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

Example 56 with Feature

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

the class AutomationUtil method deleteRelationAnnotation.

public static void deleteRelationAnnotation(AnnotatorState aBModel, DocumentService aDocumentService, CorrectionDocumentService aCorrectionDocumentService, AnnotationSchemaService aAnnotationService, AnnotationFS fs, AnnotationFeature aFeature, String aValue) throws UIMAException, ClassNotFoundException, IOException, AnnotationException {
    for (SourceDocument d : aDocumentService.listSourceDocuments(aBModel.getProject())) {
        loadDocument(d, aAnnotationService, aDocumentService, aCorrectionDocumentService, aBModel.getUser());
        JCas jCas = aCorrectionDocumentService.readCorrectionCas(d);
        ArcAdapter adapter = (ArcAdapter) aAnnotationService.getAdapter(aFeature.getLayer());
        String sourceFName = adapter.getSourceFeatureName();
        String targetFName = adapter.getTargetFeatureName();
        Type type = getType(jCas.getCas(), aFeature.getLayer().getName());
        Type spanType = getType(jCas.getCas(), adapter.getAttachTypeName());
        Feature arcSpanFeature = spanType.getFeatureByBaseName(adapter.getAttachFeatureName());
        Feature dependentFeature = type.getFeatureByBaseName(targetFName);
        Feature governorFeature = type.getFeatureByBaseName(sourceFName);
        AnnotationFS dependentFs = null;
        AnnotationFS governorFs = null;
        if (adapter.getAttachFeatureName() != null) {
            dependentFs = (AnnotationFS) fs.getFeatureValue(dependentFeature).getFeatureValue(arcSpanFeature);
            governorFs = (AnnotationFS) fs.getFeatureValue(governorFeature).getFeatureValue(arcSpanFeature);
        } else {
            dependentFs = (AnnotationFS) fs.getFeatureValue(dependentFeature);
            governorFs = (AnnotationFS) fs.getFeatureValue(governorFeature);
        }
        int beginOffset = 0;
        int endOffset = jCas.getDocumentText().length() - 1;
        String depCoveredText = dependentFs.getCoveredText();
        String govCoveredText = governorFs.getCoveredText();
        adapter.delete(aBModel, jCas, aFeature, beginOffset, endOffset, depCoveredText, govCoveredText, aValue);
        aCorrectionDocumentService.writeCorrectionCas(jCas, d);
    }
}

Example 57 with Feature

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

the class MergeCas method getRelAnnosOnPosition.

private static List<AnnotationFS> getRelAnnosOnPosition(AnnotationFS aFs, AnnotationFS aOriginFs, AnnotationFS aTargetFs, JCas aJcas) {
    Type type = aFs.getType();
    Feature sourceFeat = type.getFeatureByBaseName(WebAnnoConst.FEAT_REL_SOURCE);
    Feature targetFeat = type.getFeatureByBaseName(WebAnnoConst.FEAT_REL_TARGET);
    return selectCovered(aJcas.getCas(), type, aFs.getBegin(), aFs.getEnd()).stream().filter(fs -> fs.getFeatureValue(sourceFeat).equals(aOriginFs) && fs.getFeatureValue(targetFeat).equals(aTargetFs)).collect(Collectors.toList());
}

Example 58 with Feature

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

the class MergeCas method modifyRelationAnnotation.

private static void modifyRelationAnnotation(AnnotationFS aOldFs, AnnotationFS aNewFs, JCas aJCas) {
    Feature[] features = getAllFeatures(aOldFs);
    Type type = aOldFs.getType();
    Feature sourceFeat = type.getFeatureByBaseName(WebAnnoConst.FEAT_REL_SOURCE);
    Feature targetFeat = type.getFeatureByBaseName(WebAnnoConst.FEAT_REL_TARGET);
    for (Feature f : features) {
        if (isLinkOrBasicFeatures(aOldFs, f)) {
            continue;
        }
        if (f.equals(sourceFeat)) {
            continue;
        } else if (f.equals(targetFeat)) {
            continue;
        }
        setFeatureValue(aNewFs, f, getFeatureValue(aOldFs, f));
    }
    aJCas.addFsToIndexes(aNewFs);
}

Example 59 with Feature

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

the class MergeCas method reMergeCas.

