/**
* @param inputAS input annotation set
* @param outputAS output annotation set
* @param term String matched
* @param startOffset match start offset
* @param endOffset match end offset
*/
private void addLookup(
AnnotationSet inputAS,
AnnotationSet outputAS,
String term,
String outputASType,
Long startOffset,
Long endOffset,
boolean useNounChunk) {
if (useNounChunk && nounChunkType != null && !nounChunkType.isEmpty()) {
AnnotationSet nounChunkAS = inputAS.getCovering(nounChunkType, startOffset, endOffset);
if (!nounChunkAS.isEmpty()) {
startOffset = nounChunkAS.firstNode().getOffset();
endOffset = nounChunkAS.lastNode().getOffset();
}
}
try {
AnnotationSet diseaseAS = inputAS.get(outputASType, startOffset, endOffset);
if (diseaseAS.isEmpty()) {
FeatureMap fm = Factory.newFeatureMap();
fm.put("match", term);
outputAS.add(startOffset, endOffset, outputASType, fm);
} else {
Annotation disease = diseaseAS.iterator().next();
FeatureMap fm = disease.getFeatures();
String meta = (String) fm.get("match");
if (meta != null) {
meta = meta + " " + term;
}
fm.put("match", meta);
}
} catch (InvalidOffsetException ie) {
// shouldn't happen
gate.util.Err.println(ie);
}
}
/**
* Rename annotation
*
* @param outputAS output annotation set
* @param oldType old annotation name
* @param newType new annotation name
*/
private void renameAnnotations(AnnotationSet outputAS, String oldType, String newType) {
AnnotationSet tmpAnatomyAS = outputAS.get(oldType);
for (Annotation tmpAnn : tmpAnatomyAS) {
Long startOffset = tmpAnn.getStartNode().getOffset();
Long endOffset = tmpAnn.getEndNode().getOffset();
AnnotationSet existingAS = outputAS.getCovering(newType, startOffset, endOffset);
// If we've already got an annotation of the same name in the same place, don't add a new one
// just delete the old one
if (existingAS.isEmpty()) {
FeatureMap tmpFm = tmpAnn.getFeatures();
FeatureMap fm = Factory.newFeatureMap();
fm.putAll(tmpFm);
try {
outputAS.add(startOffset, endOffset, newType, fm);
outputAS.remove(tmpAnn);
} catch (InvalidOffsetException ie) {
// shouldn't happen
}
} else {
outputAS.remove(tmpAnn);
}
}
}
@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);
}