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

Example 1 with Entry

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

the class VCMetaData method compareEquals.

public boolean compareEquals(VCMetaData vcMetaData) {
    if (!getRdfData().equals(vcMetaData.getRdfData())) {
        return false;
    }
    if (!registry.compareEquals(vcMetaData.registry)) {
        return false;
    }
    Set<Entry> oeSet = nonRDFAnnotationMap.keySet();
    Set<VCID> vcidSet = new HashSet<VCID>();
    for (Entry oe : oeSet) {
        VCID vcid = identifiableProvider.getVCID(oe.getIdentifiable());
        vcidSet.add(vcid);
    }
    Set<Entry> otherOeSet = vcMetaData.nonRDFAnnotationMap.keySet();
    for (Entry oe : otherOeSet) {
        VCID vcid = vcMetaData.identifiableProvider.getVCID(oe.getIdentifiable());
        vcidSet.add(vcid);
    }
    NonRDFAnnotation emtpyAnnotation = new NonRDFAnnotation();
    for (VCID vcid : vcidSet) {
        Identifiable myIdentifiable = identifiableProvider.getIdentifiableObject(vcid);
        Identifiable otherIdentifiable = vcMetaData.identifiableProvider.getIdentifiableObject(vcid);
        if ((otherIdentifiable == null && myIdentifiable != null) || (myIdentifiable == null && otherIdentifiable != null)) {
            return false;
        }
        NonRDFAnnotation nonRDFAnnotation = nonRDFAnnotationMap.get(registry.getEntry(myIdentifiable));
        if (nonRDFAnnotation == null) {
            nonRDFAnnotation = emtpyAnnotation;
        }
        NonRDFAnnotation otherNonRDFAnnotation = vcMetaData.nonRDFAnnotationMap.get(vcMetaData.registry.getEntry(otherIdentifiable));
        if (otherNonRDFAnnotation == null) {
            otherNonRDFAnnotation = emtpyAnnotation;
        }
        if (!Compare.isEqual(nonRDFAnnotation, otherNonRDFAnnotation)) {
            return false;
        }
    }
    return true;
}

Example 2 with Entry

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

the class VCMetaData method cleanupMetadata.

public void cleanupMetadata() {
    Set<Registry.Entry> entries = registry.getAllEntries();
    for (Registry.Entry entry : entries) {
        Identifiable entryIdentifiable = entry.getIdentifiable();
        VCID vcid = identifiableProvider.getVCID(entryIdentifiable);
        Identifiable identifiable = identifiableProvider.getIdentifiableObject(vcid);
        if (identifiable == null) {
            // use miriamManager to remove RDF statements from resource for identifiable
            try {
                Map<MiriamRefGroup, MIRIAMQualifier> miriamRefGps = getMiriamManager().getAllMiriamRefGroups(entryIdentifiable);
                if (miriamRefGps != null) {
                    for (Map.Entry<MiriamRefGroup, MIRIAMQualifier> groupEntry : miriamRefGps.entrySet()) {
                        MiriamRefGroup refGroup = groupEntry.getKey();
                        MIRIAMQualifier qualifier = groupEntry.getValue();
                        getMiriamManager().remove(entryIdentifiable, qualifier, refGroup);
                    }
                }
            } catch (URNParseFailureException e) {
                e.printStackTrace(System.out);
            }
            // set nonRDF annotations to null
            NonRDFAnnotation nonRDFAnnotation = getExistingNonRDFAnnotation(entryIdentifiable);
            if (nonRDFAnnotation != null) {
                nonRDFAnnotation.setFreeTextAnnotation(null);
                nonRDFAnnotation.setXhtmlNotes(null);
                nonRDFAnnotation.setXmlAnnotations(null);
            }
            System.err.println("Deleting resource for identifiable '" + entryIdentifiable.toString() + "' since it is not found in " + identifiableProvider.getClass().getName());
        }
    }
}

Example 3 with Entry

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

the class VCMetaDataMiriamManager method remove.

public void remove(Identifiable identifiable, MIRIAMQualifier miriamQualifier, MiriamRefGroup miriamRefGroup) throws URNParseFailureException {
    Entry openEntry = vcMetaData.getRegistry().getEntry(identifiable);
    Resource resource = openEntry.getResource();
    MIRIAMizer miriamizer = new MIRIAMizer();
    RefGroup sybilRefGroup = miriamizer.newRefGroup(vcMetaData.getRdfData(), resource, miriamQualifier);
    Set<MIRIAMRef> sybilMiriamRefs = new HashSet<MIRIAMRef>();
    Set<MiriamResource> miriamResources = miriamRefGroup.getMiriamRefs();
    for (MiriamResource miriamResource : miriamResources) {
        sybilMiriamRefs.add(MIRIAMRef.createFromURN(miriamResource.getMiriamURN()));
    }
    for (MIRIAMRef sybilMiriamRef : sybilMiriamRefs) {
        sybilRefGroup.add(vcMetaData.getRdfData(), sybilMiriamRef);
    }
    miriamizer.deleteRefGroup(vcMetaData.getRdfData(), resource, sybilRefGroup);
    invalidateCache(identifiable);
    vcMetaData.fireAnnotationEventListener(new VCMetaData.AnnotationEvent(identifiable));
}

Example 4 with Entry

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

the class VCMetaDataMiriamManager method addDate.

public void addDate(Identifiable identifiable, DateQualifier dateQualifier, DublinCoreDate date) {
    Entry entry = vcMetaData.getRegistry().getEntry(identifiable);
    if (entry.getResource() == null) {
        String newURI = vcMetaData.getRegistry().generateFreeURI(identifiable);
        entry.setURI(vcMetaData.getRdfData(), newURI);
    }
    Graph rdfData = vcMetaData.getRdfData();
    Literal dateLiteral = rdfData.getValueFactory().createLiteral(date.getDateString());
    rdfData.add(entry.getResource(), dateQualifier.getProperty(), dateLiteral);
    vcMetaData.fireAnnotationEventListener(new VCMetaData.AnnotationEvent(identifiable));
}

Example 5 with Entry

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

the class VCMetaDataMiriamManager method getMiriamTreeMap.

public synchronized TreeMap<Identifiable, Map<MiriamRefGroup, MIRIAMQualifier>> getMiriamTreeMap() {
    if (miriamTreeMap == null) {
        final IdentifiableProvider identifiableProvider = vcMetaData.getIdentifiableProvider();
        miriamTreeMap = new TreeMap<Identifiable, Map<MiriamRefGroup, MIRIAMQualifier>>(new IdentifiableComparator(identifiableProvider));
        Set<Entry> allEntries = vcMetaData.getRegistry().getAllEntries();
        for (Entry entry : allEntries) {
            if (entry.getResource() != null) {
                Map<MiriamRefGroup, MIRIAMQualifier> refGroupMap = queryAllMiriamRefGroups(entry.getIdentifiable());
                if (refGroupMap.size() > 0) {
                    miriamTreeMap.put(entry.getIdentifiable(), refGroupMap);
                }
            }
        }
    }
    return miriamTreeMap;
}