Examples with AnnotationLayer de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer used on opensource projects

Example 56 with AnnotationLayer

use of de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer in project webanno by webanno.

the class LinksReachableThroughChainsCheck method check.

@Override
public boolean check(Project aProject, CAS aCas, List<LogMessage> aMessages) {
    boolean ok = true;
    for (AnnotationLayer layer : annotationService.listAnnotationLayer(aProject)) {
        if (!WebAnnoConst.CHAIN_TYPE.equals(layer.getType())) {
            continue;
        }
        Type chainType;
        Type linkType;
        try {
            chainType = getType(aCas, layer.getName() + "Chain");
            linkType = getType(aCas, layer.getName() + "Link");
        } catch (IllegalArgumentException e) {
            // check
            continue;
        }
        List<FeatureStructure> chains = new ArrayList<>(selectFS(aCas, chainType));
        List<AnnotationFS> links = new ArrayList<>(select(aCas, linkType));
        for (FeatureStructure chain : chains) {
            AnnotationFS link = FSUtil.getFeature(chain, "first", AnnotationFS.class);
            while (link != null) {
                links.remove(link);
                link = FSUtil.getFeature(link, "next", AnnotationFS.class);
            }
        }
        if (!links.isEmpty()) {
            ok = false;
            aMessages.add(new LogMessage(this, LogLevel.ERROR, "CoreferenceLinks not reachable through chains: %d", links.size()));
            for (AnnotationFS link : links) {
                aMessages.add(new LogMessage(this, LogLevel.ERROR, "Unreachable CoreferenceLink [%s]", link));
            }
        }
    }
    return ok;
}

Example 57 with AnnotationLayer

use of de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer in project webanno by webanno.

the class RelationOffsetsCheck method check.

@Override
public boolean check(Project aProject, CAS aCas, List<LogMessage> aMessages) {
    boolean ok = true;
    for (AnnotationLayer layer : annotationService.listAnnotationLayer(aProject)) {
        if (!WebAnnoConst.RELATION_TYPE.equals(layer.getType())) {
            continue;
        }
        Type type;
        try {
            type = getType(aCas, layer.getName());
        } catch (IllegalArgumentException e) {
            // can skip checking the layer because there will be no annotations anyway.
            continue;
        }
        for (AnnotationFS rel : select(aCas, type)) {
            AnnotationFS target = getFeature(rel, WebAnnoConst.FEAT_REL_TARGET, AnnotationFS.class);
            if ((rel.getBegin() != target.getBegin()) || (rel.getEnd() != target.getEnd())) {
                aMessages.add(new LogMessage(this, LogLevel.ERROR, "Relation offsets [%d,%d] to not match target offsets [%d,%d]", rel.getBegin(), rel.getEnd(), target.getBegin(), target.getEnd()));
                ok = false;
            }
        }
    }
    return ok;
}

Example 58 with AnnotationLayer

use of de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer in project webanno by webanno.

the class BratRenderer method render.

