public void importAnnotationMapping(AnnotationMapping iam) {
List<VersionMetadata> metadata =
APIFactory.getInstance()
.getAnnotationAPI()
.checkInvolvedVersion(iam.getSrcVersion(), iam.getTargetVersion());
APIFactory.getInstance().getAnnotationAPI().importMapping(metadata, iam);
}
public static Map<Integer, List<EntityAnnotation>> groupByItem(AnnotationMapping corSet) {
HashMap<Integer, List<EntityAnnotation>> groups =
new HashMap<Integer, List<EntityAnnotation>>();
for (EntityAnnotation cor : corSet.getAnnotations()) {
List<EntityAnnotation> umlsCon = groups.get(cor.getSrcId());
if (umlsCon == null) {
umlsCon = new ArrayList<EntityAnnotation>();
groups.put(cor.getSrcId(), umlsCon);
}
umlsCon.add(cor);
}
return groups;
}
public static HashMap<Integer, List<Integer>> groupSimilarUMLSConsByCommonToken(
EncodedEntityStructure umlsGroup, int srcId, AnnotationMapping am) {
HashMap<Integer, List<Integer>> umlsGroups = new HashMap<Integer, List<Integer>>();
Map<Integer, Set<Integer>> conceptToEvidenceSet = new HashMap<Integer, Set<Integer>>();
for (int targetId : umlsGroup.getObjIds().keySet()) {
long anid = CantorDecoder.code(srcId, targetId);
Set<Integer> evidence = am.getEvidenceMap().get(anid);
conceptToEvidenceSet.put(targetId, evidence);
for (int tid : evidence) {
List<Integer> group = umlsGroups.get(tid);
if (group == null) {
group = new ArrayList<Integer>();
umlsGroups.put(tid, group);
}
group.add(targetId);
}
}
Map<Integer, Set<Integer>> conceptTosupersets =
getSupersetConceptRelationships(conceptToEvidenceSet);
for (Entry<Integer, List<Integer>> entry : umlsGroups.entrySet()) {
for (int i = 0; i < entry.getValue().size(); i++) {
int concept = entry.getValue().get(i);
if (conceptTosupersets.containsKey(concept)) {
boolean found = false;
Set<Integer> supersetConcepts = conceptTosupersets.get(concept);
for (int superConcept : entry.getValue()) {
if (supersetConcepts.contains(superConcept)) {
found = true;
break;
}
}
if (found) {
entry.getValue().remove(i);
i--;
}
}
}
}
return umlsGroups;
}