Examples with FeatureStructure org.apache.uima.cas.FeatureStructure used on opensource projects

Example 31 with FeatureStructure

use of org.apache.uima.cas.FeatureStructure in project webanno by webanno.

the class ImportExportServiceImpl method updateCasWithTagSet.

/**
 * A Helper method to add {@link TagsetDescription} to {@link CAS}
 *
 * @param aCas
 *            the CAA.
 * @param aLayer
 *            the layer.
 * @param aTagSetName
 *            the tagset.
 */
private static void updateCasWithTagSet(CAS aCas, String aLayer, String aTagSetName) {
    Type TagsetType = CasUtil.getType(aCas, TagsetDescription.class);
    Feature layerFeature = TagsetType.getFeatureByBaseName("layer");
    Feature nameFeature = TagsetType.getFeatureByBaseName("name");
    boolean tagSetModified = false;
    // modify existing tagset Name
    for (FeatureStructure fs : CasUtil.select(aCas, TagsetType)) {
        String layer = fs.getStringValue(layerFeature);
        String tagSetName = fs.getStringValue(nameFeature);
        if (layer.equals(aLayer)) {
            // only if the tagset name is changed
            if (!aTagSetName.equals(tagSetName)) {
                fs.setStringValue(nameFeature, aTagSetName);
                aCas.addFsToIndexes(fs);
            }
            tagSetModified = true;
            break;
        }
    }
    if (!tagSetModified) {
        FeatureStructure fs = aCas.createFS(TagsetType);
        fs.setStringValue(layerFeature, aLayer);
        fs.setStringValue(nameFeature, aTagSetName);
        aCas.addFsToIndexes(fs);
    }
}

Example 32 with FeatureStructure

use of org.apache.uima.cas.FeatureStructure in project webanno by webanno.

the class ChainRenderer method render.

@Override
public void render(JCas aJcas, List<AnnotationFeature> aFeatures, VDocument aResponse, AnnotatorState aState) {
    List<AnnotationFeature> visibleFeatures = aFeatures.stream().filter(f -> f.isVisible() && f.isEnabled()).collect(Collectors.toList());
    // Find the features for the arc and span labels - it is possible that we do not find a
    // feature for arc/span labels because they may have been disabled.
    AnnotationFeature spanLabelFeature = null;
    AnnotationFeature arcLabelFeature = null;
    for (AnnotationFeature f : visibleFeatures) {
        if (WebAnnoConst.COREFERENCE_TYPE_FEATURE.equals(f.getName())) {
            spanLabelFeature = f;
        }
        if (WebAnnoConst.COREFERENCE_RELATION_FEATURE.equals(f.getName())) {
            arcLabelFeature = f;
        }
    }
    // At this point arc and span feature labels must have been found! If not, the later code
    // will crash.
    ChainAdapter typeAdapter = getTypeAdapter();
    Type chainType = typeAdapter.getAnnotationType(aJcas.getCas());
    Feature chainFirst = chainType.getFeatureByBaseName(typeAdapter.getChainFirstFeatureName());
    int colorIndex = 0;
    // Iterate over the chains
    for (FeatureStructure chainFs : selectFS(aJcas.getCas(), chainType)) {
        AnnotationFS linkFs = (AnnotationFS) chainFs.getFeatureValue(chainFirst);
        AnnotationFS prevLinkFs = null;
        // Iterate over the links of the chain
        while (linkFs != null) {
            Feature linkNext = linkFs.getType().getFeatureByBaseName(typeAdapter.getLinkNextFeatureName());
            AnnotationFS nextLinkFs = (AnnotationFS) linkFs.getFeatureValue(linkNext);
            // Is link after window? If yes, we can skip the rest of the chain
            if (linkFs.getBegin() >= aState.getWindowEndOffset()) {
                // Go to next chain
                break;
            }
            // end within the window
            if (!(linkFs.getBegin() >= aState.getWindowBeginOffset()) && (linkFs.getEnd() <= aState.getWindowEndOffset())) {
                // prevLinkFs remains null until we enter the window
                linkFs = nextLinkFs;
                // Go to next link
                continue;
            }
            String bratTypeName = TypeUtil.getUiTypeName(typeAdapter);
            // Render span
            {
                String bratLabelText = TypeUtil.getUiLabelText(typeAdapter, linkFs, (spanLabelFeature != null) ? asList(spanLabelFeature) : emptyList());
                String bratHoverText = TypeUtil.getUiHoverText(typeAdapter, linkFs, (spanLabelFeature != null) ? asList(spanLabelFeature) : emptyList());
                VRange offsets = new VRange(linkFs.getBegin() - aState.getWindowBeginOffset(), linkFs.getEnd() - aState.getWindowBeginOffset());
                aResponse.add(new VSpan(typeAdapter.getLayer(), linkFs, bratTypeName, offsets, colorIndex, singletonMap("label", bratLabelText), singletonMap("label", bratHoverText)));
            }
            // and last link are within the window ;)
            if (prevLinkFs != null) {
                String bratLabelText = null;
                if (typeAdapter.isLinkedListBehavior() && arcLabelFeature != null) {
                    // Render arc label
                    bratLabelText = TypeUtil.getUiLabelText(typeAdapter, prevLinkFs, asList(arcLabelFeature));
                } else {
                    // Render only chain type
                    bratLabelText = TypeUtil.getUiLabelText(typeAdapter, prevLinkFs, emptyList());
                }
                aResponse.add(new VArc(typeAdapter.getLayer(), new VID(prevLinkFs, 1, VID.NONE, VID.NONE), bratTypeName, prevLinkFs, linkFs, colorIndex, singletonMap("label", bratLabelText)));
            }
            // Render errors if required features are missing
            renderRequiredFeatureErrors(visibleFeatures, linkFs, aResponse);
            // if (BratAjaxCasUtil.isSame(linkFs, nextLinkFs)) {
            // log.error("Loop in CAS detected, aborting rendering of chains");
            // break;
            // }
            prevLinkFs = linkFs;
            linkFs = nextLinkFs;
        }
        // The color index is updated even for chains that have no visible links in the current
        // window because we would like the chain color to be independent of visibility. In
        // particular the color of a chain should not change when switching pages/scrolling.
        colorIndex++;
    }
}

