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);
}
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);
}
@Override
public void renderHead(IHeaderResponse response) {
super.renderHead(response);
if (firstLoad) {
firstLoad = false;
} else if (bModel.getProject() != null) {
// mergeVisualizer.setModelObject(bratAnnotatorModel);
annotator.setCollection("#" + bModel.getProject().getName() + "/");
annotator.bratInitRenderLater(response);
}
}
public static void savePreference(BratAnnotatorModel aBModel, RepositoryService aRepository)
throws FileNotFoundException, IOException {
AnnotationPreference preference = aBModel.getPreferences();
ArrayList<Long> layers = new ArrayList<Long>();
for (AnnotationLayer layer : aBModel.getAnnotationLayers()) {
layers.add(layer.getId());
}
preference.setAnnotationLayers(layers);
String username = SecurityContextHolder.getContext().getAuthentication().getName();
aRepository.saveUserSettings(username, aBModel.getProject(), aBModel.getMode(), preference);
}
/** for the first time the page is accessed, open the <b>open document dialog</b> */
@Override
public void renderHead(IHeaderResponse response) {
super.renderHead(response);
String jQueryString = "";
if (firstLoad) {
jQueryString += "jQuery('#showOpenDocumentModal').trigger('click');";
firstLoad = false;
}
response.render(OnLoadHeaderItem.forScript(jQueryString));
if (bModel.getProject() != null) {
mergeVisualizer.setModelObject(bModel);
mergeVisualizer.setCollection("#" + bModel.getProject().getName() + "/");
mergeVisualizer.bratInitRenderLater(response);
}
}
/**
* Set annotation preferences of users for a given project such as window size, annotation
* layers,... reading from the file system.
*
* @param aUsername The {@link User} for whom we need to read the preference (preferences are
* stored per user)
* @param aRepositoryService the repository service.
* @param aAnnotationService the annotation service.
* @param aBModel The {@link BratAnnotatorModel} that will be populated with preferences from the
* file
* @param aMode the mode.
* @throws BeansException hum?
* @throws IOException hum?
*/
public static void setAnnotationPreference(
String aUsername,
RepositoryService aRepositoryService,
AnnotationService aAnnotationService,
BratAnnotatorModel aBModel,
Mode aMode)
throws BeansException, IOException {
AnnotationPreference preference = new AnnotationPreference();
BeanWrapper wrapper = new BeanWrapperImpl(preference);
// get annotation preference from file system
try {
Properties props = aRepositoryService.loadUserSettings(aUsername, aBModel.getProject());
for (Entry<Object, Object> entry : props.entrySet()) {
String property = entry.getKey().toString();
int index = property.lastIndexOf(".");
String propertyName = property.substring(index + 1);
String mode = property.substring(0, index);
if (wrapper.isWritableProperty(propertyName) && mode.equals(aMode.getName())) {
if (AnnotationPreference.class.getDeclaredField(propertyName).getGenericType()
instanceof ParameterizedType) {
List<String> value =
Arrays.asList(
StringUtils.replaceChars(entry.getValue().toString(), "[]", "").split(","));
if (!value.get(0).equals("")) {
wrapper.setPropertyValue(propertyName, value);
}
} else {
wrapper.setPropertyValue(propertyName, entry.getValue());
}
}
}
aBModel.setPreferences(preference);
// Get tagset using the id, from the properties file
aBModel.getAnnotationLayers().clear();
if (preference.getAnnotationLayers() != null) {
for (Long id : preference.getAnnotationLayers()) {
aBModel.getAnnotationLayers().add(aAnnotationService.getLayer(id));
}
} else {
// If no layer preferences are defined, then just assume all layers are enabled
List<AnnotationLayer> layers = aAnnotationService.listAnnotationLayer(aBModel.getProject());
aBModel.setAnnotationLayers(layers);
}
}
// no preference found
catch (Exception e) {
// If no layer preferences are defined, then just assume all layers are enabled
List<AnnotationLayer> layers = aAnnotationService.listAnnotationLayer(aBModel.getProject());
aBModel.setAnnotationLayers(layers);
}
}
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 JCas createCorrectionCas(
JCas mergeJCas,
BratAnnotatorModel aBratAnnotatorModel,
AnnotationDocument randomAnnotationDocument)
throws UIMAException, ClassNotFoundException, IOException {
User userLoggedIn =
userRepository.get(SecurityContextHolder.getContext().getAuthentication().getName());
mergeJCas = repository.readAnnotationCas(aBratAnnotatorModel.getDocument(), userLoggedIn);
repository.writeCorrectionCas(mergeJCas, randomAnnotationDocument.getDocument(), userLoggedIn);
return mergeJCas;
}
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()));
}
/**
* 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)) {
*
* } }
*/
}
/**
* Fetches the CAS that the user will be able to edit. In AUTOMATION/CORRECTION mode, this is the
* CAS for the CORRECTION_USER and in CURATION mode it is the CAS for the CURATION user.
*
* @param aBratAnnotatorModel the model.
* @param aDocument the source document.
