@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);
}
}
}