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 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 Map<String, JCas> listJcasesforCuration(
List<AnnotationDocument> annotationDocuments,
AnnotationDocument randomAnnotationDocument,
Mode aMode)
throws UIMAException, ClassNotFoundException, IOException {
Map<String, JCas> jCases = new HashMap<String, JCas>();
for (AnnotationDocument annotationDocument : annotationDocuments) {
String username = annotationDocument.getUser();
if (!annotationDocument.getState().equals(AnnotationDocumentState.FINISHED)) {
continue;
}
if (randomAnnotationDocument == null) {
randomAnnotationDocument = annotationDocument;
}
// 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(annotationDocument.getDocument(), aMode, username);
JCas jCas = repository.readAnnotationCas(annotationDocument);
jCases.put(username, jCas);
}
return jCases;
}
public Map<String, JCas> listJcasesforCorrection(
AnnotationDocument randomAnnotationDocument, SourceDocument aDocument, Mode aMode)
throws UIMAException, ClassNotFoundException, IOException {
Map<String, JCas> jCases = new HashMap<String, JCas>();
User user =
userRepository.get(SecurityContextHolder.getContext().getAuthentication().getName());
randomAnnotationDocument = repository.getAnnotationDocument(aDocument, user);
// 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, aMode, user.getUsername());
JCas jCas = repository.readAnnotationCas(randomAnnotationDocument);
jCases.put(user.getUsername(), jCas);
return jCases;
}
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);
}
/**
* 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;
}
/**
* 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);
}
}
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 a curation page is opened, create a MergeCas that contains only agreeing
* annotations Using the CAS of the curator user.
*
* @param aProject the project
* @param randomAnnotationDocument an annotation document.
* @param jCases the JCases
* @param aAnnotationLayers the layers.
* @return the JCas.
* @throws IOException if an I/O error occurs.
*/
public JCas createCurationCas(
Project aProject,
AnnotationDocument randomAnnotationDocument,
Map<String, JCas> jCases,
List<AnnotationLayer> aAnnotationLayers)
throws IOException {
User userLoggedIn =
userRepository.get(SecurityContextHolder.getContext().getAuthentication().getName());
JCas mergeJCas = repository.readAnnotationCas(randomAnnotationDocument);
jCases.put(CurationPanel.CURATION_USER, mergeJCas);
List<Type> entryTypes = getEntryTypes(mergeJCas, aAnnotationLayers, annotationService);
DiffResult diff =
CasDiff2.doDiffSingle(
annotationService,
aProject,
entryTypes,
jCases,
0,
mergeJCas.getDocumentText().length());
for (Entry<Position, ConfigurationSet> diffEntry :
diff.getDifferingConfigurationSets().entrySet()) {
// Remove FSes with differences from the merge CAS
List<Configuration> cfgsForCurationUser =
diffEntry.getValue().getConfigurations(CurationPanel.CURATION_USER);
for (Configuration cfg : cfgsForCurationUser) {
FeatureStructure fs = cfg.getFs(CurationPanel.CURATION_USER, jCases);
mergeJCas.removeFsFromIndexes(fs);
}
}
repository.writeCurationCas(mergeJCas, randomAnnotationDocument.getDocument(), userLoggedIn);
return mergeJCas;
}
private void addJCas(List<JCas> jCases, User user, SourceDocument sourceDocument) {
try {
// Check if there is an annotation document entry in the database. If there is none,
// create one.
AnnotationDocument annotationDocument =
repository.createOrGetAnnotationDocument(sourceDocument, user);
// Read the CAS
JCas jcas = repository.readAnnotationCas(annotationDocument);
// Update the annotation document CAS
repository.upgradeCas(jcas.getCas(), annotationDocument);
// After creating an new CAS or upgrading the CAS, we need to save it
repository.writeAnnotationCas(
jcas.getCas().getJCas(), annotationDocument.getDocument(), user);
jCases.add(jcas);
} catch (UIMAException e) {
error(e.getMessage() + " : " + ExceptionUtils.getRootCauseMessage(e));
} catch (IOException e) {
error(e.getMessage());
}
}
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());
}
@Override
protected String getDocumentData() {
if (!dirty) {
return docData;
}
dirty = false;
// Clear the rendered document
docData = EMPTY_DOC;
// Check if a document is set
if (getModelObject() == null) {
return docData;
}
// Get CAS from the repository
JCas jCas = null;
try {
jCas = repository.readAnnotationCas(getModelObject());
} catch (IOException | DataRetrievalFailureException e) {
LOG.error("Unable to read annotation document", e);
error("Unable to read annotation document: " + ExceptionUtils.getRootCauseMessage(e));
}
// Generate BRAT object model from CAS
GetDocumentResponse response = new GetDocumentResponse();
response.setText(jCas.getDocumentText());
BratAnnotatorModel bratAnnotatorModel = new BratAnnotatorModel();
SpanAdapter.renderTokenAndSentence(jCas, response, bratAnnotatorModel);
Map<String[], Queue<String>> colorQueues = new HashMap<>();
for (AnnotationLayer layer : bratAnnotatorModel.getAnnotationLayers()) {
if (layer.getName().equals(Token.class.getName())) {
continue;
}
List<AnnotationFeature> features = annotationService.listAnnotationFeature(layer);
List<AnnotationFeature> invisibleFeatures = new ArrayList<AnnotationFeature>();
for (AnnotationFeature feature : features) {
if (!feature.isVisible()) {
invisibleFeatures.add(feature);
}
}
features.removeAll(invisibleFeatures);
ColoringStrategy coloringStrategy =
ColoringStrategy.getBestStrategy(
annotationService, layer, bratAnnotatorModel.getPreferences(), colorQueues);
getAdapter(annotationService, layer)
.render(jCas, features, response, bratAnnotatorModel, coloringStrategy);
}
// Serialize BRAT object model to JSON
try {
StringWriter out = new StringWriter();
JsonGenerator jsonGenerator =
JSONUtil.getJsonConverter().getObjectMapper().getFactory().createGenerator(out);
jsonGenerator.writeObject(response);
docData = out.toString();
} catch (IOException e) {
error(ExceptionUtils.getRootCauseMessage(e));
}
return docData;
}
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;
}