* @param jCases the JCases.
* @param randomAnnotationDocument an annotation document.
* @return the JCas.
* @throws UIMAException hum?
* @throws ClassNotFoundException hum?
* @throws IOException if an I/O error occurs.
* @throws BratAnnotationException hum?
*/
public JCas getMergeCas(
BratAnnotatorModel aBratAnnotatorModel,
SourceDocument aDocument,
Map<String, JCas> jCases,
AnnotationDocument randomAnnotationDocument)
throws UIMAException, ClassNotFoundException, IOException, BratAnnotationException {
JCas mergeJCas = null;
try {
if (aBratAnnotatorModel.getMode().equals(Mode.AUTOMATION)
|| aBratAnnotatorModel.getMode().equals(Mode.CORRECTION)) {
// Upgrading should be an explicit action during the opening of a document at the
// end
// of the open dialog - it must not happen during editing because the CAS addresses
// are used as IDs in the UI
// repository.upgradeCasAndSave(aDocument, aBratAnnotatorModel.getMode(),
// aBratAnnotatorModel.getUser().getUsername());
mergeJCas = repository.readCorrectionCas(aDocument);
} else {
// Upgrading should be an explicit action during the opening of a document at the
// end
// of the open dialog - it must not happen during editing because the CAS addresses
// are used as IDs in the UI
// repository.upgradeCasAndSave(aDocument, aBratAnnotatorModel.getMode(),
// aBratAnnotatorModel.getUser().getUsername());
mergeJCas = repository.readCurationCas(aDocument);
}
}
// Create jcas, if it could not be loaded from the file system
catch (Exception e) {
if (aBratAnnotatorModel.getMode().equals(Mode.AUTOMATION)
|| aBratAnnotatorModel.getMode().equals(Mode.CORRECTION)) {
mergeJCas = createCorrectionCas(mergeJCas, aBratAnnotatorModel, randomAnnotationDocument);
} else {
mergeJCas =
createCurationCas(
aBratAnnotatorModel.getProject(),
randomAnnotationDocument,
jCases,
aBratAnnotatorModel.getAnnotationLayers());
}
}
return mergeJCas;
}
public AutomationPage() {
bModel = new BratAnnotatorModel();
bModel.setMode(Mode.AUTOMATION);
LinkedList<CurationUserSegmentForAnnotationDocument> sentences =
new LinkedList<CurationUserSegmentForAnnotationDocument>();
CurationUserSegmentForAnnotationDocument curationUserSegmentForAnnotationDocument =
new CurationUserSegmentForAnnotationDocument();
if (bModel.getDocument() != null) {
curationUserSegmentForAnnotationDocument.setAnnotationSelectionByUsernameAndAddress(
annotationSelectionByUsernameAndAddress);
curationUserSegmentForAnnotationDocument.setBratAnnotatorModel(bModel);
sentences.add(curationUserSegmentForAnnotationDocument);
}
automateView =
new SuggestionViewPanel(
"automateView",
new Model<LinkedList<CurationUserSegmentForAnnotationDocument>>(sentences)) {
private static final long serialVersionUID = 2583509126979792202L;
@Override
public void onChange(AjaxRequestTarget aTarget) {
try {
// update begin/end of the curationsegment based on bratAnnotatorModel changes
// (like sentence change in auto-scroll mode,....
aTarget.addChildren(getPage(), FeedbackPanel.class);
curationContainer.setBratAnnotatorModel(bModel);
setCurationSegmentBeginEnd();
CuratorUtil.updatePanel(
aTarget,
this,
curationContainer,
mergeVisualizer,
repository,
annotationSelectionByUsernameAndAddress,
curationSegment,
annotationService,
userRepository);
} catch (UIMAException e) {
error(ExceptionUtils.getRootCause(e));
} catch (ClassNotFoundException e) {
error(e.getMessage());
} catch (IOException e) {
error(e.getMessage());
} catch (BratAnnotationException e) {
error(e.getMessage());
}
mergeVisualizer.bratRenderLater(aTarget);
aTarget.add(numberOfPages);
update(aTarget);
}
};
automateView.setOutputMarkupId(true);
add(automateView);
annotationDetailEditorPanel =
new AnnotationDetailEditorPanel(
"annotationDetailEditorPanel", new Model<BratAnnotatorModel>(bModel)) {
private static final long serialVersionUID = 2857345299480098279L;
@Override
protected void onChange(AjaxRequestTarget aTarget, BratAnnotatorModel aBModel) {
aTarget.addChildren(getPage(), FeedbackPanel.class);
try {
mergeVisualizer.bratRender(aTarget, getCas(aBModel));
