public void updatePanel(AjaxRequestTarget aTarget, CurationContainer aCC)
throws UIMAException, ClassNotFoundException, IOException, BratAnnotationException {
JCas jCas = repository.readCurationCas(bModel.getDocument());
final int sentenceAddress =
getAddr(
selectSentenceAt(jCas, bModel.getSentenceBeginOffset(), bModel.getSentenceEndOffset()));
bModel.setSentenceAddress(sentenceAddress);
final Sentence sentence = selectByAddr(jCas, Sentence.class, sentenceAddress);
List<Sentence> followingSentences =
selectFollowing(jCas, Sentence.class, sentence, bModel.getPreferences().getWindowSize());
// Check also, when getting the last sentence address in the display window, if this is the
// last sentence or the ONLY sentence in the document
Sentence lastSentenceAddressInDisplayWindow =
followingSentences.size() == 0
? sentence
: followingSentences.get(followingSentences.size() - 1);
if (curationView == null) {
curationView = new SourceListView();
}
curationView.setCurationBegin(sentence.getBegin());
curationView.setCurationEnd(lastSentenceAddressInDisplayWindow.getEnd());
int ws = bModel.getPreferences().getWindowSize();
Sentence fs =
BratAjaxCasUtil.selectSentenceAt(
jCas, bModel.getSentenceBeginOffset(), bModel.getSentenceEndOffset());
int l = BratAjaxCasUtil.getLastSentenceAddressInDisplayWindow(jCas, getAddr(fs), ws);
Sentence ls = (Sentence) selectByAddr(jCas, FeatureStructure.class, l);
fSn = BratAjaxCasUtil.getSentenceNumber(jCas, fs.getBegin());
lSn = BratAjaxCasUtil.getSentenceNumber(jCas, ls.getBegin());
sentencesListView.addOrReplace(sentenceList);
aTarget.add(sentencesListView);
/*
* corssSentAnnoView.addOrReplace(crossSentAnnoList); aTarget.add(corssSentAnnoView);
*/
aTarget.add(suggestionViewPanel);
if (annotate) {
annotator.bratRender(aTarget, editor.getCas(bModel));
annotator.bratSetHighlight(aTarget, bModel.getSelection().getAnnotation());
} else {
annotator.bratRenderLater(aTarget);
}
annotate = false;
CuratorUtil.updatePanel(
aTarget,
suggestionViewPanel,
aCC,
annotator,
repository,
annotationSelectionByUsernameAndAddress,
curationView,
annotationService,
userRepository);
}
private void verifySentence(Sentence sentence, TestSentenceInfo info)
throws LAPVerificationException {
if (!info.text.equals(sentence.getCoveredText()))
throw new LAPVerificationException(
"Bad sentence text, expected \""
+ info.text
+ "\", got \""
+ sentence.getCoveredText()
+ "\"");
if (info.begin != sentence.getBegin())
throw new LAPVerificationException(
"Bad sentence begin index, expected " + info.begin + ", got " + sentence.getBegin());
if (info.end != sentence.getEnd())
throw new LAPVerificationException(
"Bad sentence end index, expected " + info.end + ", got " + sentence.getEnd());
System.out.println("Verified sentence: " + info);
}
/**
* Puts JCases into a list and get a random annotation document that will be used as a base for
* the diff.
