Examples with MIRIAMRef org.vcell.sybil.models.miriam.MIRIAMRef used on opensource projects

Example 1 with MIRIAMRef

use of org.vcell.sybil.models.miriam.MIRIAMRef 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 2 with MIRIAMRef

use of org.vcell.sybil.models.miriam.MIRIAMRef in project vcell by virtualcell.

the class VCMetaDataMiriamManager method addMiriamRefGroup.

public void addMiriamRefGroup(Identifiable identifiable, MIRIAMQualifier miriamQualifier, Set<MiriamResource> miriamResources) throws URNParseFailureException {
    Entry entry = vcMetaData.getRegistry().getEntry(identifiable);
    Resource resource = entry.getResource();
    if (resource == null) {
        String newURIString = vcMetaData.getRegistry().generateFreeURI(identifiable);
        resource = entry.setURI(vcMetaData.getRdfData(), newURIString);
    }
    MIRIAMizer miriamizer = new MIRIAMizer();
    RefGroup sybilRefGroup = miriamizer.newRefGroup(vcMetaData.getRdfData(), resource, miriamQualifier);
    Set<MIRIAMRef> sybilMiriamRefs = new HashSet<MIRIAMRef>();
    for (MiriamResource miriamResource : miriamResources) {
        sybilMiriamRefs.add(MIRIAMRef.createFromURN(miriamResource.getMiriamURN()));
    }
    for (MIRIAMRef sybilMiriamRef : sybilMiriamRefs) {
        sybilRefGroup.add(vcMetaData.getRdfData(), sybilMiriamRef);
    }
    invalidateCache(identifiable);
    vcMetaData.fireAnnotationEventListener(new VCMetaData.AnnotationEvent(identifiable));
}