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