*
* @throws IOException
* @throws ClassNotFoundException
* @throws UIMAException
*/
private void updateSegment(
BratAnnotatorModel aBratAnnotatorModel,
Map<Integer, Integer> segmentBeginEnd,
Map<Integer, Integer> segmentNumber,
Map<String, Map<Integer, Integer>> segmentAdress,
JCas jCas,
String username,
int aWinSize)
throws UIMAException, ClassNotFoundException, IOException {
Sentence firstSentence =
selectSentenceAt(
jCas,
aBratAnnotatorModel.getSentenceBeginOffset(),
aBratAnnotatorModel.getSentenceEndOffset());
Sentence lastSentence =
selectByAddr(
jCas,
Sentence.class,
getLastSentenceAddressInDisplayWindow(jCas, getAddr(firstSentence), aWinSize));
begin = firstSentence.getBegin();
end = lastSentence.getEnd();
sentenceNumber = getFirstSentenceNumber(jCas, getAddr(firstSentence));
segmentAdress.put(username, new HashMap<Integer, Integer>());
for (Sentence sentence : selectCovered(jCas, Sentence.class, begin, end)) {
sentenceNumber += 1;
segmentBeginEnd.put(sentence.getBegin(), sentence.getEnd());
segmentNumber.put(sentence.getBegin(), sentenceNumber);
segmentAdress.get(username).put(sentence.getBegin(), getAddr(sentence));
}
/*
* if (segmentBeginEnd.isEmpty()) { for (Sentence sentence : selectCovered(mergeJCas,
* Sentence.class, begin, end)) {
*
* } }
*/
}
private void ubdateSentenceNumber(JCas aJCas, int aAddress) {
bModel.setSentenceAddress(aAddress);
Sentence sentence = selectByAddr(aJCas, Sentence.class, aAddress);
bModel.setSentenceBeginOffset(sentence.getBegin());
bModel.setSentenceEndOffset(sentence.getEnd());
bModel.setSentenceNumber(BratAjaxCasUtil.getSentenceNumber(aJCas, sentence.getBegin()));
Sentence firstSentence =
selectSentenceAt(aJCas, bModel.getSentenceBeginOffset(), bModel.getSentenceEndOffset());
int lastAddressInPage =
getLastSentenceAddressInDisplayWindow(
aJCas, getAddr(firstSentence), bModel.getPreferences().getWindowSize());
// the last sentence address in the display window
Sentence lastSentenceInPage =
(Sentence) selectByAddr(aJCas, FeatureStructure.class, lastAddressInPage);
bModel.setFSN(BratAjaxCasUtil.getSentenceNumber(aJCas, firstSentence.getBegin()));
bModel.setLSN(BratAjaxCasUtil.getSentenceNumber(aJCas, lastSentenceInPage.getBegin()));
}
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);
}
}
private void setCurationSegmentBeginEnd()
throws UIMAException, ClassNotFoundException, IOException {
JCas jCas = repository.readAnnotationCas(bModel.getDocument(), bModel.getUser());
final int sentenceAddress =
getAddr(
selectSentenceAt(jCas, bModel.getSentenceBeginOffset(), bModel.getSentenceEndOffset()));
final Sentence sentence = selectByAddr(jCas, Sentence.class, sentenceAddress);
List<Sentence> followingSentences =
selectFollowing(jCas, Sentence.class, sentence, bModel.getPreferences().getWindowSize());
// Check also, when getting the last sentence address in the display window, if this is the
// last sentence or the ONLY sentence in the document
Sentence lastSentenceAddressInDisplayWindow =
followingSentences.size() == 0
? sentence
: followingSentences.get(followingSentences.size() - 1);
curationSegment.setBegin(sentence.getBegin());
curationSegment.setEnd(lastSentenceAddressInDisplayWindow.getEnd());
}
private void updateCurationView(
final CurationContainer curationContainer,
final SourceListView curationViewItem,
AjaxRequestTarget aTarget,
JCas jCas) {
int currentSentAddress =
BratAjaxCasUtil.getCurrentSentence(
jCas, curationViewItem.getBegin(), curationViewItem.getEnd())
.getAddress();
bModel.setSentenceAddress(
BratAjaxCasUtil.getSentenceBeginAddress(
jCas,