/**
 * wrap JSON responses to BRAT visualizer
 *
 * @param aResponse
 *            the response.
 * @param aState
 *            the annotator model.
 * @param aJCas
 *            the JCas.
 * @param aAnnotationService
 *            the annotation service.s
 */
public static void render(GetDocumentResponse aResponse, AnnotatorState aState, VDocument aVDoc, JCas aJCas, AnnotationSchemaService aAnnotationService, ColoringStrategy aColoringStrategy) {
    aResponse.setRtlMode(ScriptDirection.RTL.equals(aState.getScriptDirection()));
    aResponse.setFontZoom(aState.getPreferences().getFontZoom());
    // Render invisible baseline annotations (sentence, tokens)
    renderTokenAndSentence(aJCas, aResponse, aState);
    // Render visible (custom) layers
    Map<String[], Queue<String>> colorQueues = new HashMap<>();
    for (AnnotationLayer layer : aVDoc.getAnnotationLayers()) {
        ColoringStrategy coloringStrategy = aColoringStrategy != null ? aColoringStrategy : ColoringStrategy.getStrategy(aAnnotationService, layer, aState.getPreferences(), colorQueues);
        TypeAdapter typeAdapter = aAnnotationService.getAdapter(layer);
        for (VSpan vspan : aVDoc.spans(layer.getId())) {
            List<Offsets> offsets = toOffsets(vspan.getRanges());
            String bratLabelText = TypeUtil.getUiLabelText(typeAdapter, vspan.getFeatures());
            String bratHoverText = TypeUtil.getUiHoverText(typeAdapter, vspan.getHoverFeatures());
            String color;
            if (vspan.getColorHint() == null) {
                color = getColor(vspan, coloringStrategy, bratLabelText);
            } else {
                color = vspan.getColorHint();
            }
            aResponse.addEntity(new Entity(vspan.getVid(), vspan.getType(), offsets, bratLabelText, color, bratHoverText));
        }
        for (VArc varc : aVDoc.arcs(layer.getId())) {
            String bratLabelText;
            if (varc.getLabelHint() == null) {
                bratLabelText = TypeUtil.getUiLabelText(typeAdapter, varc.getFeatures());
            } else {
                bratLabelText = varc.getLabelHint();
            }
            String color;
            if (varc.getColorHint() == null) {
                color = getColor(varc, coloringStrategy, bratLabelText);
            } else {
                color = varc.getColorHint();
            }
            aResponse.addRelation(new Relation(varc.getVid(), varc.getType(), getArgument(varc.getSource(), varc.getTarget()), bratLabelText, color));
        }
    }
    List<Sentence> sentences = new ArrayList<>(select(aJCas, Sentence.class));
    for (VComment vcomment : aVDoc.comments()) {
        String type;
        switch(vcomment.getCommentType()) {
            case ERROR:
                type = AnnotationComment.ANNOTATION_ERROR;
                break;
            case INFO:
                type = AnnotationComment.ANNOTATOR_NOTES;
                break;
            case YIELD:
                type = "Yield";
                break;
            default:
                type = AnnotationComment.ANNOTATOR_NOTES;
                break;
        }
        AnnotationFS fs;
        if (!vcomment.getVid().isSynthetic() && ((fs = selectByAddr(aJCas, vcomment.getVid().getId())) instanceof Sentence)) {
            int index = sentences.indexOf(fs) + 1;
            aResponse.addComment(new SentenceComment(index, type, vcomment.getComment()));
        } else {
            aResponse.addComment(new AnnotationComment(vcomment.getVid(), type, vcomment.getComment()));
        }
    }
    // Render markers
    for (VMarker vmarker : aVDoc.getMarkers()) {
        if (vmarker instanceof VAnnotationMarker) {
            VAnnotationMarker marker = (VAnnotationMarker) vmarker;
            aResponse.addMarker(new AnnotationMarker(vmarker.getType(), marker.getVid()));
        } else if (vmarker instanceof VSentenceMarker) {
            VSentenceMarker marker = (VSentenceMarker) vmarker;
            aResponse.addMarker(new SentenceMarker(vmarker.getType(), marker.getIndex()));
        } else if (vmarker instanceof VTextMarker) {
            VTextMarker marker = (VTextMarker) vmarker;
            aResponse.addMarker(new TextMarker(marker.getType(), marker.getBegin(), marker.getEnd()));
        } else {
            LOG.warn("Unknown how to render marker: [" + vmarker + "]");
        }
    }
}

Example 59 with AnnotationLayer

use of de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer in project webanno by webanno.

the class BratRenderer method buildEntityTypes.

/**
 * Generates brat type definitions from the WebAnno layer definitions.
 *
 * @param aAnnotationLayers
 *            the layers
 * @param aAnnotationService
 *            the annotation service
 * @return the brat type definitions
 */
public static Set<EntityType> buildEntityTypes(List<AnnotationLayer> aAnnotationLayers, AnnotationSchemaService aAnnotationService) {
    // Sort layers
    List<AnnotationLayer> layers = new ArrayList<>(aAnnotationLayers);
    layers.sort(Comparator.comparing(AnnotationLayer::getName));
    // Now build the actual configuration
    Set<EntityType> entityTypes = new LinkedHashSet<>();
    for (AnnotationLayer layer : layers) {
        EntityType entityType = configureEntityType(layer);
        List<RelationType> arcs = new ArrayList<>();
        // For link features, we also need to configure the arcs, even though there is no arc
        // layer here.
        boolean hasLinkFeatures = false;
        for (AnnotationFeature f : aAnnotationService.listAnnotationFeature(layer)) {
            if (!LinkMode.NONE.equals(f.getLinkMode())) {
                hasLinkFeatures = true;
                break;
            }
        }
        if (hasLinkFeatures) {
            String bratTypeName = getBratTypeName(layer);
            arcs.add(new RelationType(layer.getName(), layer.getUiName(), bratTypeName, bratTypeName, null, "triangle,5", "3,3"));
        }
        // Styles for the remaining relation and chain layers
        for (AnnotationLayer attachingLayer : getAttachingLayers(layer, layers, aAnnotationService)) {
            arcs.add(configureRelationType(layer, attachingLayer));
        }
        entityType.setArcs(arcs);
        entityTypes.add(entityType);
    }
    return entityTypes;
}