/**
 * Using {@code DiffResult}, determine the annotations to be deleted from the randomly generated
 * MergeCase. The initial Merge CAs is stored under a name {@code CurationPanel#CURATION_USER}.
 * <p>
 * Any similar annotations stacked in a {@code CasDiff2.Position} will be assumed a difference
 * <p>
 * Any two annotation with different value will be assumed a difference
 * <p>
 * Any non stacked empty/null annotations are assumed agreement
 * <p>
 * Any non stacked annotations with similar values for each of the features are assumed
 * agreement
 * <p>
 * Any two link mode / slotable annotations which agree on the base features are assumed
 * agreement
 *
 * @param aDiff
 *            the {@code CasDiff2.DiffResult}
 * @param aJCases
 *            a map of{@code JCas}s for each users and the random merge
 * @return the actual merge {@code JCas}
 */
public static JCas reMergeCas(DiffResult aDiff, Map<String, JCas> aJCases) {
    Set<FeatureStructure> slotFeaturesToReset = new HashSet<>();
    Set<FeatureStructure> annotationsToDelete = new HashSet<>();
    Set<String> users = aJCases.keySet();
    for (Position position : aDiff.getPositions()) {
        Map<String, List<FeatureStructure>> annosPerUser = new HashMap<>();
        ConfigurationSet cfgs = aDiff.getConfigurtionSet(position);
        if (cfgs.getConfigurations(WebAnnoConst.CURATION_USER).isEmpty()) {
            // annotations
            continue;
        }
        AnnotationFS mergeAnno = (AnnotationFS) cfgs.getConfigurations(WebAnnoConst.CURATION_USER).get(0).getFs(WebAnnoConst.CURATION_USER, aJCases);
        // Get Annotations per user in this position
        getAllAnnosOnPosition(aJCases, annosPerUser, users, mergeAnno);
        for (FeatureStructure mergeFs : annosPerUser.get(WebAnnoConst.CURATION_USER)) {
            // incomplete annotations
            if (aJCases.size() != annosPerUser.size()) {
                annotationsToDelete.add(mergeFs);
            } else // agreed and not stacked
            if (isAgree(mergeFs, annosPerUser)) {
                Type t = mergeFs.getType();
                Feature sourceFeat = t.getFeatureByBaseName(WebAnnoConst.FEAT_REL_SOURCE);
                Feature targetFeat = t.getFeatureByBaseName(WebAnnoConst.FEAT_REL_TARGET);
                // Is this a relation?
                if (sourceFeat != null && targetFeat != null) {
                    AnnotationFS source = (AnnotationFS) mergeFs.getFeatureValue(sourceFeat);
                    AnnotationFS target = (AnnotationFS) mergeFs.getFeatureValue(targetFeat);
                    // all span anno on this source positions
                    Map<String, List<FeatureStructure>> sourceAnnosPerUser = new HashMap<>();
                    // all span anno on this target positions
                    Map<String, List<FeatureStructure>> targetAnnosPerUser = new HashMap<>();
                    getAllAnnosOnPosition(aJCases, sourceAnnosPerUser, users, source);
                    getAllAnnosOnPosition(aJCases, targetAnnosPerUser, users, target);
                    if (isAgree(source, sourceAnnosPerUser) && isAgree(target, targetAnnosPerUser)) {
                        slotFeaturesToReset.add(mergeFs);
                    } else {
                        annotationsToDelete.add(mergeFs);
                    }
                } else {
                    slotFeaturesToReset.add(mergeFs);
                }
            } else // disagree or stacked annotations
            {
                annotationsToDelete.add(mergeFs);
            }
        // remove dangling rels
        // setDanglingRelToDel(aJCases.get(CurationPanel.CURATION_USER),
        // mergeFs, annotationsToDelete);
        }
    }
    // remove annotations that do not agree or are a stacked ones
    for (FeatureStructure fs : annotationsToDelete) {
        if (!slotFeaturesToReset.contains(fs)) {
            JCas mergeCas = aJCases.get(WebAnnoConst.CURATION_USER);
            // Check if this difference is on POS, STEM and LEMMA (so remove from the token too)
            Type type = fs.getType();
            int fsBegin = ((AnnotationFS) fs).getBegin();
            int fsEnd = ((AnnotationFS) fs).getEnd();
            if (type.getName().equals(POS.class.getName())) {
                Token t = JCasUtil.selectCovered(mergeCas, Token.class, fsBegin, fsEnd).get(0);
                t.setPos(null);
            }
            if (type.getName().equals(Stem.class.getName())) {
                Token t = JCasUtil.selectCovered(mergeCas, Token.class, fsBegin, fsEnd).get(0);
                t.setStem(null);
            }
            if (type.getName().equals(Lemma.class.getName())) {
                Token t = JCasUtil.selectCovered(mergeCas, Token.class, fsBegin, fsEnd).get(0);
                t.setLemma(null);
            }
            if (type.getName().equals(MorphologicalFeatures.class.getName())) {
                Token t = JCasUtil.selectCovered(mergeCas, Token.class, fsBegin, fsEnd).get(0);
                t.setMorph(null);
            }
            mergeCas.removeFsFromIndexes(fs);
        }
    }
    // if slot bearing annotation, clean
    for (FeatureStructure baseFs : slotFeaturesToReset) {
        for (Feature roleFeature : baseFs.getType().getFeatures()) {
            if (isLinkMode(baseFs, roleFeature)) {
                // FeatureStructure roleFs = baseFs.getFeatureValue(f);
                ArrayFS roleFss = (ArrayFS) WebAnnoCasUtil.getFeatureFS(baseFs, roleFeature.getShortName());
                if (roleFss == null) {
                    continue;
                }
                Map<String, ArrayFS> roleAnnosPerUser = new HashMap<>();
                setAllRoleAnnosOnPosition(aJCases, roleAnnosPerUser, users, baseFs, roleFeature);
                List<FeatureStructure> linkFSes = new LinkedList<>(Arrays.asList(roleFss.toArray()));
                for (FeatureStructure roleFs : roleFss.toArray()) {
                    if (isRoleAgree(roleFs, roleAnnosPerUser)) {
                        for (Feature targetFeature : roleFs.getType().getFeatures()) {
                            if (isBasicFeature(targetFeature)) {
                                continue;
                            }
                            if (!targetFeature.getShortName().equals("target")) {
                                continue;
                            }
                            AnnotationFS targetFs = (AnnotationFS) roleFs.getFeatureValue(targetFeature);
                            if (targetFs == null) {
                                continue;
                            }
                            Map<String, List<FeatureStructure>> targetAnnosPerUser = new HashMap<>();
                            getAllAnnosOnPosition(aJCases, targetAnnosPerUser, users, targetFs);
                            // do not agree on targets
                            if (!isAgree(targetFs, targetAnnosPerUser)) {
                                linkFSes.remove(roleFs);
                            }
                        }
                    } else // do not agree on some role features
                    {
                        linkFSes.remove(roleFs);
                    }
                }
                ArrayFS array = baseFs.getCAS().createArrayFS(linkFSes.size());
                array.copyFromArray(linkFSes.toArray(new FeatureStructure[linkFSes.size()]), 0, 0, linkFSes.size());
                baseFs.setFeatureValue(roleFeature, array);
            }
        }
    }
    return aJCases.get(WebAnnoConst.CURATION_USER);
}