currentSentAddress,
curationViewItem.getBegin(),
bModel.getProject(),
bModel.getDocument(),
bModel.getPreferences().getWindowSize()));
Sentence sentence = selectByAddr(jCas, Sentence.class, bModel.getSentenceAddress());
bModel.setSentenceBeginOffset(sentence.getBegin());
bModel.setSentenceEndOffset(sentence.getEnd());
Sentence firstSentence =
selectSentenceAt(jCas, bModel.getSentenceBeginOffset(), bModel.getSentenceEndOffset());
int lastAddressInPage =
getLastSentenceAddressInDisplayWindow(
jCas, getAddr(firstSentence), bModel.getPreferences().getWindowSize());
// the last sentence address in the display window
Sentence lastSentenceInPage =
(Sentence) selectByAddr(jCas, FeatureStructure.class, lastAddressInPage);
bModel.setFSN(BratAjaxCasUtil.getSentenceNumber(jCas, firstSentence.getBegin()));
bModel.setLSN(BratAjaxCasUtil.getSentenceNumber(jCas, lastSentenceInPage.getBegin()));
curationContainer.setBratAnnotatorModel(bModel);
onChange(aTarget);
}
@Override
public void process(JCas aJCas) throws AnalysisEngineProcessException {
// Convert UIMA to LIF Container
Container container = new Container();
container.setLanguage(aJCas.getDocumentLanguage());
container.setText(aJCas.getDocumentText());
View view = container.newView();
// Paragraph
for (Paragraph p : select(aJCas, Paragraph.class)) {
view.newAnnotation(id(PARAGRAPH, p), Discriminators.Uri.PARAGRAPH, p.getBegin(), p.getEnd());
}
// Sentence
for (Sentence s : select(aJCas, Sentence.class)) {
view.newAnnotation(id(SENTENCE, s), Discriminators.Uri.SENTENCE, s.getBegin(), s.getEnd());
}
// Token, POS, Lemma
for (Token t : select(aJCas, Token.class)) {
Annotation a =
view.newAnnotation(id(TOKEN, t), Discriminators.Uri.TOKEN, t.getBegin(), t.getEnd());
if (t.getPos() != null) {
a.addFeature(Features.Token.POS, t.getPos().getPosValue());
}
if (t.getLemma() != null) {
a.addFeature(Features.Token.LEMMA, t.getLemma().getValue());
}
}
// NamedEntity
for (NamedEntity neAnno : select(aJCas, NamedEntity.class)) {
Annotation ne =
view.newAnnotation(
id(NAMED_ENTITY, neAnno), Discriminators.Uri.NE, neAnno.getBegin(), neAnno.getEnd());
ne.setLabel(neAnno.getValue());
}
// Dependency
for (Sentence s : select(aJCas, Sentence.class)) {
Set<String> depRelIds = new TreeSet<>();
for (Dependency dep : selectCovered(Dependency.class, s)) {
String depRelId = id(DEPENDENCY, dep);
// LAPPS dependencies inherit from Relation which has no offsets
Annotation depRel = view.newAnnotation(depRelId, Discriminators.Uri.DEPENDENCY);
depRel.setLabel(dep.getDependencyType());
depRel.addFeature(Features.Dependency.GOVERNOR, id(TOKEN, dep.getGovernor()));
depRel.addFeature(Features.Dependency.DEPENDENT, id(TOKEN, dep.getDependent()));
depRelIds.add(depRelId);
}
if (!depRelIds.isEmpty()) {
Annotation depStruct =
view.newAnnotation(
id(DEPENDENCY_STRUCTURE, s),
Discriminators.Uri.DEPENDENCY_STRUCTURE,
s.getBegin(),
s.getEnd());
depStruct.addFeature(Features.DependencyStructure.DEPENDENCIES, depRelIds);
}
}
// Constituents
for (ROOT r : select(aJCas, ROOT.class)) {
Set<String> constituents = new LinkedHashSet<>();
convertConstituent(view, r, constituents);
Annotation phraseStruct =
view.newAnnotation(
id(PHRASE_STRUCTURE, r),
Discriminators.Uri.PHRASE_STRUCTURE,
r.getBegin(),
r.getEnd());
phraseStruct.addFeature(Features.PhraseStructure.CONSTITUENTS, constituents);
}
try (OutputStream docOS = getOutputStream(aJCas, filenameSuffix)) {
String json = Serializer.toPrettyJson(container);
IOUtils.write(json, docOS, encoding);
} catch (Exception e) {
throw new AnalysisEngineProcessException(e);
}
}
