Examples with AnnotationException de.tudarmstadt.ukp.clarin.webanno.api.annotation.exception.AnnotationException used on opensource projects

Example 6 with AnnotationException

use of de.tudarmstadt.ukp.clarin.webanno.api.annotation.exception.AnnotationException in project webanno by webanno.

the class AnnotationDetailEditorPanel method actionCreateOrUpdate.

@Override
public void actionCreateOrUpdate(AjaxRequestTarget aTarget, JCas aJCas) throws IOException, AnnotationException {
    LOG.trace("actionAnnotate");
    if (isAnnotationFinished()) {
        throw new AnnotationException("This document is already closed. Please ask your " + "project manager to re-open it via the Monitoring page");
    }
    AnnotatorState state = getModelObject();
    // switches from the selected span layer to the relation layer that is attached to the span
    if (state.getSelection().isArc()) {
        LOG.trace("actionAnnotate() relation annotation - looking for attached layer");
        // FIXME REC I think this whole section which meddles around with the selected
        // annotation layer should be moved out of there to the place where we originally set
        // the annotation layer...!
        AnnotationFS originFS = selectByAddr(aJCas, state.getSelection().getOrigin());
        AnnotationLayer spanLayer = annotationService.getLayer(state.getProject(), originFS);
        if (state.getPreferences().isRememberLayer() && // i.e. new annotation
        state.getSelection().getAnnotation().isNotSet() && !spanLayer.equals(state.getDefaultAnnotationLayer())) {
            throw new AnnotationException("No relation annotation allowed on layer [" + state.getDefaultAnnotationLayer().getUiName() + "]");
        }
        AnnotationLayer previousLayer = state.getSelectedAnnotationLayer();
        // Chain layers consist of arcs and spans
        if (spanLayer.getType().equals(WebAnnoConst.CHAIN_TYPE)) {
            // one layer both for the span and arc annotation
            state.setSelectedAnnotationLayer(spanLayer);
        } else // Otherwise, look up the possible relation layer(s) in the database.
        {
            for (AnnotationLayer l : annotationService.listAnnotationLayer(state.getProject())) {
                if ((l.getAttachType() != null && l.getAttachType().equals(spanLayer)) || (l.getAttachFeature() != null && l.getAttachFeature().getType().equals(spanLayer.getName()))) {
                    if (state.getAnnotationLayers().contains(l)) {
                        state.setSelectedAnnotationLayer(l);
                    } else {
                        state.setSelectedAnnotationLayer(null);
                    }
                    break;
                }
            }
        }
        state.setDefaultAnnotationLayer(spanLayer);
        // If we switched layers, we need to initialize the feature editors for the new layer
        if (!Objects.equals(previousLayer, state.getSelectedAnnotationLayer())) {
            LOG.trace("Layer changed from {} to {} - need to reload feature editors", previousLayer, state.getSelectedAnnotationLayer());
            loadFeatureEditorModels(aJCas, aTarget);
        }
    } else {
        // Re-set the selected layer from the drop-down since it might have changed if we
        // have previously created a relation annotation
        state.setSelectedAnnotationLayer(annotationFeatureForm.getLayerSelector().getModelObject());
    }
    internalCommitAnnotation(aTarget, aJCas);
    internalCompleteAnnotation(aTarget, aJCas);
}

Example 7 with AnnotationException

use of de.tudarmstadt.ukp.clarin.webanno.api.annotation.exception.AnnotationException in project webanno by webanno.

the class MergeCas method addRelationArcAnnotation.