} catch (UIMAException | ClassNotFoundException | IOException e) {
LOG.info("Error reading CAS " + e.getMessage());
error("Error reading CAS " + e.getMessage());
return;
}
mergeVisualizer.bratRenderHighlight(aTarget, aBModel.getSelection().getAnnotation());
mergeVisualizer.onChange(aTarget, aBModel);
mergeVisualizer.onAnnotate(
aTarget,
aBModel,
aBModel.getSelection().getBegin(),
aBModel.getSelection().getEnd());
if (!aBModel.getSelection().isAnnotate()) {
mergeVisualizer.onDelete(
aTarget,
aBModel,
aBModel.getSelection().getBegin(),
aBModel.getSelection().getEnd());
}
}
};
annotationDetailEditorPanel.setOutputMarkupId(true);
add(annotationDetailEditorPanel);
mergeVisualizer =
new BratAnnotator(
"mergeView", new Model<BratAnnotatorModel>(bModel), annotationDetailEditorPanel) {
private static final long serialVersionUID = 7279648231521710155L;
@Override
public void onChange(AjaxRequestTarget aTarget, BratAnnotatorModel aBratAnnotatorModel) {
try {
aTarget.addChildren(getPage(), FeedbackPanel.class);
// info(bratAnnotatorModel.getMessage());
aTarget.addChildren(getPage(), FeedbackPanel.class);
bModel = aBratAnnotatorModel;
SuggestionBuilder builder =
new SuggestionBuilder(repository, annotationService, userRepository);
curationContainer = builder.buildCurationContainer(bModel);
setCurationSegmentBeginEnd();
curationContainer.setBratAnnotatorModel(bModel);
CuratorUtil.updatePanel(
aTarget,
automateView,
curationContainer,
this,
repository,
annotationSelectionByUsernameAndAddress,
curationSegment,
annotationService,
userRepository);
aTarget.add(automateView);
aTarget.add(numberOfPages);
} catch (UIMAException e) {
error(ExceptionUtils.getRootCause(e));
} catch (ClassNotFoundException e) {
error(e.getMessage());
} catch (IOException e) {
error(e.getMessage());
} catch (BratAnnotationException e) {
error(e.getMessage());
}
update(aTarget);
}
@Override
public void onAnnotate(
AjaxRequestTarget aTarget,
BratAnnotatorModel aBratAnnotatorModel,
int aStart,
int aEnd) {
MiraTemplate template;
Set<AnnotationFeature> features = bModel.getRememberedSpanFeatures().keySet();
AnnotationFeature autoFeature = null;
for (AnnotationFeature feature : features) {
autoFeature = feature;
break;
}
try {
template = automationService.getMiraTemplate(autoFeature);
if (!template.isAnnotateAndPredict()) {
return;
}
/*
* Tag tag = annotationService.getTag(bratAnnotatorModel
* .getRememberedSpanFeatures().get(autoFeature), autoFeature.getTagset());
*/
AutomationUtil.repeateAnnotation(
bModel,
repository,
userRepository,
annotationService,
automationService,
aStart,
aEnd,
autoFeature);
} catch (UIMAException e) {
error(ExceptionUtils.getRootCause(e));
} catch (ClassNotFoundException e) {
error(e.getMessage());
} catch (IOException e) {
error(e.getMessage());
} catch (BratAnnotationException e) {
error(e.getMessage());
} catch (NoResultException e) { // no automation layer is configured yet.
template = null;
return;
}
update(aTarget);
}
@Override
public void onDelete(
AjaxRequestTarget aTarget,
BratAnnotatorModel aBratAnnotatorModel,
int aStart,
int aEnd) {
MiraTemplate template;
Set<AnnotationFeature> features = bModel.getRememberedSpanFeatures().keySet();
AnnotationFeature autoFeature = null;
for (AnnotationFeature feature : features) {
autoFeature = feature;
break;
}
if (autoFeature == null) {
return;
}
try {
template = automationService.getMiraTemplate(autoFeature);
if (!template.isAnnotateAndPredict()) {
return;
}
/*
* Tag tag = annotationService.getTag(bratAnnotatorModel
* .getRememberedSpanFeatures().get(autoFeature), autoFeature.getTagset());
*/
AutomationUtil.deleteAnnotation(
bModel,
repository,
annotationService,
automationService,
userRepository,
aStart,
aEnd,
autoFeature);
} catch (UIMAException e) {
error(ExceptionUtils.getRootCause(e));
} catch (ClassNotFoundException e) {
error(e.getMessage());
} catch (IOException e) {
error(e.getMessage());
} catch (BratAnnotationException e) {
error(e.getMessage());
} catch (NoResultException e) { // no automation layer is configured yet.