Example 60 with AnnotationLayer

use of de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer in project webanno by webanno.

the class ImportUtil method exportLayerDetails.

public static de.tudarmstadt.ukp.clarin.webanno.export.model.AnnotationLayer exportLayerDetails(Map<AnnotationLayer, de.tudarmstadt.ukp.clarin.webanno.export.model.AnnotationLayer> aLayerToExLayer, Map<AnnotationFeature, de.tudarmstadt.ukp.clarin.webanno.export.model.AnnotationFeature> aFeatureToExFeature, AnnotationLayer aLayer, AnnotationSchemaService aAnnotationService) {
    de.tudarmstadt.ukp.clarin.webanno.export.model.AnnotationLayer exLayer = new de.tudarmstadt.ukp.clarin.webanno.export.model.AnnotationLayer();
    exLayer.setAllowStacking(aLayer.isAllowStacking());
    exLayer.setBuiltIn(aLayer.isBuiltIn());
    exLayer.setReadonly(aLayer.isReadonly());
    exLayer.setCrossSentence(aLayer.isCrossSentence());
    exLayer.setDescription(aLayer.getDescription());
    exLayer.setEnabled(aLayer.isEnabled());
    exLayer.setLockToTokenOffset(aLayer.isLockToTokenOffset());
    exLayer.setMultipleTokens(aLayer.isMultipleTokens());
    exLayer.setLinkedListBehavior(aLayer.isLinkedListBehavior());
    exLayer.setName(aLayer.getName());
    exLayer.setProjectName(aLayer.getProject().getName());
    exLayer.setType(aLayer.getType());
    exLayer.setUiName(aLayer.getUiName());
    if (aLayerToExLayer != null) {
        aLayerToExLayer.put(aLayer, exLayer);
    }
    List<de.tudarmstadt.ukp.clarin.webanno.export.model.AnnotationFeature> exFeatures = new ArrayList<>();
    for (AnnotationFeature feature : aAnnotationService.listAnnotationFeature(aLayer)) {
        de.tudarmstadt.ukp.clarin.webanno.export.model.AnnotationFeature exFeature = new de.tudarmstadt.ukp.clarin.webanno.export.model.AnnotationFeature();
        exFeature.setDescription(feature.getDescription());
        exFeature.setEnabled(feature.isEnabled());
        exFeature.setRemember(feature.isRemember());
        exFeature.setRequired(feature.isRequired());
        exFeature.setHideUnconstraintFeature(feature.isHideUnconstraintFeature());
        exFeature.setName(feature.getName());
        exFeature.setProjectName(feature.getProject().getName());
        exFeature.setType(feature.getType());
        exFeature.setUiName(feature.getUiName());
        exFeature.setVisible(feature.isVisible());
        exFeature.setMultiValueMode(feature.getMultiValueMode());
        exFeature.setLinkMode(feature.getLinkMode());
        exFeature.setLinkTypeName(feature.getLinkTypeName());
        exFeature.setLinkTypeRoleFeatureName(feature.getLinkTypeRoleFeatureName());
        exFeature.setLinkTypeTargetFeatureName(feature.getLinkTypeTargetFeatureName());
        if (feature.getTagset() != null) {
            TagSet tagSet = feature.getTagset();
            ExportedTagSet exTagSet = new ExportedTagSet();
            exTagSet.setDescription(tagSet.getDescription());
            exTagSet.setLanguage(tagSet.getLanguage());
            exTagSet.setName(tagSet.getName());
            exTagSet.setCreateTag(tagSet.isCreateTag());
            List<ExportedTag> exportedTags = new ArrayList<>();
            for (Tag tag : aAnnotationService.listTags(tagSet)) {
                ExportedTag exTag = new ExportedTag();
                exTag.setDescription(tag.getDescription());
                exTag.setName(tag.getName());
                exportedTags.add(exTag);
            }
            exTagSet.setTags(exportedTags);
            exFeature.setTagSet(exTagSet);
        }
        exFeatures.add(exFeature);
        if (aFeatureToExFeature != null) {
            aFeatureToExFeature.put(feature, exFeature);
        }
    }
    exLayer.setFeatures(exFeatures);
    return exLayer;
}