Example 33 with FeatureStructure

use of org.apache.uima.cas.FeatureStructure in project webanno by webanno.

the class RelationRenderer method getRelationLinks.

/**
 * Get relation links to display in relation yield
 */
private Map<Integer, Set<Integer>> getRelationLinks(JCas aJcas, int aWindowBegin, int aWindowEnd, Type type, Feature dependentFeature, Feature governorFeature, Feature arcSpanFeature) {
    ArcAdapter typeAdapter = getTypeAdapter();
    FeatureStructure dependentFs;
    FeatureStructure governorFs;
    Map<Integer, Set<Integer>> relations = new ConcurrentHashMap<>();
    for (AnnotationFS fs : selectCovered(aJcas.getCas(), type, aWindowBegin, aWindowEnd)) {
        if (typeAdapter.getAttachFeatureName() != null) {
            dependentFs = fs.getFeatureValue(dependentFeature).getFeatureValue(arcSpanFeature);
            governorFs = fs.getFeatureValue(governorFeature).getFeatureValue(arcSpanFeature);
        } else {
            dependentFs = fs.getFeatureValue(dependentFeature);
            governorFs = fs.getFeatureValue(governorFeature);
        }
        if (dependentFs == null || governorFs == null) {
            log.warn("Relation [" + typeAdapter.getLayer().getName() + "] with id [" + getAddr(fs) + "] has loose ends - cannot render.");
            continue;
        }
        Set<Integer> links = relations.get(getAddr(governorFs));
        if (links == null) {
            links = new ConcurrentSkipListSet<>();
        }
        links.add(getAddr(dependentFs));
        relations.put(getAddr(governorFs), links);
    }
    // Update other subsequent links
    for (int i = 0; i < relations.keySet().size(); i++) {
        for (Integer fs : relations.keySet()) {
            updateLinks(relations, fs);
        }
    }
    // to start displaying the text from the governor, include it
    for (Integer fs : relations.keySet()) {
        relations.get(fs).add(fs);
    }
    return relations;
}

Example 34 with FeatureStructure

use of org.apache.uima.cas.FeatureStructure in project webanno by webanno.

the class SpanRenderer method render.