template = null;
return;
}
update(aTarget);
}
};
// reset sentenceAddress and lastSentenceAddress to the orginal once
mergeVisualizer.setOutputMarkupId(true);
add(mergeVisualizer);
curationContainer = new CurationContainer();
curationContainer.setBratAnnotatorModel(bModel);
add(
documentNamePanel =
new DocumentNamePanel("documentNamePanel", new Model<BratAnnotatorModel>(bModel)));
add(
numberOfPages =
(Label)
new Label(
"numberOfPages",
new LoadableDetachableModel<String>() {
private static final long serialVersionUID = 891566759811286173L;
@Override
protected String load() {
if (bModel.getDocument() != null) {
JCas mergeJCas = null;
try {
mergeJCas = repository.readCorrectionCas(bModel.getDocument());
totalNumberOfSentence = getNumberOfPages(mergeJCas);
// If only one page, start displaying from sentence 1
/*
* if (totalNumberOfSentence == 1) {
* bratAnnotatorModel.setSentenceAddress(bratAnnotatorModel
* .getFirstSentenceAddress()); }
*/
int address =
getAddr(
selectSentenceAt(
mergeJCas,
bModel.getSentenceBeginOffset(),
bModel.getSentenceEndOffset()));
sentenceNumber = getFirstSentenceNumber(mergeJCas, address);
int firstSentenceNumber = sentenceNumber + 1;
int lastSentenceNumber;
if (firstSentenceNumber
+ bModel.getPreferences().getWindowSize()
- 1
< totalNumberOfSentence) {
lastSentenceNumber =
firstSentenceNumber
+ bModel.getPreferences().getWindowSize()
- 1;
} else {
lastSentenceNumber = totalNumberOfSentence;
}
return "showing "
+ firstSentenceNumber
+ "-"
+ lastSentenceNumber
+ " of "
+ totalNumberOfSentence
+ " sentences";
} catch (UIMAException e) {
return "";
} catch (DataRetrievalFailureException e) {
return "";
} catch (ClassNotFoundException e) {
return "";
} catch (FileNotFoundException e) {
return "";
} catch (IOException e) {
return "";
}
} else {
return ""; // no document yet selected
}
}
})
.setOutputMarkupId(true));
final ModalWindow openDocumentsModal;
add(openDocumentsModal = new ModalWindow("openDocumentsModal"));
openDocumentsModal.setOutputMarkupId(true);
openDocumentsModal.setInitialWidth(500);
openDocumentsModal.setInitialHeight(300);
openDocumentsModal.setResizable(true);
openDocumentsModal.setWidthUnit("px");
openDocumentsModal.setHeightUnit("px");
openDocumentsModal.setTitle("Open document");
add(
new AjaxLink<Void>("showOpenDocumentModal") {
private static final long serialVersionUID = 7496156015186497496L;
@Override
public void onClick(AjaxRequestTarget aTarget) {
openDocumentsModal.setContent(
new OpenModalWindowPanel(
openDocumentsModal.getContentId(),
bModel,
openDocumentsModal,
Mode.AUTOMATION));
openDocumentsModal.setWindowClosedCallback(
new ModalWindow.WindowClosedCallback() {
private static final long serialVersionUID = -1746088901018629567L;
@Override
public void onClose(AjaxRequestTarget target) {
if (bModel.getDocument() == null) {
setResponsePage(WelcomePage.class);
return;
}
try {
target.addChildren(getPage(), FeedbackPanel.class);
bModel.setDocument(bModel.getDocument());
bModel.setProject(bModel.getProject());
String username =
SecurityContextHolder.getContext().getAuthentication().getName();
repository.upgradeCasAndSave(bModel.getDocument(), Mode.AUTOMATION, username);
loadDocumentAction();
setCurationSegmentBeginEnd();
update(target);
} catch (UIMAException e) {
target.addChildren(getPage(), FeedbackPanel.class);
error(ExceptionUtils.getRootCause(e));
} catch (ClassNotFoundException e) {
target.addChildren(getPage(), FeedbackPanel.class);
error(e.getMessage());
} catch (IOException e) {
target.addChildren(getPage(), FeedbackPanel.class);
error(e.getMessage());
} catch (BratAnnotationException e) {
error(e.getMessage());
}
finish.setModelObject(bModel);
target.add(finish.setOutputMarkupId(true));
target.appendJavaScript(
"Wicket.Window.unloadConfirmation=false;window.location.reload()");
target.add(documentNamePanel.setOutputMarkupId(true));
target.add(numberOfPages);
}
});
openDocumentsModal.show(aTarget);
}
});
add(
new AnnotationLayersModalPanel(
"annotationLayersModalPanel", new Model<BratAnnotatorModel>(bModel)) {
private static final long serialVersionUID = -4657965743173979437L;
@Override
protected void onChange(AjaxRequestTarget aTarget) {
curationContainer.setBratAnnotatorModel(bModel);
try {
aTarget.addChildren(getPage(), FeedbackPanel.class);
setCurationSegmentBeginEnd();
} catch (UIMAException e) {
error(ExceptionUtils.getRootCauseMessage(e));
} catch (ClassNotFoundException e) {
error(e.getMessage());
} catch (IOException e) {
error(e.getMessage());
}
update(aTarget);
