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;
}
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 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());
}
}
/**
* 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;
}
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;
}