/**
* 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);
}
}
@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;
}