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;
}
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;
}
/**
* 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 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()
+ "]");
}