static void addRelationArcAnnotation(JCas aJcas, AnnotationFS aClickedFS, boolean aIsAttachType, boolean aIsAllowStacking, AnnotationFS originFsClicked, AnnotationFS targetFsClicked) throws AnnotationException {
    List<AnnotationFS> merges = MergeCas.getMergeFS(aClickedFS, aJcas).collect(Collectors.toList());
    List<AnnotationFS> origins = MergeCas.getMergeFS(originFsClicked, aJcas).collect(Collectors.toList());
    List<AnnotationFS> targets = MergeCas.getMergeFS(targetFsClicked, aJcas).collect(Collectors.toList());
    // check if target/source exists in the mergeview
    if (origins.size() == 0 || targets.size() == 0) {
        throw new AnnotationException("Both the source and target annotation" + " should exist on the mergeview. Please first copy/create them");
    }
    AnnotationFS originFs = origins.get(0);
    AnnotationFS targetFs = targets.get(0);
    if (origins.size() > 1) {
        throw new AnnotationException("Stacked sources exist in mergeview. Cannot copy this relation.");
    }
    if (targets.size() > 1) {
        throw new AnnotationException("Stacked targets exist in mergeview. Cannot copy this relation.");
    }
    if (merges.size() > 0) {
        throw new AnnotationException("The annotation already exists on the mergeview. " + "Add this manually to have stacked annotations");
    }
    // TODO: DKPro Core Dependency layer -> It should be done differently
    if (aIsAttachType) {
        Type type = aClickedFS.getType();
        Feature sourceFeature = type.getFeatureByBaseName(WebAnnoConst.FEAT_REL_SOURCE);
        originFsClicked = (AnnotationFS) aClickedFS.getFeatureValue(sourceFeature);
        Feature targetFeature = type.getFeatureByBaseName(WebAnnoConst.FEAT_REL_TARGET);
        targetFsClicked = (AnnotationFS) aClickedFS.getFeatureValue(targetFeature);
        origins = MergeCas.getMergeFS(originFsClicked, aJcas).collect(Collectors.toList());
        targets = MergeCas.getMergeFS(targetFsClicked, aJcas).collect(Collectors.toList());
        originFs = origins.get(0);
        targetFs = targets.get(0);
    }
    List<AnnotationFS> existingAnnos = MergeCas.getRelAnnosOnPosition(aClickedFS, originFs, targetFs, aJcas);
    if (existingAnnos.size() == 0 || aIsAllowStacking) {
        MergeCas.copyRelationAnnotation(aClickedFS, originFs, targetFs, aJcas);
    } else {
        MergeCas.modifyRelationAnnotation(aClickedFS, existingAnnos.get(0), aJcas);
    }
}

Example 8 with AnnotationException

use of de.tudarmstadt.ukp.clarin.webanno.api.annotation.exception.AnnotationException in project webanno by webanno.

the class SuggestionViewPanel method mergeArc.

private void mergeArc(IRequestParameters aRequest, UserAnnotationSegment aCurationUserSegment, JCas aJcas) throws AnnotationException, IOException, UIMAException, ClassNotFoundException {
    int addressOriginClicked = aRequest.getParameterValue(PARAM_ORIGIN_SPAN_ID).toInt();
    int addressTargetClicked = aRequest.getParameterValue(PARAM_TARGET_SPAN_ID).toInt();
    String arcType = removePrefix(aRequest.getParameterValue(PARAM_TYPE).toString());
    String fsArcaddress = aRequest.getParameterValue(PARAM_ARC_ID).toString();
    AnnotatorState bModel = aCurationUserSegment.getAnnotatorState();
    SourceDocument sourceDocument = bModel.getDocument();
    // for correction and automation, the lower panel is the clickedJcase, from the suggestions
    JCas clickedJCas;
    if (!aCurationUserSegment.getAnnotatorState().getMode().equals(Mode.CURATION)) {
        clickedJCas = correctionDocumentService.readCorrectionCas(sourceDocument);
    } else {
        User user = userRepository.get(aCurationUserSegment.getUsername());
        AnnotationDocument clickedAnnotationDocument = documentService.getAnnotationDocument(sourceDocument, user);
        clickedJCas = getJCas(bModel, clickedAnnotationDocument);
    }
    long layerId = TypeUtil.getLayerId(arcType);
    AnnotationLayer layer = annotationService.getLayer(layerId);
    TypeAdapter adapter = annotationService.getAdapter(layer);
    int address = Integer.parseInt(fsArcaddress.split("\\.")[0]);
    AnnotationFS clickedFS = selectByAddr(clickedJCas, address);
    if (isCorefType(clickedFS)) {
        throw new AnnotationException(" Coreference Annotation not supported in curation");
    }
    MergeCas.addArcAnnotation(adapter, aJcas, addressOriginClicked, addressTargetClicked, fsArcaddress, clickedJCas, clickedFS);
    writeEditorCas(bModel, aJcas);
    int sentenceNumber = getSentenceNumber(clickedJCas, clickedFS.getBegin());
    bModel.setFocusUnitIndex(sentenceNumber);
    // Update timestamp
    bModel.getDocument().setSentenceAccessed(sentenceNumber);
    if (bModel.getPreferences().isScrollPage()) {
        Sentence sentence = selectSentenceAt(aJcas, bModel.getFirstVisibleUnitBegin(), bModel.getFirstVisibleUnitEnd());
        sentence = findWindowStartCenteringOnSelection(aJcas, sentence, clickedFS.getBegin(), bModel.getProject(), bModel.getDocument(), bModel.getPreferences().getWindowSize());
        bModel.setFirstVisibleUnit(sentence);
    }
}