// mergeVisualizer.reloadContent(aTarget);
aTarget.appendJavaScript(
"Wicket.Window.unloadConfirmation = false;window.location.reload()");
}
});
add(new ExportModalPanel("exportModalPanel", new Model<BratAnnotatorModel>(bModel)));
gotoPageTextField =
(NumberTextField<Integer>)
new NumberTextField<Integer>("gotoPageText", new Model<Integer>(0));
Form<Void> gotoPageTextFieldForm = new Form<Void>("gotoPageTextFieldForm");
gotoPageTextFieldForm.add(
new AjaxFormSubmitBehavior(gotoPageTextFieldForm, "onsubmit") {
private static final long serialVersionUID = -4549805321484461545L;
@Override
protected void onSubmit(AjaxRequestTarget aTarget) {
if (gotoPageAddress == 0) {
aTarget.appendJavaScript("alert('The sentence number entered is not valid')");
return;
}
JCas mergeJCas = null;
try {
aTarget.addChildren(getPage(), FeedbackPanel.class);
mergeJCas = repository.readCorrectionCas(bModel.getDocument());
if (bModel.getSentenceAddress() != gotoPageAddress) {
ubdateSentenceNumber(mergeJCas, gotoPageAddress);
SuggestionBuilder builder =
new SuggestionBuilder(repository, annotationService, userRepository);
curationContainer = builder.buildCurationContainer(bModel);
setCurationSegmentBeginEnd();
curationContainer.setBratAnnotatorModel(bModel);
update(aTarget);
mergeVisualizer.bratRenderLater(aTarget);
}
} catch (UIMAException e) {
error(ExceptionUtils.getRootCause(e));
} catch (ClassNotFoundException e) {
error(e.getMessage());
} catch (IOException e) {
error(e.getMessage());
} catch (BratAnnotationException e) {
error(e.getMessage());
}
}
});
gotoPageTextField.setType(Integer.class);
gotoPageTextField.setMinimum(1);
gotoPageTextField.setDefaultModelObject(1);
add(gotoPageTextFieldForm.add(gotoPageTextField));
gotoPageTextField.add(
new AjaxFormComponentUpdatingBehavior("onchange") {
private static final long serialVersionUID = -3853194405966729661L;
@Override
protected void onUpdate(AjaxRequestTarget target) {
JCas mergeJCas = null;
try {
mergeJCas = repository.readCorrectionCas(bModel.getDocument());
gotoPageAddress = getSentenceAddress(mergeJCas, gotoPageTextField.getModelObject());
} catch (UIMAException e) {
error(ExceptionUtils.getRootCause(e));
} catch (ClassNotFoundException e) {
error(ExceptionUtils.getRootCause(e));
} catch (IOException e) {
error(e.getMessage());
}
}
});
add(
new AjaxLink<Void>("gotoPageLink") {
private static final long serialVersionUID = 7496156015186497496L;
@Override
public void onClick(AjaxRequestTarget aTarget) {
if (gotoPageAddress == 0) {
aTarget.appendJavaScript("alert('The sentence number entered is not valid')");
return;
}
if (bModel.getDocument() == null) {
aTarget.appendJavaScript("alert('Please open a document first!')");
return;
}
JCas mergeJCas = null;
try {
aTarget.addChildren(getPage(), FeedbackPanel.class);
mergeJCas = repository.readCorrectionCas(bModel.getDocument());
if (bModel.getSentenceAddress() != gotoPageAddress) {
ubdateSentenceNumber(mergeJCas, gotoPageAddress);
SuggestionBuilder builder =
new SuggestionBuilder(repository, annotationService, userRepository);
curationContainer = builder.buildCurationContainer(bModel);
setCurationSegmentBeginEnd();
curationContainer.setBratAnnotatorModel(bModel);
update(aTarget);
mergeVisualizer.bratRenderLater(aTarget);
}
} catch (UIMAException e) {
error(ExceptionUtils.getRootCause(e));
} catch (ClassNotFoundException e) {
error(e.getMessage());
} catch (IOException e) {
error(e.getMessage());
} catch (BratAnnotationException e) {
error(e.getMessage());
}
}
});
finish =
new FinishImage(
"finishImage",
new LoadableDetachableModel<BratAnnotatorModel>() {
private static final long serialVersionUID = -2737326878793568454L;
@Override
protected BratAnnotatorModel load() {
return bModel;
}
});
add(
new FinishLink("showYesNoModalPanel", new Model<BratAnnotatorModel>(bModel), finish) {
private static final long serialVersionUID = -4657965743173979437L;
});
// Show the previous document, if exist
add(
new AjaxLink<Void>("showPreviousDocument") {
private static final long serialVersionUID = 7496156015186497496L;
/**
* Get the current beginning sentence address and add on it the size of the display window
*/
@Override
public void onClick(AjaxRequestTarget target) {
target.addChildren(getPage(), FeedbackPanel.class);
// List of all Source Documents in the project
List<SourceDocument> listOfSourceDocuements =
repository.listSourceDocuments(bModel.getProject());
String username = SecurityContextHolder.getContext().getAuthentication().getName();
User user = userRepository.get(username);
