@Override
public int compare(AnnotationFS arg0, AnnotationFS arg1) {
int beginDiff = arg0.getBegin() - arg1.getBegin();
if (beginDiff == 0) {
return arg1.getEnd() - arg0.getEnd();
} else {
return beginDiff;
}
}
@Override
public void process(JCas jcas) throws AnalysisEngineProcessException {
// sentenceCount = 0;
tokenCount = 0;
String text = jcas.getDocumentText();
String[] zones = getZoneTypes();
if (isStrictZoning()) {
if (zones == null || zones.length == 0) {
process(jcas, text.substring(0, text.length()), 0);
} else if (zones.length != 1) {
throw new AnalysisEngineProcessException(
new IllegalStateException("Strict zoning cannot use multiple zone types"));
} else {
CAS cas = jcas.getCas();
for (AnnotationFS zone : select(cas, getType(cas, zones[0]))) {
int[] adjusted = limit(text, zone.getBegin(), zone.getEnd());
process(jcas, text.substring(adjusted[0], adjusted[1]), adjusted[0]);
}
}
} else {
// This set collects all zone boundaries.
SortedSet<Integer> boundarySet = new TreeSet<Integer>();
boundarySet.add(0); // Add start boundary
boundarySet.add(text.length()); // Add end boundary
// If zoneTypes have been define then get the boundaries, otherwise we will
// simply have one big zone covering the whole document.
if (zones != null) {
// Iterate over all the zone indices and create sentences respecting
// the zone boundaries. If the zoneTypes overlap... well... bad luck!
for (String zoneName : zones) {
CAS cas = jcas.getCas();
for (AnnotationFS zone : select(cas, getType(cas, zoneName))) {
int[] adjusted = limit(text, zone.getBegin(), zone.getEnd());
boundarySet.add(adjusted[0]);
boundarySet.add(adjusted[1]);
}
}
}
// Now process all zoneTypes. There will be at least two entries in the
// boundary set (see above).
Iterator<Integer> bi = boundarySet.iterator();
int begin = bi.next();
while (bi.hasNext()) {
int end = bi.next();
process(jcas, text.substring(begin, end), begin);
begin = end;
}
}
}
@Override
public boolean incrementToken() throws IOException {
if (iterator == null) {
initializeIterator();
}
if (iterator.hasNext()) {
clearAttributes();
AnnotationFS next = iterator.next();
termAttr.append(next.getCoveredText());
offsetAttr.setOffset(correctOffset(next.getBegin()), correctOffset(next.getEnd()));
return true;
} else {
return false;
}
}
private void updateCrossSentAnnoList(
Map<Integer, Integer> segmentBeginEnd, Map<String, JCas> jCases, List<Type> entryTypes) {
crossSentenceLists = new HashMap<>();
for (Integer begin : segmentBeginEnd.keySet()) {
int thisSent = -1;
Set<Integer> crossSents = new HashSet<>();
for (Type t : entryTypes) {
for (JCas c : jCases.values()) {
if (thisSent == -1) {
thisSent = BratAjaxCasUtil.getSentenceNumber(c, begin);
}
// update cross-sentence annotation lists
for (AnnotationFS fs : selectCovered(c.getCas(), t, this.begin, end)) {
// CASE 1. annotation begins here
if (fs.getBegin() >= begin && fs.getBegin() <= segmentBeginEnd.get(begin)) {
if (fs.getEnd() > segmentBeginEnd.get(begin) || fs.getEnd() < begin) {
Sentence s = BratAjaxCasUtil.getSentenceByAnnoEnd(c, fs.getEnd());
int thatSent = BratAjaxCasUtil.getSentenceNumber(c, s.getBegin());
crossSents.add(thatSent);
}
}
// CASE 2. Annotation ends here
else if (fs.getEnd() >= begin && fs.getEnd() <= segmentBeginEnd.get(begin)) {
if (fs.getBegin() > segmentBeginEnd.get(begin) || fs.getBegin() < begin) {
int thatSent = BratAjaxCasUtil.getSentenceNumber(c, fs.getBegin());
crossSents.add(thatSent);
}
}
}
for (AnnotationFS fs : selectCovered(c.getCas(), t, begin, end)) {
if (fs.getBegin() <= segmentBeginEnd.get(begin)
&& fs.getEnd() > segmentBeginEnd.get(begin)) {
Sentence s = BratAjaxCasUtil.getSentenceByAnnoEnd(c, fs.getEnd());
segmentBeginEnd.put(begin, s.getEnd());
}
}
}
}
crossSentenceLists.put(thisSent, crossSents);
}
}
/**
* Creates a Stem annotation with same begin and end as the AnnotationFS fs, the value is the
* stemmed value derived by applying the featurepath.
