@Override
public void execute() throws ExecutionException {
AnnotationSet inputAS = document.getAnnotations(inputASName);
AnnotationSet outputAS = document.getAnnotations(outputASName);
AnnotationSet tagAS = document.getAnnotations(tagASName);
AnnotationSet annotsToTransfer = null;
boolean newID = copyAnnotations && inputAS.equals(outputAS);
mappings.clear();
// TODO clean this up so we don't have to repeat ourselves
if (configURL != null) {
BufferedReader in = null;
try {
in = new BomStrippingInputStreamReader(configURL.openStream());
String line = in.readLine();
while (line != null) {
if (!line.trim().equals("")) {
String[] data = line.split("=", 2);
String oldName = data[0].trim();
String newName = data.length == 2 ? data[1].trim() : null;
mappings.put(oldName, new Mapping(oldName, newName));
}
line = in.readLine();
}
} catch (IOException ioe) {
ioe.printStackTrace();
} finally {
IOUtils.closeQuietly(in);
}
} else if (annotationTypes != null) {
for (String type : annotationTypes) {
String[] data = type.split("=", 2);
String oldName = data[0].trim();
String newName = data.length == 2 ? data[1].trim() : null;
mappings.put(oldName, new Mapping(oldName, newName));
}
}
// else
// throw new
// ExecutionException("The annotation list and URL cannot both be null");
if (mappings.size() > 0) {
annotsToTransfer = inputAS.get(mappings.keySet());
} else {
// transfer everything
annotsToTransfer = inputAS.get();
}
// in case of no one annotation from some of annotationTypes
if (annotsToTransfer == null || annotsToTransfer.size() == 0) return;
// check if we have a BODY annotation
// if not, just copy all
if (textTagName == null || textTagName.equals("")) {
// remove from input set unless we copy only
if (!copyAnnotations) inputAS.removeAll(annotsToTransfer);
transferAnnotations(new ArrayList<Annotation>(annotsToTransfer), outputAS, newID);
return;
}
// get the BODY annotation
bodyAnnotations = tagAS.get(textTagName);
if (bodyAnnotations == null || bodyAnnotations.isEmpty()) {
// outputAS.addAll(inputAS);
if (transferAllUnlessFound) {
// remove from input set unless we copy only
if (!copyAnnotations) inputAS.removeAll(annotsToTransfer);
transferAnnotations(new ArrayList<Annotation>(annotsToTransfer), outputAS, newID);
}
return;
}
List<Annotation> annots2Move = new ArrayList<Annotation>();
Iterator<Annotation> bodyIter = bodyAnnotations.iterator();
while (bodyIter.hasNext()) {
Annotation bodyAnn = bodyIter.next();
Long start = bodyAnn.getStartNode().getOffset();
Long end = bodyAnn.getEndNode().getOffset();
// get all annotations we want transferred
AnnotationSet annots2Copy = annotsToTransfer.getContained(start, end);
// copy them to the new set and delete them from the old one
annots2Move.addAll(annots2Copy);
}
if (!copyAnnotations) inputAS.removeAll(annots2Move);
transferAnnotations(annots2Move, outputAS, newID);
}