List<SourceDocument> sourceDocumentsinIgnorState = new ArrayList<SourceDocument>();
for (SourceDocument sourceDocument : listOfSourceDocuements) {
if (repository.existsAnnotationDocument(sourceDocument, user)
&& repository
.getAnnotationDocument(sourceDocument, user)
.getState()
.equals(AnnotationDocumentState.IGNORE)) {
sourceDocumentsinIgnorState.add(sourceDocument);
} else if (sourceDocument.isTrainingDocument()) {
sourceDocumentsinIgnorState.add(sourceDocument);
}
}
listOfSourceDocuements.removeAll(sourceDocumentsinIgnorState);
// Index of the current source document in the list
int currentDocumentIndex = listOfSourceDocuements.indexOf(bModel.getDocument());
// If the first the document
if (currentDocumentIndex == 0) {
target.appendJavaScript("alert('This is the first document!')");
} else {
bModel.setDocumentName(
listOfSourceDocuements.get(currentDocumentIndex - 1).getName());
bModel.setDocument(listOfSourceDocuements.get(currentDocumentIndex - 1));
try {
repository.upgradeCasAndSave(
bModel.getDocument(), Mode.AUTOMATION, bModel.getUser().getUsername());
loadDocumentAction();
setCurationSegmentBeginEnd();
update(target);
} catch (UIMAException e) {
error(ExceptionUtils.getRootCause(e));
} catch (ClassNotFoundException e) {
error(ExceptionUtils.getRootCause(e));
} catch (IOException e) {
error(ExceptionUtils.getRootCause(e));
} catch (BratAnnotationException e) {
target.addChildren(getPage(), FeedbackPanel.class);
error(e.getMessage());
}
finish.setModelObject(bModel);
target.add(finish.setOutputMarkupId(true));
target.add(numberOfPages);
target.add(documentNamePanel);
mergeVisualizer.bratRenderLater(target);
}
}
}.add(new InputBehavior(new KeyType[] {KeyType.Shift, KeyType.Page_up}, EventType.click)));
// Show the next document if exist
add(
new AjaxLink<Void>("showNextDocument") {
private static final long serialVersionUID = 7496156015186497496L;
/**
* Get the current beginning sentence address and add on it the size of the display window
*/
@Override
public void onClick(AjaxRequestTarget target) {
target.addChildren(getPage(), FeedbackPanel.class);
// List of all Source Documents in the project
List<SourceDocument> listOfSourceDocuements =
repository.listSourceDocuments(bModel.getProject());
String username = SecurityContextHolder.getContext().getAuthentication().getName();
User user = userRepository.get(username);
List<SourceDocument> sourceDocumentsinIgnorState = new ArrayList<SourceDocument>();
for (SourceDocument sourceDocument : listOfSourceDocuements) {
if (repository.existsAnnotationDocument(sourceDocument, user)
&& repository
.getAnnotationDocument(sourceDocument, user)
.getState()
.equals(AnnotationDocumentState.IGNORE)) {
sourceDocumentsinIgnorState.add(sourceDocument);
} else if (sourceDocument.isTrainingDocument()) {
sourceDocumentsinIgnorState.add(sourceDocument);
}
}
listOfSourceDocuements.removeAll(sourceDocumentsinIgnorState);
// Index of the current source document in the list
int currentDocumentIndex = listOfSourceDocuements.indexOf(bModel.getDocument());
// If the first document
if (currentDocumentIndex == listOfSourceDocuements.size() - 1) {
target.appendJavaScript("alert('This is the last document!')");
return;
}
bModel.setDocumentName(listOfSourceDocuements.get(currentDocumentIndex + 1).getName());
bModel.setDocument(listOfSourceDocuements.get(currentDocumentIndex + 1));
try {
repository.upgradeCasAndSave(
bModel.getDocument(), Mode.AUTOMATION, bModel.getUser().getUsername());
loadDocumentAction();
setCurationSegmentBeginEnd();
update(target);
} catch (UIMAException e) {
error(ExceptionUtils.getRootCause(e));
} catch (ClassNotFoundException e) {
error(ExceptionUtils.getRootCause(e));
} catch (IOException e) {
error(ExceptionUtils.getRootCause(e));
} catch (BratAnnotationException e) {
target.addChildren(getPage(), FeedbackPanel.class);
error(e.getMessage());
}
finish.setModelObject(bModel);
target.add(finish.setOutputMarkupId(true));
target.add(numberOfPages);
target.add(documentNamePanel);
mergeVisualizer.bratRenderLater(target);
}
}.add(
new InputBehavior(new KeyType[] {KeyType.Shift, KeyType.Page_down}, EventType.click)));
// Show the next page of this document
add(
new AjaxLink<Void>("showNext") {
private static final long serialVersionUID = 7496156015186497496L;
/**
* Get the current beginning sentence address and add on it the size of the display window
*/
@Override
public void onClick(AjaxRequestTarget aTarget) {
if (bModel.getDocument() != null) {
JCas mergeJCas = null;
try {
