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

Example 26 with JsonParser

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

the class R5ToR5Loader method loadBundle.

@Override
public Bundle loadBundle(InputStream stream, boolean isJson) throws FHIRException, IOException {
    Resource r5 = null;
    if (isJson)
        r5 = new JsonParser().parse(stream);
    else
        r5 = new XmlParser().parse(stream);
    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 : cslist) {
        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_R4));
                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 27 with JsonParser

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

the class CountryCodesConverter method execute.

private void execute() throws ParserConfigurationException, SAXException, IOException {
    Document src = load();
    CodeSystem cs1 = new CodeSystem();
    CodeSystem cs2 = new CodeSystem();
    CodeSystem cs3 = new CodeSystem();
    setMetadata(src, cs1, "iso3166", "urn:iso:std:iso:3166", "", "");
    setMetadata(src, cs2, "iso3166-2", "urn:iso:std:iso:3166:-2", "Part2", " Part 2");
    cs1.addProperty().setCode("canonical").setDescription("The 2 letter code that identifies the same country (so 2/3/numeric codes can be aligned)").setType(PropertyType.CODE);
    cs2.addProperty().setCode("country").setDescription("The 2 letter code that identifies the country for the subdivision").setType(PropertyType.CODE);
    for (Element e : XMLUtil.getNamedChildren(src.getDocumentElement(), "country")) {
        System.out.println(e.getAttribute("id"));
        String c2 = XMLUtil.getNamedChildText(e, "alpha-2-code");
        String c3 = XMLUtil.getNamedChildText(e, "alpha-3-code");
        String cN = XMLUtil.getNamedChildText(e, "numeric-code");
        Element n = XMLUtil.getNamedChildByAttribute(e, "short-name", "lang3code", "eng");
        if (n == null)
            n = XMLUtil.getNamedChildByAttribute(e, "short-name-upper-case", "lang3code", "eng");
        if (n == null)
            continue;
        String name = n.getTextContent();
        n = XMLUtil.getNamedChildByAttribute(e, "full-name", "lang3code", "eng");
        if (n == null)
            n = XMLUtil.getNamedChildByAttribute(e, "full-name-upper-case", "lang3code", "eng");
        if (n == null)
            n = XMLUtil.getNamedChildByAttribute(e, "short-name", "lang3code", "eng");
        if (n == null)
            n = XMLUtil.getNamedChildByAttribute(e, "short-name-upper-case", "lang3code", "eng");
        String desc = n.getTextContent();
        ConceptDefinitionComponent cc = cs1.addConcept();
        cc.setCode(c2);
        cc.setDisplay(name);
        cc.setDefinition(desc);
        poplang(e, cc);
        if (c3 != null) {
            cc = cs1.addConcept();
            cc.setCode(c3);
            cc.setDisplay(name);
            cc.setDefinition(desc);
            cc.addProperty().setCode("canonical").setValue(new CodeType(c2));
            poplang(e, cc);
        }
        if (cN != null) {
            cc = cs1.addConcept();
            cc.setCode(cN);
            cc.setDisplay(name);
            cc.setDefinition(desc);
            cc.addProperty().setCode("canonical").setValue(new CodeType(c2));
            poplang(e, cc);
        }
        for (Element sd : XMLUtil.getNamedChildren(e, "subdivision")) {
            cc = cs2.addConcept();
            cc.setCode(XMLUtil.getNamedChildText(sd, "subdivision-code"));
            Element l = XMLUtil.getNamedChild(sd, "subdivision-locale");
            cc.setDisplay(XMLUtil.getNamedChildText(l, "subdivision-locale-name"));
            cc.addProperty().setCode("country").setValue(new CodeType(c2));
        }
    }
    cs1.setCount(cs1.getConcept().size());
    cs2.setCount(cs2.getConcept().size());
    throw new Error("Needs revisiting");
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "4.0.1", "package", "CodeSstem-iso3166.json")), cs1);
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "3.0.2", "package", "CodeSstem-iso3166.json")), cs1); // format hasn't changed
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "4.0.1", "package", "CodeSstem-iso3166-2.json")), cs2);
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "3.0.2", "package", "CodeSstem-iso3166-2.json")), cs2); // format hasn't changed
}

Example 28 with JsonParser

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

the class ArgonautConverter method saveResource.

private void saveResource(Resource resource, String extraType) throws Exception {
    if (!WANT_SAVE)
        return;
    DomainResource dr = null;
    if (resource instanceof DomainResource) {
        dr = (DomainResource) resource;
        if (!dr.hasText()) {
            NarrativeGenerator generator = new NarrativeGenerator("", "", context);
            generator.generate(dr);
        }
    }
    XmlParser xparser = new XmlParser();
    xparser.setOutputStyle(OutputStyle.PRETTY);
    JsonParser jparser = new JsonParser();
    jparser.setOutputStyle(OutputStyle.PRETTY);
    ByteArrayOutputStream ba = new ByteArrayOutputStream();
    xparser.compose(ba, resource);
    ba.close();
    byte[] srcX = ba.toByteArray();
    ba = new ByteArrayOutputStream();
    jparser.compose(ba, resource);
    ba.close();
    byte[] srcJ = ba.toByteArray();
    String rn = resource.getResourceType().toString();
    if (extraType != null)
        rn = rn + extraType;
    zipX.addBytes(resource.getId() + ".xml", srcX, false);
    zipJ.addBytes(resource.getId() + ".json", srcJ, false);
    if (!zipsX.containsKey(rn)) {
        zipsX.put(rn, new ZipGenerator(Utilities.path(destFolder, "xml/type", rn + ".xml.zip")));
        zipsJ.put(rn, new ZipGenerator(Utilities.path(destFolder, "json/type", rn + ".json.zip")));
        stats.put(rn, new Stats());
    }
    zipsJ.get(rn).addBytes(resource.getId() + ".json", srcJ, false);
    zipsX.get(rn).addBytes(resource.getId() + ".xml", srcX, false);
    Stats ss = stats.get(rn);
    ss.setInstances(ss.getInstances() + 1);
    String profile = resource.getUserString("profile");
    validate(srcX, profile, resource, ss);
}

Example 29 with JsonParser

use of org.hl7.fhir.r5.formats.JsonParser 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 30 with JsonParser

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

the class R2016MayToR5Loader method loadResource.

@Override
public org.hl7.fhir.r5.model.Resource loadResource(InputStream stream, boolean isJson) throws FHIRException, IOException {
    Resource r2016may = null;
    if (isJson)
        r2016may = new JsonParser().parse(stream);
    else
        r2016may = new XmlParser().parse(stream);
    org.hl7.fhir.r5.model.Resource r5 = VersionConvertorFactory_14_50.convertResource(r2016may);
    setPath(r5);
    if (!advisor.getCslist().isEmpty()) {
        throw new FHIRException("Error: Cannot have included code systems");
    }
    if (killPrimitives) {
        throw new FHIRException("Cannot kill primitives when using deferred loading");
    }
    if (patchUrls) {
        if (r5 instanceof StructureDefinition) {
            StructureDefinition sd = (StructureDefinition) r5;
            sd.setUrl(sd.getUrl().replace(URL_BASE, URL_R4));
            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 r5;
}