Examples with Annotation org.exquery.xquery3.Annotation used on opensource projects

Example 16 with Annotation

use of org.exquery.xquery3.Annotation in project exist by eXist-db.

the class RegistryFunctions method serializeAnnotations.

private static void serializeAnnotations(final MemTreeBuilder builder, final ResourceFunction resourceFn) {
    final List<Annotation> annotations = new ArrayList<>();
    annotations.addAll(resourceFn.getHttpMethodAnnotations());
    annotations.addAll(resourceFn.getConsumesAnnotations());
    annotations.addAll(resourceFn.getProducesAnnotations());
    for (final Annotation annotation : annotations) {
        builder.startElement(QName.fromJavaQName(annotation.getName()), null);
        final Literal[] literals = annotation.getLiterals();
        if (literals != null) {
            for (final Literal literal : literals) {
                if (annotation instanceof ConsumesAnnotation || annotation instanceof ProducesAnnotation) {
                    builder.startElement(INTERNET_MEDIA_TYPE, null);
                    builder.characters(literal.getValue());
                    builder.endElement();
                }
            }
        }
        builder.endElement();
    }
    // path annotation
    if (resourceFn.getPathAnnotation() != null) {
        final PathAnnotation pathAnnotation = resourceFn.getPathAnnotation();
        final AttributesImpl attrs = new AttributesImpl();
        attrs.addAttribute(null, SPECIFICITY_METRIC, "", "string", Long.toString(pathAnnotation.getPathSpecificityMetric()));
        builder.startElement(QName.fromJavaQName(pathAnnotation.getName()), attrs);
        final String[] segments = pathAnnotation.getLiterals()[0].getValue().split("/");
        for (final String segment : segments) {
            if (!segment.isEmpty()) {
                builder.startElement(SEGMENT, null);
                builder.characters(segment);
                builder.endElement();
            }
        }
        builder.endElement();
    }
    // parameter annotations
    for (final ParameterAnnotation parameterAnnotation : resourceFn.getParameterAnnotations()) {
        final Literal[] literals = parameterAnnotation.getLiterals();
        final AttributesImpl attrs = new AttributesImpl();
        attrs.addAttribute(null, NAME, "", "string", literals[0].getValue());
        attrs.addAttribute(null, ARGUMENT, "", "string", literals[1].getValue());
        if (literals.length == 3) {
            attrs.addAttribute(null, DEFAULT_VALUE, "", "string", literals[2].getValue());
        }
        builder.startElement(QName.fromJavaQName(parameterAnnotation.getName()), attrs);
        builder.endElement();
    }
    // serialization annotations
    for (final SerializationAnnotation serializationAnnotation : resourceFn.getSerializationAnnotations()) {
        serializeSerializationAnnotation(builder, serializationAnnotation);
    }
}

Example 17 with Annotation

use of org.exquery.xquery3.Annotation in project libSBOLj by SynBioDex.

the class AnnotationTest method test_toString.

@Test
public void test_toString() throws SBOLValidationException {
    Annotation CD_annot = gRNA_b_gene.createAnnotation(new QName(prURI, "protein", "pr"), true);
    // System.out.println(CD_annot.toString());
    assertTrue(CD_annot.toString().contains("value=" + true));
}

Example 18 with Annotation

use of org.exquery.xquery3.Annotation in project libSBOLj by SynBioDex.

the class AnnotationOutput method main.

public static void main(String[] args) throws Exception {
    String prURI = "http://partsregistry.org/";
    String prPrefix = "pr";
    SBOLDocument document = new SBOLDocument();
    document.setDefaultURIprefix(prURI);
    document.setTypesInURIs(true);
    document.addNamespace(URI.create(prURI), prPrefix);
    ComponentDefinition promoter = document.createComponentDefinition("BBa_J23119", "", new HashSet<URI>(Arrays.asList(URI.create("http://www.biopax.org/release/biopax-level3.owl#DnaRegion"))));
    promoter.addRole(SequenceOntology.PROMOTER);
    promoter.setName("J23119");
    promoter.setDescription("Constitutive promoter");
    promoter.createAnnotation(new QName(prURI, "group", prPrefix), "iGEM2006_Berkeley");
    promoter.createAnnotation(new QName(prURI, "experience", prPrefix), URI.create("http://parts.igem.org/cgi/partsdb/part_info.cgi?part_name=BBa_J23119"));
    Annotation sigmaFactor = new Annotation(QName(prURI, "sigmafactor", prPrefix), "//rnap/prokaryote/ecoli/sigma70");
    Annotation regulation = new Annotation(QName(prURI, "regulation", prPrefix), "//regulation/constitutive");
    promoter.createAnnotation(new QName(prURI, "information", prPrefix), new QName(prURI, "Information", prPrefix), "information", new ArrayList<Annotation>(Arrays.asList(sigmaFactor, regulation)));
    SBOLWriter.write(document, (System.out));
}