@Override
public void render(JCas aJcas, List<AnnotationFeature> aFeatures, VDocument aResponse, AnnotatorState aBratAnnotatorModel) {
    List<AnnotationFeature> visibleFeatures = aFeatures.stream().filter(f -> f.isVisible() && f.isEnabled()).collect(Collectors.toList());
    SpanAdapter typeAdapter = getTypeAdapter();
    Type type = getType(aJcas.getCas(), typeAdapter.getAnnotationTypeName());
    int windowBegin = aBratAnnotatorModel.getWindowBeginOffset();
    int windowEnd = aBratAnnotatorModel.getWindowEndOffset();
    List<Sentence> visibleSentences = selectCovered(aJcas, Sentence.class, windowBegin, windowEnd);
    for (AnnotationFS fs : selectCovered(aJcas.getCas(), type, windowBegin, windowEnd)) {
        String bratTypeName = TypeUtil.getUiTypeName(typeAdapter);
        Map<String, String> features = getFeatures(typeAdapter, fs, visibleFeatures);
        Map<String, String> hoverFeatures = getHoverFeatures(typeAdapter, fs, aFeatures);
        Sentence beginSent = null;
        Sentence endSent = null;
        // the visible window
        for (Sentence sent : visibleSentences) {
            if (beginSent == null) {
                // offset of the current annotation.
                if (sent.getBegin() <= fs.getBegin() && fs.getBegin() <= sent.getEnd()) {
                    beginSent = sent;
                }
                // second sentence.
                if (fs.getBegin() == fs.getEnd()) {
                    endSent = sent;
                }
            }
            if (endSent == null) {
                if (sent.getBegin() <= fs.getEnd() && fs.getEnd() <= sent.getEnd()) {
                    endSent = sent;
                }
            }
            if (beginSent != null && endSent != null) {
                break;
            }
        }
        if (beginSent == null || endSent == null) {
            throw new IllegalStateException("Unable to determine sentences in which the annotation starts/ends: " + fs);
        }
        List<Sentence> sentences = selectCovered(aJcas, Sentence.class, beginSent.getBegin(), endSent.getEnd());
        List<VRange> ranges = new ArrayList<>();
        if (sentences.size() > 1) {
            for (Sentence sentence : sentences) {
                if (sentence.getBegin() <= fs.getBegin() && fs.getBegin() < sentence.getEnd()) {
                    ranges.add(new VRange(fs.getBegin() - windowBegin, sentence.getEnd() - windowBegin));
                } else if (sentence.getBegin() <= fs.getEnd() && fs.getEnd() <= sentence.getEnd()) {
                    ranges.add(new VRange(sentence.getBegin() - windowBegin, fs.getEnd() - windowBegin));
                } else {
                    ranges.add(new VRange(sentence.getBegin() - windowBegin, sentence.getEnd() - windowBegin));
                }
            }
            aResponse.add(new VSpan(typeAdapter.getLayer(), fs, bratTypeName, ranges, features, hoverFeatures));
        } else {
            // FIXME It should be possible to remove this case and the if clause because
            // the case that a FS is inside a single sentence is just a special case
            aResponse.add(new VSpan(typeAdapter.getLayer(), fs, bratTypeName, new VRange(fs.getBegin() - windowBegin, fs.getEnd() - windowBegin), features, hoverFeatures));
        }
        // Render errors if required features are missing
        renderRequiredFeatureErrors(visibleFeatures, fs, aResponse);
        // Render slots
        int fi = 0;
        for (AnnotationFeature feat : typeAdapter.listFeatures()) {
            if (MultiValueMode.ARRAY.equals(feat.getMultiValueMode()) && LinkMode.WITH_ROLE.equals(feat.getLinkMode())) {
                List<LinkWithRoleModel> links = typeAdapter.getFeatureValue(feat, fs);
                for (int li = 0; li < links.size(); li++) {
                    LinkWithRoleModel link = links.get(li);
                    FeatureStructure targetFS = selectByAddr(fs.getCAS(), link.targetAddr);
                    aResponse.add(new VArc(typeAdapter.getLayer(), new VID(fs, fi, li), bratTypeName, fs, targetFS, link.role, features));
                }
            }
            fi++;
        }
    }
}

Example 35 with FeatureStructure

use of org.apache.uima.cas.FeatureStructure in project webanno by webanno.

the class ChainAdapter method newChain.

/**
 * Create a new chain head feature structure. Already adds the chain to the CAS.
 */
private FeatureStructure newChain(JCas aJCas, AnnotationFS aFirstLink) {
    Type chainType = getAnnotationType(aJCas.getCas());
    FeatureStructure newChain = aJCas.getCas().createFS(chainType);
    newChain.setFeatureValue(chainType.getFeatureByBaseName(chainFirstFeatureName), aFirstLink);
    aJCas.addFsToIndexes(newChain);
    return newChain;
}