aTarget.addChildren(getPage(), FeedbackPanel.class);
mergeJCas = repository.readCorrectionCas(bModel.getDocument());
int address =
getAddr(
selectSentenceAt(
mergeJCas,
bModel.getSentenceBeginOffset(),
bModel.getSentenceEndOffset()));
int nextSentenceAddress =
getNextPageFirstSentenceAddress(
mergeJCas, address, bModel.getPreferences().getWindowSize());
if (address != nextSentenceAddress) {
ubdateSentenceNumber(mergeJCas, nextSentenceAddress);
SuggestionBuilder builder =
new SuggestionBuilder(repository, annotationService, userRepository);
curationContainer = builder.buildCurationContainer(bModel);
setCurationSegmentBeginEnd();
curationContainer.setBratAnnotatorModel(bModel);
update(aTarget);
mergeVisualizer.bratRenderLater(aTarget);
} else {
aTarget.appendJavaScript("alert('This is last page!')");
}
} catch (UIMAException e) {
error(ExceptionUtils.getRootCause(e));
} catch (ClassNotFoundException e) {
error(e.getMessage());
} catch (IOException e) {
error(e.getMessage());
} catch (BratAnnotationException e) {
error(e.getMessage());
}
} else {
aTarget.appendJavaScript("alert('Please open a document first!')");
}
}
}.add(new InputBehavior(new KeyType[] {KeyType.Page_down}, EventType.click)));
// SHow the previous page of this document
add(
new AjaxLink<Void>("showPrevious") {
private static final long serialVersionUID = 7496156015186497496L;
@Override
public void onClick(AjaxRequestTarget aTarget) {
if (bModel.getDocument() != null) {
JCas mergeJCas = null;
try {
aTarget.addChildren(getPage(), FeedbackPanel.class);
mergeJCas = repository.readCorrectionCas(bModel.getDocument());
int previousSentenceAddress =
BratAjaxCasUtil.getPreviousDisplayWindowSentenceBeginAddress(
mergeJCas,
bModel.getSentenceAddress(),
bModel.getPreferences().getWindowSize());
if (bModel.getSentenceAddress() != previousSentenceAddress) {
ubdateSentenceNumber(mergeJCas, previousSentenceAddress);
SuggestionBuilder builder =
new SuggestionBuilder(repository, annotationService, userRepository);
curationContainer = builder.buildCurationContainer(bModel);
setCurationSegmentBeginEnd();
curationContainer.setBratAnnotatorModel(bModel);
update(aTarget);
mergeVisualizer.bratRenderLater(aTarget);
} else {
aTarget.appendJavaScript("alert('This is First Page!')");
}
} catch (UIMAException e) {
error(ExceptionUtils.getRootCause(e));
} catch (ClassNotFoundException e) {
error(e.getMessage());
} catch (IOException e) {;
error(e.getMessage());
} catch (BratAnnotationException e) {
error(e.getMessage());
}
} else {
aTarget.appendJavaScript("alert('Please open a document first!')");
}
}
}.add(new InputBehavior(new KeyType[] {KeyType.Page_up}, EventType.click)));
add(
new AjaxLink<Void>("showFirst") {
private static final long serialVersionUID = 7496156015186497496L;
@Override
public void onClick(AjaxRequestTarget aTarget) {
if (bModel.getDocument() != null) {
JCas mergeJCas = null;
try {
aTarget.addChildren(getPage(), FeedbackPanel.class);
mergeJCas = repository.readCorrectionCas(bModel.getDocument());
int address =
getAddr(
selectSentenceAt(
mergeJCas,
bModel.getSentenceBeginOffset(),
bModel.getSentenceEndOffset()));
int firstAddress = getFirstSentenceAddress(mergeJCas);
if (firstAddress != address) {
ubdateSentenceNumber(mergeJCas, firstAddress);
SuggestionBuilder builder =
new SuggestionBuilder(repository, annotationService, userRepository);
curationContainer = builder.buildCurationContainer(bModel);
setCurationSegmentBeginEnd();
curationContainer.setBratAnnotatorModel(bModel);
update(aTarget);
mergeVisualizer.bratRenderLater(aTarget);
} else {
aTarget.appendJavaScript("alert('This is first page!')");
}
} catch (UIMAException e) {
error(ExceptionUtils.getRootCause(e));
} catch (ClassNotFoundException e) {
error(e.getMessage());
} catch (IOException e) {
error(e.getMessage());
} catch (BratAnnotationException e) {
error(e.getMessage());
}
} else {
aTarget.appendJavaScript("alert('Please open a document first!')");
}
}
}.add(new InputBehavior(new KeyType[] {KeyType.Home}, EventType.click)));
add(
new AjaxLink<Void>("showLast") {
private static final long serialVersionUID = 7496156015186497496L;
@Override
public void onClick(AjaxRequestTarget aTarget) {
if (bModel.getDocument() != null) {
JCas mergeJCas = null;
try {
aTarget.addChildren(getPage(), FeedbackPanel.class);
mergeJCas = repository.readCorrectionCas(bModel.getDocument());
int lastDisplayWindowBeginingSentenceAddress =
BratAjaxCasUtil.getLastDisplayWindowFirstSentenceAddress(
mergeJCas, bModel.getPreferences().getWindowSize());
