private void update(AjaxRequestTarget target) {
JCas jCas = null;
try {
CuratorUtil.updatePanel(
target,
automateView,
curationContainer,
mergeVisualizer,
repository,
annotationSelectionByUsernameAndAddress,
curationSegment,
annotationService,
userRepository);
jCas = repository.readCorrectionCas(bModel.getDocument());
} catch (UIMAException e) {
error(ExceptionUtils.getRootCauseMessage(e));
} catch (ClassNotFoundException e) {
error(e.getMessage());
} catch (IOException e) {
error(e.getMessage());
} catch (BratAnnotationException e) {
error(e.getMessage());
}
gotoPageTextField.setModelObject(getFirstSentenceNumber(jCas, bModel.getSentenceAddress()) + 1);
gotoPageAddress = getSentenceAddress(jCas, gotoPageTextField.getModelObject());
target.add(gotoPageTextField);
target.add(automateView);
target.add(numberOfPages);
}
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);
}
private void loadDocumentAction()
throws UIMAException, ClassNotFoundException, IOException, BratAnnotationException {
String username = SecurityContextHolder.getContext().getAuthentication().getName();
User logedInUser =
userRepository.get(SecurityContextHolder.getContext().getAuthentication().getName());
bModel.setUser(logedInUser);
JCas jCas = null;
try {
AnnotationDocument logedInUserAnnotationDocument =
repository.getAnnotationDocument(bModel.getDocument(), logedInUser);
jCas = repository.readAnnotationCas(logedInUserAnnotationDocument);
} catch (IOException e) {
throw e;
}
// Get information to be populated to bratAnnotatorModel from the JCAS of the logged in user
//
catch (DataRetrievalFailureException e) {
jCas = repository.readAnnotationCas(bModel.getDocument(), logedInUser);
// This is the auto annotation, save it under CORRECTION_USER, Only if it is not created
// by another annotater
if (!repository.existsCorrectionCas(bModel.getDocument())) {
repository.writeCorrectionCas(jCas, bModel.getDocument(), logedInUser);
}
} catch (NoResultException e) {
jCas = repository.readAnnotationCas(bModel.getDocument(), logedInUser);
// This is the auto annotation, save it under CORRECTION_USER, Only if it is not created
// by another annotater
if (!repository.existsCorrectionCas(bModel.getDocument())) {
repository.writeCorrectionCas(jCas, bModel.getDocument(), logedInUser);
}
}
// (Re)initialize brat model after potential creating / upgrading CAS
bModel.initForDocument(jCas);
// Load user preferences
PreferencesUtil.setAnnotationPreference(
username, repository, annotationService, bModel, Mode.AUTOMATION);
// if project is changed, reset some project specific settings
if (currentprojectId != bModel.getProject().getId()) {
bModel.initForProject();
}
currentprojectId = bModel.getProject().getId();
currentDocumentId = bModel.getDocument().getId();
LOG.debug(
"Configured BratAnnotatorModel for user ["
+ bModel.getUser()
+ "] f:["
+ bModel.getFirstSentenceAddress()
+ "] l:["
+ bModel.getLastSentenceAddress()
+ "] s:["
+ bModel.getSentenceAddress()
+ "]");
}
/**
* 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;
}
}
}