@Override
public synchronized Annotation getOrCreateAnnotation(
Collection<BiologicalEntity> biologicalEntities,
Property property,
AnnotationProvenance annotationProvenance,
Collection<URI> semanticTags) {
List<String> idContents = new ArrayList<>();
for (BiologicalEntity biologicalEntity : biologicalEntities) {
for (Study s : biologicalEntity.getStudies()) {
idContents.add(s.getAccession());
}
if (biologicalEntity.getName() != null) {
idContents.add(biologicalEntity.getName());
}
if (biologicalEntity.getTypes() != null) {
for (URI type : biologicalEntity.getTypes()) {
idContents.add(type.toString());
}
}
}
if (property instanceof TypedProperty) {
idContents.add(((TypedProperty) property).getPropertyType());
}
idContents.add(property.getPropertyValue());
for (URI semanticTag : semanticTags) {
idContents.add(semanticTag.toString());
}
idContents.add(
annotationProvenance.getAnnotator() != null ? annotationProvenance.getAnnotator() : "");
idContents.add(
annotationProvenance.getGeneratedDate() != null
? annotationProvenance.getGeneratedDate().toString()
: "");
idContents.add(
annotationProvenance.getAnnotationDate() != null
? annotationProvenance.getAnnotationDate().toString()
: "");
idContents.add(
annotationProvenance.getEvidence() != null
? annotationProvenance.getEvidence().toString()
: "");
idContents.add(
annotationProvenance.getSource() != null
? annotationProvenance.getSource().getURI().toString()
: "");
String annotationID = generateIDFromContent(idContents.toArray(new String[idContents.size()]));
return getOrCreateAnnotation(
annotationID, biologicalEntities, property, annotationProvenance, semanticTags);
}
@Override
public synchronized BiologicalEntity getOrCreateBiologicalEntity(
String bioentityName,
Collection<String> bioentityTypeName,
Collection<URI> bioentityTypeURI,
Study... studies) {
List<String> ids = new ArrayList<>();
for (Study s : studies) {
ids.add(s.getAccession());
}
ids.add(bioentityName);
String hashID = generateIDFromContent(ids.toArray(new String[ids.size()]));
return getOrCreateBiologicalEntity(
bioentityName, hashID, bioentityTypeName, bioentityTypeURI, studies);
}
