Examples with Resource org.openrdf.model.Resource used on opensource projects

Example 11 with Resource

use of org.openrdf.model.Resource in project vcell by virtualcell.

the class RefGroup method remove.

public RefGroup remove(Graph graph, MIRIAMRef ref) {
    Resource resourceRef = graph.getValueFactory().createURI(ref.urn());
    Iterator<Statement> stmtIter = graph.match(getResource(), null, resourceRef);
    while (stmtIter.hasNext()) {
        stmtIter.next();
        stmtIter.remove();
    }
    return this;
}

Example 12 with Resource

use of org.openrdf.model.Resource in project vcell by virtualcell.

the class RefGroup method contains.

public boolean contains(Graph graph, MIRIAMRef ref) {
    Resource rRef = graph.getValueFactory().createURI(ref.urn());
    Statement statement = graph.getValueFactory().createStatement(getResource(), RDF.LI, rRef);
    return graph.contains(statement);
}

Example 13 with Resource

use of org.openrdf.model.Resource in project vcell by virtualcell.

the class RefGroup method add.

public RefGroup add(Graph graph, MIRIAMRef ref) {
    Resource rRef = graph.getValueFactory().createURI(ref.urn());
    graph.add(getResource(), RDF.LI, rRef);
    return this;
}

Example 14 with Resource

use of org.openrdf.model.Resource in project vcell by virtualcell.

the class SBMLAnnotationUtil method writeAnnotation.

public void writeAnnotation(Identifiable identifiable, SBase sBase, Element vcellImportRelatedElement) throws XMLStreamException {
    // Deal with RDF annotation
    XMLNode rootAnnotation = new XMLNode(tripleAnnotation, new XMLAttributes());
    Resource resource = metaData.getRegistry().getEntry(identifiable).getResource();
    Graph rdfChunk = null;
    if (resource != null) {
        rdfChunk = chopper.getChops().get(resource);
    }
    if (identifiable == root && rdfChunk != null) {
        rdfChunk.addAll(chopper.getRemains());
    }
    XMLNode rootRDF = null;
    if (rdfChunk != null && metaData.getBaseURIExtended() != null) {
        Element element = XMLRDFWriter.createElement(rdfChunk, nsSBML);
        XMLNamespaces xmlnss = new XMLNamespaces();
        xmlnss.add(DefaultNameSpaces.RDF.uri, DefaultNameSpaces.RDF.prefix);
        rootRDF = XMLNode.convertStringToXMLNode(XmlUtil.xmlToString(element), xmlnss);
    }
    if (rootRDF != null && rootRDF.getNumChildren() > 0) {
        rootAnnotation.addChild(rootRDF);
    }
    // Deal with the non-RDF; VCell free-text annotations
    // get free text annotation from NonRDFAnnotation (associated with identifiable); create XMLNode
    XMLNode rootVCellInfo = new XMLNode(tripleVCellInfo, new XMLAttributes());
    rootVCellInfo.addNamespace(XMLTags.SBML_VCELL_NS, XMLTags.VCELL_NS_PREFIX);
    String freeTextStr = metaData.getFreeTextAnnotation(identifiable);
    if (freeTextStr != null && freeTextStr.length() > 0) {
        XMLNode contentFreeText = new XMLNode(freeTextStr);
        XMLNode rootFreeText = new XMLNode(tripleFreeText, new XMLAttributes());
        rootFreeText.addChild(contentFreeText);
        rootVCellInfo.addChild(rootFreeText);
    }
    // VCell specific info to be exported to SBML as annotation - used for import, not needed for metadata
    if (vcellImportRelatedElement != null) {
        XMLNode xn = elementToXMLNode(vcellImportRelatedElement);
        if (xn != null) {
            xn.removeNamespace(XMLTags.VCELL_NS_PREFIX);
            rootVCellInfo.addChild(xn);
        }
    }
    if (rootVCellInfo.getNumChildren() > 0) {
        rootAnnotation.addChild(rootVCellInfo);
    }
    // Deal with the non-RDF (other tool-related?) annotation
    Element[] elementsXML = metaData.getXmlAnnotations(identifiable);
    if (elementsXML != null) {
        for (Element elementXML : elementsXML) {
            XMLTriple tripleXML = new XMLTriple(elementXML.getName(), elementXML.getNamespaceURI(), elementXML.getNamespacePrefix());
            XMLNode contentXML = elementToXMLNode(elementXML);
            XMLNode rootXML = new XMLNode(tripleXML, new XMLAttributes());
            rootXML.addChild(contentXML);
            rootAnnotation.addChild(rootXML);
        }
    }
    if (rootAnnotation.getNumChildren() > 0) {
        sBase.setAnnotation(rootAnnotation);
    }
    writeMetaID(identifiable, sBase);
}

Example 15 with Resource

use of org.openrdf.model.Resource in project vcell by virtualcell.

the class SBMLAnnotationUtil method writeMetaID.

public void writeMetaID(Identifiable identifiable, SBase sBase) {
    Resource resource = metaData.getRegistry().getEntry(identifiable).getResource();
    if (resource != null) {
        Resource mappedResource = namespaceAssimilator.map(resource);
        if (mappedResource instanceof URI) {
            String metaID = ((URI) mappedResource).getLocalName();
            sBase.setMetaId(metaID);
        }
    }
}