 + "\" \"" + f2 + "\"");
    ProcessBuilder builder = new ProcessBuilder(command);
    builder.directory(new CSFile(Utilities.path("[tmp]")));
    builder.start();
}

Example 55 with XmlParser

use of org.hl7.fhir.r4.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class ProfileUtilitiesTests method compare.

private void compare(String fn1, String fn2) throws FHIRFormatError, FileNotFoundException, IOException, DefinitionException {
    System.out.println("Compare " + fn1 + " to " + fn2);
    System.out.println("  .. load");
    StructureDefinition left = (StructureDefinition) new XmlParser().parse(new FileInputStream(Utilities.path(root, fn1)));
    StructureDefinition right = (StructureDefinition) new XmlParser().parse(new FileInputStream(Utilities.path(root, fn2)));
    System.out.println(" .. compare");
    comp.compareProfiles(left, right);
}