if (lastDisplayWindowBeginingSentenceAddress != bModel.getSentenceAddress()) {
ubdateSentenceNumber(mergeJCas, lastDisplayWindowBeginingSentenceAddress);
SuggestionBuilder builder =
new SuggestionBuilder(repository, annotationService, userRepository);
curationContainer = builder.buildCurationContainer(bModel);
setCurationSegmentBeginEnd();
curationContainer.setBratAnnotatorModel(bModel);
update(aTarget);
mergeVisualizer.bratRenderLater(aTarget);
} else {
aTarget.appendJavaScript("alert('This is last Page!')");
}
} catch (UIMAException e) {
error(ExceptionUtils.getRootCause(e));
} catch (ClassNotFoundException e) {
error(e.getMessage());
} catch (IOException e) {
error(e.getMessage());
} catch (BratAnnotationException e) {
error(e.getMessage());
}
} else {
aTarget.appendJavaScript("alert('Please open a document first!')");
}
}
}.add(new InputBehavior(new KeyType[] {KeyType.End}, EventType.click)));
add(new GuidelineModalPanel("guidelineModalPanel", new Model<BratAnnotatorModel>(bModel)));
}
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()
+ "]");
}
public CurationContainer buildCurationContainer(BratAnnotatorModel aBModel)
throws UIMAException, ClassNotFoundException, IOException, BratAnnotationException {
CurationContainer curationContainer = new CurationContainer();
// initialize Variables
SourceDocument sourceDocument = aBModel.getDocument();
Map<Integer, Integer> segmentBeginEnd = new HashMap<Integer, Integer>();
Map<Integer, Integer> segmentNumber = new HashMap<Integer, Integer>();
Map<String, Map<Integer, Integer>> segmentAdress = new HashMap<String, Map<Integer, Integer>>();
// get annotation documents
List<AnnotationDocument> finishedAnnotationDocuments = new ArrayList<AnnotationDocument>();
for (AnnotationDocument annotationDocument :
repository.listAnnotationDocuments(aBModel.getDocument())) {
if (annotationDocument.getState().equals(AnnotationDocumentState.FINISHED)) {
finishedAnnotationDocuments.add(annotationDocument);
}
}
Map<String, JCas> jCases = new HashMap<String, JCas>();
AnnotationDocument randomAnnotationDocument = null;
JCas mergeJCas;
// get the correction/automation JCas for the logged in user
if (aBModel.getMode().equals(Mode.AUTOMATION) || aBModel.getMode().equals(Mode.CORRECTION)) {
jCases = listJcasesforCorrection(randomAnnotationDocument, sourceDocument, aBModel.getMode());
mergeJCas = getMergeCas(aBModel, sourceDocument, jCases, randomAnnotationDocument);
String username = jCases.keySet().iterator().next();
updateSegment(
aBModel,
segmentBeginEnd,
segmentNumber,
segmentAdress,
jCases.get(username),
username,
aBModel.getPreferences().getWindowSize());
} else {
jCases =
listJcasesforCuration(
finishedAnnotationDocuments, randomAnnotationDocument, aBModel.getMode());
mergeJCas = getMergeCas(aBModel, sourceDocument, jCases, randomAnnotationDocument);
updateSegment(
aBModel,
segmentBeginEnd,
segmentNumber,
segmentAdress,
mergeJCas,
CurationPanel.CURATION_USER,
aBModel.getPreferences().getCurationWindowSize());
}
List<Type> entryTypes = null;
segmentAdress.put(CurationPanel.CURATION_USER, new HashMap<Integer, Integer>());
for (Sentence sentence : selectCovered(mergeJCas, Sentence.class, begin, end)) {
segmentAdress.get(CurationPanel.CURATION_USER).put(sentence.getBegin(), getAddr(sentence));
}
if (entryTypes == null) {
entryTypes = getEntryTypes(mergeJCas, aBModel.getAnnotationLayers(), annotationService);
}
// for cross-sentences annotation, update the end of the segment
if (firstload) {
updateCrossSentAnnoList(segmentBeginEnd, jCases, entryTypes);
firstload = false;
}
for (Integer begin : segmentBeginEnd.keySet()) {
Integer end = segmentBeginEnd.get(begin);
DiffResult diff =
CasDiff2.doDiffSingle(
annotationService, aBModel.getProject(), entryTypes, jCases, begin, end);
SourceListView curationSegment = new SourceListView();
curationSegment.setBegin(begin);
curationSegment.setEnd(end);
if (diff.hasDifferences() || !diff.getIncompleteConfigurationSets().isEmpty()) {
curationSegment.setSentenceState(SentenceState.DISAGREE);
} else {
curationSegment.setSentenceState(SentenceState.AGREE);
}
curationSegment.setSentenceNumber(segmentNumber.get(begin));
for (String username : segmentAdress.keySet()) {
curationSegment.getSentenceAddress().put(username, segmentAdress.get(username).get(begin));
}
curationContainer.getCurationViewByBegin().put(begin, curationSegment);
}
return curationContainer;
}
/**
* 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;
}
}
}
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);
}