@Override
protected void align() throws Exception {
super.align(); // do the schema matching part .. if any.
if (alignInstances == true
&& (sourceOntology.getInstances() == null || targetOntology.getInstances() == null)) {
// the source ontology or target ontology have no instances
for (MatchingProgressListener mpd : progressDisplays) {
mpd.appendToReport("Instances were NOT matched since they were not loaded properly.");
}
} else if (alignInstances && !this.isCancelled()) {
sourceInstanceDataset = sourceOntology.getInstances();
targetInstanceDataset = targetOntology.getInstances();
// compile a list of source instances
if (!sourceInstanceDataset.isIterable() && !targetInstanceDataset.isIterable()) {
throw new AMException(
"Neither the source or the target instance datasets are iterable. We cannot instance match.");
}
if (!sourceInstanceDataset.isIterable()) {
throw new AMException("The source MUST be an iterable instance dataset.");
}
Iterator<Instance> sourceInstances = sourceInstanceDataset.getInstances();
// for every individual in the source list, look for candidate individuals in the target
instanceAlignmentSet = alignInstances(sourceInstances);
}
}
@Override
protected void setupProgress() {
super.setupProgress();
if (alignInstances) {
try {
InstanceDataset instances = sourceOntology.getInstances();
if (instances != null && instances.isIterable())
stepsTotal += sourceOntology.getInstances().size();
} catch (Exception e) {
sLog.error("", e);
}
}
}
/**
* @param sourceInstances
* @return
* @throws Exception
*/
protected MatchingPairAlignment alignInstances(Iterator<Instance> sourceInstances)
throws Exception {
MatchingPairAlignment mappings = new MatchingPairAlignment();
while (sourceInstances.hasNext()) {
Instance currentInstance = sourceInstances.next();
Set<String> labelList = currentInstance.getProperty(Instance.INST_LABEL);
if (labelList == null) continue;
// FIXME: Manage multiple labels.
String label = labelList.iterator().next();
label = processLabelBeforeCandidatesGeneration(label, currentInstance.getType());
String sourceType = currentInstance.getTypeValue();
List<MatchingPair> targetTypes = null;
if (sourceType != null) {
if (isUseInstanceSchemaMappings() && sourceOntology.getInstanceTypeMapping() != null) {
HashMap<String, List<MatchingPair>> typeMapping = sourceOntology.getInstanceTypeMapping();
if (typeMapping.containsKey(sourceType)) {
targetTypes = typeMapping.get(sourceType);
} else {
targetTypes = null;
// targetTypes = new ArrayList<MatchingPair>();
// targetTypes.add( new MatchingPair(sourceType, sourceType)); // same type in the
// target
}
}
}
// targetTypes = null;
List<Instance> allCandidates = new ArrayList<Instance>();
MatchingPair mapping = null;
if (targetTypes != null) {
for (MatchingPair mp : targetTypes) {
Collection<Instance> targetCandidates =
targetInstanceDataset.getCandidateInstances(label, mp.targetURI);
allCandidates.addAll(targetCandidates);
}
mapping = alignInstanceCandidates(currentInstance, allCandidates);
} else {
Collection<Instance> targetCandidates =
targetInstanceDataset.getCandidateInstances(label, null);
allCandidates.addAll(targetCandidates);
mapping = alignInstanceCandidates(currentInstance, allCandidates);
}
if (mapping != null) {
System.out.println("Found mapping: " + mapping);
mappings.add(mapping);
}
// stepDone();
// updateProgress();
}
return mappings;
}