Examples with Entry cbit.vcell.biomodel.meta.registry.Registry.Entry used on opensource projects

Example 6 with Entry

use of cbit.vcell.biomodel.meta.registry.Registry.Entry in project vcell by virtualcell.

the class VCMetaDataMiriamManager method queryAllMiriamRefGroups.

private Map<MiriamRefGroup, MIRIAMQualifier> queryAllMiriamRefGroups(Identifiable identifiable) {
    Entry entry = vcMetaData.getRegistry().getEntry(identifiable);
    if (entry.getResource() == null) {
        return null;
    }
    MIRIAMizer miriamizer = new MIRIAMizer();
    Map<RefGroup, MIRIAMQualifier> allRefGroups = miriamizer.getAllRefGroups(vcMetaData.getRdfData(), entry.getResource());
    Map<MiriamRefGroup, MIRIAMQualifier> wrappedRefGroups = new HashMap<MiriamRefGroup, MIRIAMQualifier>();
    for (RefGroup refGroup : allRefGroups.keySet()) {
        MiriamRefGroup miriamRefGroup = new VCMetaDataMiriamRefGroup(refGroup);
        MIRIAMQualifier miriamQualifier = allRefGroups.get(refGroup);
        wrappedRefGroups.put(miriamRefGroup, miriamQualifier);
    }
    return wrappedRefGroups;
}

Example 7 with Entry

use of cbit.vcell.biomodel.meta.registry.Registry.Entry in project vcell by virtualcell.

the class XMLMetaDataWriter method createNonRDFAnnotationElement.

/**
 * creating XMLMetaData element for nonRDFAnnotation element here since nonRDFAnnotation was made package level
 *	this is similar to XMLRDFWriter.createElement(metaData)
 *
 * @return the created NonRDFAnnotationListElement
 */
private static Element createNonRDFAnnotationElement(VCMetaData metaData, IdentifiableProvider identifiableProvider) {
    Set<Map.Entry<Entry, NonRDFAnnotation>> allNonRdfAnnotations = metaData.getAllNonRDFAnnotations();
    Element nonRDFAnnotationListElement = new Element(XMLMetaData.NONRDF_ANNOTATION_LIST_TAG);
    Iterator<Map.Entry<Entry, NonRDFAnnotation>> iter = allNonRdfAnnotations.iterator();
    while (iter.hasNext()) {
        Map.Entry<Entry, NonRDFAnnotation> mapEntry = iter.next();
        Entry openEntry = mapEntry.getKey();
        NonRDFAnnotation nonRDFAnnotation = mapEntry.getValue();
        VCID vcid = identifiableProvider.getVCID(openEntry.getIdentifiable());
        Identifiable identifiable = identifiableProvider.getIdentifiableObject(vcid);
        // only write out nonRDF annotation if identifiable in identifiableProvider is not null
        if (identifiable != null) {
            if (!nonRDFAnnotation.isEmpty()) {
                Element nonRDFAnnotationElement = new Element(XMLMetaData.NONRDF_ANNOTATION_TAG);
                nonRDFAnnotationElement.setAttribute(XMLMetaData.VCID_ATTR_TAG, vcid.toASCIIString());
                nonRDFAnnotationListElement.addContent(nonRDFAnnotationElement);
                String freeTextAnnotation = nonRDFAnnotation.getFreeTextAnnotation();
                if (freeTextAnnotation != null && freeTextAnnotation.length() > 0) {
                    Element freeTextAnnotationElement = new Element(XMLMetaData.FREETEXT_TAG);
                    freeTextAnnotationElement.addContent(new Text(freeTextAnnotation));
                    nonRDFAnnotationElement.addContent(freeTextAnnotationElement);
                }
                Element xhtmlNotes = nonRDFAnnotation.getXhtmlNotes();
                if (xhtmlNotes != null) {
                    // Element notesElement = new Element(XMLMetaData.NOTES_TAG);
                    // notesElement.addContent(xhtmlNotes));
                    nonRDFAnnotationElement.addContent(xhtmlNotes.detach());
                }
                Element[] otherAnnotations = nonRDFAnnotation.getXmlAnnotations();
                if (otherAnnotations != null && otherAnnotations.length > 0) {
                    Element annotationListElement = new Element(XMLMetaData.ANNOTATION_LIST_TAG);
                    nonRDFAnnotationElement.addContent(annotationListElement);
                    for (int i = 0; i < otherAnnotations.length; i++) {
                        annotationListElement.addContent(otherAnnotations[i].detach());
                    }
                }
            }
        }
    }
    return nonRDFAnnotationListElement;
}

Example 8 with Entry

use of cbit.vcell.biomodel.meta.registry.Registry.Entry in project vcell by virtualcell.

the class XMLMetaDataWriter method getElement.

public static Element getElement(VCMetaData metaData, IdentifiableProvider identifiableProvider) {
    Element element = new Element(XMLMetaData.VCMETADATA_TAG);
    Element elementRDF = metaData.createElement();
    // add RDF data
    if (elementRDF != null) {
        element.addContent(elementRDF);
    }
    Element elementNonRDFList = createNonRDFAnnotationElement(metaData, identifiableProvider);
    element.addContent(elementNonRDFList);
    // add resource binding table
    Element bindingListElement = new Element(XMLMetaData.URI_BINDING_LIST_TAG);
    Set<Registry.Entry> resources = metaData.getRegistry().getAllEntries();
    for (Registry.Entry entry : resources) {
        VCID vcid = identifiableProvider.getVCID(entry.getIdentifiable());
        Identifiable identifiable = identifiableProvider.getIdentifiableObject(vcid);
        if (identifiable != null && entry.getResource() != null) {
            Element entryElement = new Element(XMLMetaData.URI_BINDING_TAG);
            Resource resource = entry.getResource();
            if (resource != null) {
                entryElement.setAttribute(XMLMetaData.URI_ATTR_TAG, resource.stringValue());
            }
            entryElement.setAttribute(XMLMetaData.VCID_ATTR_TAG, vcid.toASCIIString());
            bindingListElement.addContent(entryElement);
        }
    }
    element.addContent(bindingListElement);
    return element;
}

Example 9 with Entry

use of cbit.vcell.biomodel.meta.registry.Registry.Entry in project vcell by virtualcell.

the class VCMetaData method getOrCreateNonRDFAnnotation.

private NonRDFAnnotation getOrCreateNonRDFAnnotation(Identifiable identifiable) {
    Entry entry = registry.getEntry(identifiable);
    NonRDFAnnotation nonRDFAnnotation = nonRDFAnnotationMap.get(entry);
    if (nonRDFAnnotation == null) {
        nonRDFAnnotation = new NonRDFAnnotation();
        nonRDFAnnotationMap.put(entry, nonRDFAnnotation);
    }
    return nonRDFAnnotation;
}

Example 10 with Entry

use of cbit.vcell.biomodel.meta.registry.Registry.Entry in project vcell by virtualcell.

the class VCMetaData method getExistingNonRDFAnnotation.

private NonRDFAnnotation getExistingNonRDFAnnotation(Identifiable identifiable) {
    Entry entry = registry.getEntry(identifiable);
    NonRDFAnnotation nonRDFAnnotation = nonRDFAnnotationMap.get(entry);
    return nonRDFAnnotation;
}