*
* @param jcas the JCas
* @param fs the AnnotationFS where the Stem annotation is created
* @throws AnalysisEngineProcessException if the {@code stem} method from the snowball stemmer
* cannot be invoked.
*/
private void createStemAnnotation(JCas jcas, AnnotationFS fs)
throws AnalysisEngineProcessException {
// Check for blank text, it makes no sense to add a stem then (and raised an exception)
String value = fp.getValue(fs);
if (!StringUtils.isBlank(value)) {
if (lowerCase) {
// Fixme - should use locale/language defined in CAS.
value = value.toLowerCase(Locale.US);
}
Stem stemAnnot = new Stem(jcas, fs.getBegin(), fs.getEnd());
SnowballProgram programm = getSnowballProgram(jcas);
programm.setCurrent(value);
try {
// The patched snowball from Lucene has this as a method on SnowballProgram
// but if we have some other snowball also in the classpath, Java might
// choose to use the other. So to be safe, we use a reflection here.
// -- REC, 2011-04-17
MethodUtils.invokeMethod(programm, "stem", null);
} catch (Exception e) {
throw new AnalysisEngineProcessException(e);
}
stemAnnot.setValue(programm.getCurrent());
stemAnnot.addToIndexes(jcas);
// Try setting the "stem" feature on Tokens.
Feature feat = fs.getType().getFeatureByBaseName("stem");
if (feat != null
&& feat.getRange() != null
&& jcas.getTypeSystem().subsumes(feat.getRange(), stemAnnot.getType())) {
fs.setFeatureValue(feat, stemAnnot);
}
}
}
public boolean isIdenticalWith(AnnotationFS anno) {
return anno.getBegin() == begin && anno.getEnd() == end;
}
public Offsets(AnnotationFS anno) {
this(anno.getBegin(), anno.getEnd());
}
/**
* Add annotations from the CAS, which is controlled by the window size, to the brat response
* {@link GetDocumentResponse}
*
* @param aJcas The JCAS object containing annotations
* @param aResponse A brat response containing annotations in brat protocol
* @param aBratAnnotatorModel Data model for brat annotations
* @param aColoringStrategy the coloring strategy to render this layer (ignored)
*/
@Override
public void render(
JCas aJcas,
List<AnnotationFeature> aFeatures,
GetDocumentResponse aResponse,
BratAnnotatorModel aBratAnnotatorModel,
ColoringStrategy aColoringStrategy) {
// Get begin and end offsets of window content
int windowBegin =
BratAjaxCasUtil.selectByAddr(
aJcas, Sentence.class, aBratAnnotatorModel.getSentenceAddress())
.getBegin();
int windowEnd =
BratAjaxCasUtil.selectByAddr(
aJcas,
Sentence.class,
BratAjaxCasUtil.getLastSentenceAddressInDisplayWindow(
aJcas,
aBratAnnotatorModel.getSentenceAddress(),
aBratAnnotatorModel.getPreferences().getWindowSize()))
.getEnd();
// Find the features for the arc and span labels - it is possible that we do not find a
// feature for arc/span labels because they may have been disabled.