Example 9 with AnnotationException

use of de.tudarmstadt.ukp.clarin.webanno.api.annotation.exception.AnnotationException in project webanno by webanno.

the class SuggestionViewPanel method createSpan.

private void createSpan(String spanType, AnnotatorState aBModel, JCas aMergeJCas, AnnotationDocument aAnnotationDocument, int aAddress) throws IOException, UIMAException, ClassNotFoundException, AnnotationException {
    JCas clickedJCas = getJCas(aBModel, aAnnotationDocument);
    AnnotationFS fsClicked = selectByAddr(clickedJCas, aAddress);
    if (isCorefType(fsClicked)) {
        throw new AnnotationException("Coreference Annotation not supported in curation");
    }
    long layerId = TypeUtil.getLayerId(spanType);
    AnnotationLayer layer = annotationService.getLayer(layerId);
    MergeCas.addSpanAnnotation(aBModel, annotationService, layer, aMergeJCas, fsClicked, layer.isAllowStacking());
    writeEditorCas(aBModel, aMergeJCas);
    // update timestamp
    int sentenceNumber = getSentenceNumber(clickedJCas, fsClicked.getBegin());
    aBModel.setFocusUnitIndex(sentenceNumber);
    aBModel.getDocument().setSentenceAccessed(sentenceNumber);
    if (aBModel.getPreferences().isScrollPage()) {
        Sentence sentence = selectSentenceAt(aMergeJCas, aBModel.getFirstVisibleUnitBegin(), aBModel.getFirstVisibleUnitEnd());
        sentence = findWindowStartCenteringOnSelection(aMergeJCas, sentence, fsClicked.getBegin(), aBModel.getProject(), aBModel.getDocument(), aBModel.getPreferences().getWindowSize());
        aBModel.setFirstVisibleUnit(sentence);
    }
}

Example 10 with AnnotationException

use of de.tudarmstadt.ukp.clarin.webanno.api.annotation.exception.AnnotationException in project webanno by webanno.

the class SuggestionBuilder method getMergeCas.

/**
 * 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 AnnotationException
 *             hum?
 */
public JCas getMergeCas(AnnotatorState aBratAnnotatorModel, SourceDocument aDocument, Map<String, JCas> jCases, AnnotationDocument randomAnnotationDocument, boolean aUpgrade) throws UIMAException, ClassNotFoundException, IOException, AnnotationException {
    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 = correctionDocumentService.readCorrectionCas(aDocument);
            if (aUpgrade) {
                correctionDocumentService.upgradeCorrectionCas(mergeJCas.getCas(), aDocument);
                correctionDocumentService.writeCorrectionCas(mergeJCas, 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 = curationDocumentService.readCurationCas(aDocument);
            if (aUpgrade) {
                curationDocumentService.upgradeCurationCas(mergeJCas.getCas(), aDocument);
                curationDocumentService.writeCurationCas(mergeJCas, aDocument, true);
            }
        }
    }// 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;
}