Example 60 with Feature

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

the class MergeCas method isSameAnno.

/**
 * Return true if these two annotations agree on every non slot features
 */
private static boolean isSameAnno(FeatureStructure aFirstFS, FeatureStructure aSeconFS) {
    for (Feature f : getAllFeatures(aFirstFS)) {
        // the annotations are already in the same position
        if (isBasicFeature(f)) {
            continue;
        }
        if (!isLinkMode(aFirstFS, f)) {
            // check if attache type exists
            try {
                FeatureStructure attachFs1 = aFirstFS.getFeatureValue(f);
                FeatureStructure attachFs2 = aSeconFS.getFeatureValue(f);
                if (!isSameAnno(attachFs1, attachFs2)) {
                    return false;
                }
            } catch (Exception e) {
            // no attach type -- continue
            }
            // assume null as equal
            if (getFeatureValue(aFirstFS, f) == null && getFeatureValue(aSeconFS, f) == null) {
                continue;
            }
            if (getFeatureValue(aFirstFS, f) == null && getFeatureValue(aSeconFS, f) != null) {
                return false;
            }
            if (getFeatureValue(aFirstFS, f) != null && getFeatureValue(aSeconFS, f) == null) {
                return false;
            }
            if (!getFeatureValue(aFirstFS, f).equals(getFeatureValue(aSeconFS, f))) {
                return false;
            }
        }
    }
    return true;
}