AnnotationFeature spanLabelFeature = null;
AnnotationFeature arcLabelFeature = null;
for (AnnotationFeature f : aFeatures) {
if (WebAnnoConst.COREFERENCE_TYPE_FEATURE.equals(f.getName())) {
spanLabelFeature = f;
}
if (WebAnnoConst.COREFERENCE_RELATION_FEATURE.equals(f.getName())) {
arcLabelFeature = f;
}
}
// At this point arc and span feature labels must have been found! If not, the later code
// will crash.
Type chainType = getAnnotationType(aJcas.getCas());
Feature chainFirst = chainType.getFeatureByBaseName(chainFirstFeatureName);
int colorIndex = 0;
// Iterate over the chains
for (FeatureStructure chainFs : selectFS(aJcas.getCas(), chainType)) {
AnnotationFS linkFs = (AnnotationFS) chainFs.getFeatureValue(chainFirst);
AnnotationFS prevLinkFs = null;
// Every chain is supposed to have a different color
String color =
ColoringStrategy.PALETTE_NORMAL_FILTERED[
colorIndex % ColoringStrategy.PALETTE_NORMAL_FILTERED.length];
// The color index is updated even for chains that have no visible links in the current
// window because we would like the chain color to be independent of visibility. In
// particular the color of a chain should not change when switching pages/scrolling.
colorIndex++;
// Iterate over the links of the chain
while (linkFs != null) {
Feature linkNext = linkFs.getType().getFeatureByBaseName(linkNextFeatureName);
AnnotationFS nextLinkFs = (AnnotationFS) linkFs.getFeatureValue(linkNext);
// Is link after window? If yes, we can skip the rest of the chain
if (linkFs.getBegin() >= windowEnd) {
break; // Go to next chain
}
// Is link before window? We only need links that being within the window and that
// end within the window
if (!(linkFs.getBegin() >= windowBegin) && (linkFs.getEnd() <= windowEnd)) {
// prevLinkFs remains null until we enter the window
linkFs = nextLinkFs;
continue; // Go to next link
}
String bratTypeName = TypeUtil.getBratTypeName(this);
// Render span
{
String bratLabelText =
TypeUtil.getBratLabelText(
this,
linkFs,
(spanLabelFeature != null) ? asList(spanLabelFeature) : Collections.EMPTY_LIST);
Offsets offsets =
new Offsets(linkFs.getBegin() - windowBegin, linkFs.getEnd() - windowBegin);
aResponse.addEntity(
new Entity(
BratAjaxCasUtil.getAddr(linkFs), bratTypeName, offsets, bratLabelText, color));
}
// Render arc (we do this on prevLinkFs because then we easily know that the current
// and last link are within the window ;)
if (prevLinkFs != null) {
String bratLabelText = null;
if (linkedListBehavior && arcLabelFeature != null) {
// Render arc label
bratLabelText = TypeUtil.getBratLabelText(this, prevLinkFs, asList(arcLabelFeature));
} else {
// Render only chain type
bratLabelText = TypeUtil.getBratLabelText(this, prevLinkFs, Collections.EMPTY_LIST);
}
List<Argument> argumentList =
asList(
new Argument("Arg1", BratAjaxCasUtil.getAddr(prevLinkFs)),
new Argument("Arg2", BratAjaxCasUtil.getAddr(linkFs)));
aResponse.addRelation(
new Relation(
BratAjaxCasUtil.getAddr(prevLinkFs),
bratTypeName,
argumentList,
bratLabelText,
color));
}
// if (BratAjaxCasUtil.isSame(linkFs, nextLinkFs)) {
// log.error("Loop in CAS detected, aborting rendering of chains");
// break;
// }
prevLinkFs = linkFs;
linkFs = nextLinkFs;
}
}
}
/** Copied and modified from {@link org.apache.uima.util.CasToInlineXml} */
private static String toXML(CAS cas, AnnotationsToElements converter) throws SAXException {
ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
XMLSerializer sax2xml = new XMLSerializer(byteArrayOutputStream, false);
// get document text
String docText = cas.getDocumentText();
char[] docCharArray = docText.toCharArray();
// get iterator over annotations sorted by increasing start position and
// decreasing end position
FSIterator<AnnotationFS> iterator = cas.getAnnotationIndex().iterator();
// This is basically a recursive algorithm that has had the recursion
// removed through the use of an explicit Stack. We iterate over the
// annotations, and if an annotation contains other annotations, we
// push the parent annotation on the stack, process the children, and
// then come back to the parent later.
