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

Example 31 with JsonParser

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

the class R2ToR5Loader method loadResource.

@Override
public org.hl7.fhir.r5.model.Resource loadResource(InputStream stream, boolean isJson) throws FHIRException, IOException {
    Resource r2 = null;
    if (isJson)
        r2 = new JsonParser().parse(stream);
    else
        r2 = new XmlParser().parse(stream);
    org.hl7.fhir.r5.model.Resource r5 = VersionConvertorFactory_10_50.convertResource(r2, advisor);
    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;
}

Example 32 with JsonParser

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

the class R2ToR5Loader method loadBundle.

@Override
public Bundle loadBundle(InputStream stream, boolean isJson) throws FHIRException, IOException {
    Resource r2 = null;
    if (isJson)
        r2 = new JsonParser().parse(stream);
    else
        r2 = new XmlParser().parse(stream);
    org.hl7.fhir.r5.model.Resource r5 = VersionConvertorFactory_10_50.convertResource(r2, 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);
    }
    // Add any code systems defined as part of processing value sets to the end of the converted Bundle
    for (CodeSystem cs : advisor.getCslist()) {
        BundleEntryComponent be = b.addEntry();
        be.setFullUrl(cs.getUrl());
        be.setResource(cs);
    }
    advisor.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) {
        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_DSTU2));
                sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
            }
        }
    }
    return b;
}

Example 33 with JsonParser

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

the class R3ToR5Loader method loadResource.

@Override
public org.hl7.fhir.r5.model.Resource loadResource(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);
    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;
}

Example 34 with JsonParser

use of org.hl7.fhir.r5.elementmodel.JsonParser 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 35 with JsonParser

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

the class DicomPackageBuilder method execute.

public void execute() throws FileNotFoundException, ParserConfigurationException, SAXException, IOException {
    CodeSystem cs = buildCodeSystem();
    String fn = Utilities.path(dest, pattern.replace("{version}", version));
    Utilities.createDirectory(Utilities.getDirectoryForFile(fn));
    NPMPackageGenerator gen = new NPMPackageGenerator(fn, buildPackage());
    int i = 2;
    gen.addFile(Category.RESOURCE, "CodeSystem-" + cs.getId() + ".json", new JsonParser().setOutputStyle(OutputStyle.NORMAL).composeBytes(cs));
    ValueSet vs = buildAllValueSet();
    gen.addFile(Category.RESOURCE, "ValueSet-" + vs.getId() + ".json", new JsonParser().setOutputStyle(OutputStyle.NORMAL).composeBytes(vs));
    Set<String> ids = new HashSet<>();
    ids.add(vs.getId());
    for (File f : new File(Utilities.path(source, "Resources", "valuesets", "fhir", "json")).listFiles()) {
        vs = (ValueSet) JsonParser.loadFile(new FileInputStream(f));
        vs.setVersion(version);
        if (vs.getId().length() > 64) {
            vs.setId(vs.getId().substring(0, 64));
        }
        if (ids.contains(vs.getId())) {
            throw new Error("Duplicate Id (note Ids cut off at 64 char): " + vs.getId());
        }
        ids.add(vs.getId());
        gen.addFile(Category.RESOURCE, "ValueSet-" + vs.getId() + ".json", new JsonParser().setOutputStyle(OutputStyle.NORMAL).composeBytes(vs));
        i++;
    }
    gen.finish();
    System.out.println("Finished - " + i + " resources");
}