Examples with Source org.hl7.fhir.utilities.validation.ValidationMessage.Source used on opensource projects

Example 51 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class RdfParser method composeDocumentManifest.

protected void composeDocumentManifest(Complex parent, String parentType, String name, DocumentManifest element, int index) {
    if (element == null)
        return;
    Complex t;
    if (Utilities.noString(parentType))
        t = parent;
    else {
        t = parent.predicate("fhir:" + parentType + '.' + name);
    }
    composeDomainResource(t, "DocumentManifest", name, element, index);
    if (element.hasMasterIdentifier())
        composeIdentifier(t, "DocumentManifest", "masterIdentifier", element.getMasterIdentifier(), -1);
    for (int i = 0; i < element.getIdentifier().size(); i++) composeIdentifier(t, "DocumentManifest", "identifier", element.getIdentifier().get(i), i);
    if (element.hasStatusElement())
        composeEnum(t, "DocumentManifest", "status", element.getStatusElement(), -1);
    if (element.hasType())
        composeCodeableConcept(t, "DocumentManifest", "type", element.getType(), -1);
    if (element.hasSubject())
        composeReference(t, "DocumentManifest", "subject", element.getSubject(), -1);
    if (element.hasCreatedElement())
        composeDateTime(t, "DocumentManifest", "created", element.getCreatedElement(), -1);
    for (int i = 0; i < element.getAuthor().size(); i++) composeReference(t, "DocumentManifest", "author", element.getAuthor().get(i), i);
    for (int i = 0; i < element.getRecipient().size(); i++) composeReference(t, "DocumentManifest", "recipient", element.getRecipient().get(i), i);
    if (element.hasSourceElement())
        composeUri(t, "DocumentManifest", "source", element.getSourceElement(), -1);
    if (element.hasDescriptionElement())
        composeString(t, "DocumentManifest", "description", element.getDescriptionElement(), -1);
    for (int i = 0; i < element.getContent().size(); i++) composeDocumentManifestDocumentManifestContentComponent(t, "DocumentManifest", "content", element.getContent().get(i), i);
    for (int i = 0; i < element.getRelated().size(); i++) composeDocumentManifestDocumentManifestRelatedComponent(t, "DocumentManifest", "related", element.getRelated().get(i), i);
}

Example 52 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source 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");
}

Example 53 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class DicomPackageBuilder method buildCodeSystem.

private CodeSystem buildCodeSystem() throws ParserConfigurationException, FileNotFoundException, SAXException, IOException {
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    factory.setNamespaceAware(true);
    DocumentBuilder builder = factory.newDocumentBuilder();
    Document doc = builder.parse(new FileInputStream(Utilities.path(source, "Resources", "Ontology", "DCM", "dcm.owl")));
    Element rdf = doc.getDocumentElement();
    Element d = XMLUtil.getFirstChild(rdf);
    version = processVersion(XMLUtil.getNamedChildText(d, "versionInfo"));
    CodeSystem cs = new CodeSystem();
    cs.setId("DCM");
    cs.setUrl("http://dicom.nema.org/resources/ontology/DCM");
    cs.setVersion(version);
    cs.setName("DICOMTerminologyDefinitions");
    cs.setTitle("DICOM Controlled Terminology Definitions");
    cs.getIdentifier().add(new Identifier().setSystem("urn:ietf:rfc:3986").setValue("urn:oid:1.2.840.10008.2.16.4"));
    cs.setStatus(PublicationStatus.ACTIVE);
    cs.setExperimental(false);
    cs.setPublisher("FHIR Project on behalf of DICOM");
    cs.setDate(new Date());
    cs.setDescription("DICOM Code Definitions (Coding Scheme Designator \"DCM\" Coding Scheme Version " + version);
    cs.setPurpose("This code system is published as part of FHIR in order to make the codes available to FHIR terminology services and so implementers can easily leverage the codes");
    cs.setCopyright("These codes are excerpted from Digital Imaging and Communications in Medicine (DICOM) Standard, Part 16: Content Mapping Resource, Copyright © 2011 by the National Electrical Manufacturers Association.");
    cs.setCaseSensitive(true);
    cs.setValueSet("http://dicom.nema.org/resources/ValueSet/all");
    cs.setContent(CodeSystemContentMode.COMPLETE);
    d = XMLUtil.getNextSibling(d);
    while (d != null) {
        String code = XMLUtil.getNamedChildText(d, "notation");
        String display = XMLUtil.getNamedChildText(d, "prefLabel");
        String definition = XMLUtil.getNamedChildText(d, "definition");
        ConceptDefinitionComponent cc = new ConceptDefinitionComponent();
        cs.getConcept().add(cc);
        cc.setCode(code);
        cc.setDisplay(display);
        cc.setDefinition(definition);
        d = XMLUtil.getNextSibling(d);
    }
    return cs;
}

Example 54 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class ResourceTest method test.

public void test() throws FHIRFormatError, FileNotFoundException, IOException {
    IParser p;
    if (isJson())
        p = new JsonParser();
    else
        p = new XmlParser(false);
    Resource rf = p.parse(new FileInputStream(source));
    FileOutputStream out = new FileOutputStream(source.getAbsoluteFile() + ".out.json");
    JsonParser json1 = new JsonParser();
    json1.setOutputStyle(OutputStyle.PRETTY);
    json1.compose(out, rf);
    out.close();
    JsonParser json = new JsonParser();
    rf = json.parse(new FileInputStream(source.getAbsoluteFile() + ".out.json"));
    out = new FileOutputStream(source.getAbsoluteFile() + ".out.xml");
    XmlParser atom = new XmlParser();
    atom.setOutputStyle(OutputStyle.PRETTY);
    atom.compose(out, rf, true);
    out.close();
}

Example 55 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class ToolsHelper method testRoundTrip.

public void testRoundTrip(String rootDir, String tmpDir, Collection<String> names) throws Throwable {
    try {
        System.err.println("Round trip from " + rootDir + " to " + tmpDir + ":" + Integer.toString(names.size()) + " files");
        for (String n : names) {
            System.err.print("  " + n);
            String source = rootDir + n + ".xml";
            // String tmpJson = tmpDir + n + ".json";
            String tmp = tmpDir + n.replace(File.separator, "-") + ".tmp";
            String dest = tmpDir + n.replace(File.separator, "-") + ".java.xml";
            FileInputStream in = new FileInputStream(source);
            XmlParser xp = new XmlParser();
            Resource r = xp.parse(in);
            System.err.print(".");
            JsonParser jp = new JsonParser();
            FileOutputStream out = new FileOutputStream(tmp);
            jp.setOutputStyle(OutputStyle.PRETTY);
            jp.compose(out, r);
            out.close();
            r = null;
            System.err.print(".");
            in = new FileInputStream(tmp);
            System.err.print(",");
            r = jp.parse(in);
            System.err.print(".");
            out = new FileOutputStream(dest);
            new XmlParser().compose(out, r, true);
            System.err.println("!");
            out.close();
            r = null;
            System.gc();
        }
    } catch (Throwable e) {
        System.err.println("Error: " + e.getMessage());
        throw e;
    }
}