List<AnnotationFS> stack = new ArrayList<AnnotationFS>();
int pos = 0;
ContentHandler handler = sax2xml.getContentHandler();
handler.startDocument();
// write the start tag
converter.startRootElement(handler);
// now use null is a placeholder for this artificial Document annotation
AnnotationFS curAnnot = null;
while (iterator.isValid()) {
AnnotationFS nextAnnot = iterator.get();
if (curAnnot == null || nextAnnot.getBegin() < curAnnot.getEnd()) {
// nextAnnot's start point is within the span of curAnnot
if (curAnnot == null || nextAnnot.getEnd() <= curAnnot.getEnd()) // crossover span check
{
// nextAnnot is contained within curAnnot
// write text between current pos and beginning of nextAnnot
try {
handler.characters(docCharArray, pos, nextAnnot.getBegin() - pos);
pos = nextAnnot.getBegin();
converter.startAnnotationElement(nextAnnot, handler);
// push parent annotation on stack
stack.add(curAnnot);
// move on to next annotation
curAnnot = nextAnnot;
} catch (StringIndexOutOfBoundsException e) {
System.err.println(
"Invalid annotation range: "
+ nextAnnot.getBegin()
+ ","
+ nextAnnot.getEnd()
+ " in document of length "
+ docText.length());
}
}
iterator.moveToNext();
} else {
// nextAnnot begins after curAnnot ends
// write text between current pos and end of curAnnot
try {
handler.characters(docCharArray, pos, curAnnot.getEnd() - pos);
pos = curAnnot.getEnd();
} catch (StringIndexOutOfBoundsException e) {
System.err.println(
"Invalid annotation range: "
+ curAnnot.getBegin()
+ ","
+ curAnnot.getEnd()
+ " in document of length "
+ docText.length());
}
converter.endAnnotationElement(curAnnot, handler);
// pop next containing annotation off stack
curAnnot = stack.remove(stack.size() - 1);
}
}
// finished writing all start tags, now finish up
if (curAnnot != null) {
try {
handler.characters(docCharArray, pos, curAnnot.getEnd() - pos);
pos = curAnnot.getEnd();
} catch (StringIndexOutOfBoundsException e) {
System.err.println(
"Invalid annotation range: "
+ curAnnot.getBegin()
+ ","
+ curAnnot.getEnd()
+ "in document of length "
+ docText.length());
}
converter.endAnnotationElement(curAnnot, handler);
while (!stack.isEmpty()) {
curAnnot = stack.remove(stack.size() - 1); // pop
if (curAnnot == null) {
break;
}
try {
handler.characters(docCharArray, pos, curAnnot.getEnd() - pos);
pos = curAnnot.getEnd();
} catch (StringIndexOutOfBoundsException e) {
System.err.println(
"Invalid annotation range: "
+ curAnnot.getBegin()
+ ","
+ curAnnot.getEnd()
+ "in document of length "
+ docText.length());
}
converter.endAnnotationElement(curAnnot, handler);
}
}
if (pos < docCharArray.length) {
handler.characters(docCharArray, pos, docCharArray.length - pos);
}
converter.endRootElement(handler);
handler.endDocument();
// return XML string
return new String(byteArrayOutputStream.toByteArray());
}