Examples with ConfigurationSet de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.CasDiff.ConfigurationSet used on opensource projects

Example 1 with ConfigurationSet

use of de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.CasDiff.ConfigurationSet in project webanno by webanno.

the class AgreementUtils method dumpAgreementConfigurationSets.

private static void dumpAgreementConfigurationSets(PrintStream aOut, AgreementResult<ICodingAnnotationStudy> aAgreement, List<ConfigurationSet> aSets) {
    for (ConfigurationSet cfgSet : aSets) {
        StringBuilder sb = new StringBuilder();
        sb.append(cfgSet.getPosition());
        for (Configuration cfg : cfgSet.getConfigurations()) {
            if (sb.length() > 0) {
                sb.append(" \t");
            }
            sb.append(cfg.toString());
        }
        aOut.println(sb);
    }
}

Example 2 with ConfigurationSet

use of de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.CasDiff.ConfigurationSet in project webanno by webanno.

the class CasMerge 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 {@link DiffResult}
 * @param aCases
 *            a map of {@code CAS}s for each users and the random merge
 */
public void reMergeCas(DiffResult aDiff, SourceDocument aTargetDocument, String aTargetUsername, CAS aTargetCas, Map<String, CAS> aCases) throws AnnotationException, UIMAException {
    silenceEvents = true;
    int updated = 0;
    int created = 0;
    Set<LogMessage> messages = new LinkedHashSet<>();
    // Remove any annotations from the target CAS - keep type system, sentences and tokens
    clearAnnotations(aTargetCas);
    // If there is nothing to merge, bail out
    if (aCases.isEmpty()) {
        return;
    }
    // Set up a cache for resolving type to layer to avoid hammering the DB as we process each
    // position
    Map<String, AnnotationLayer> type2layer = aDiff.getPositions().stream().map(Position::getType).distinct().map(type -> schemaService.findLayer(aTargetDocument.getProject(), type)).collect(toMap(AnnotationLayer::getName, identity()));
    List<String> layerNames = new ArrayList<>(type2layer.keySet());
    // Move token layer to front
    if (layerNames.contains(Token.class.getName())) {
        layerNames.remove(Token.class.getName());
        layerNames.add(0, Token.class.getName());
    }
    // Move sentence layer to front
    if (layerNames.contains(Sentence.class.getName())) {
        layerNames.remove(Sentence.class.getName());
        layerNames.add(0, Sentence.class.getName());
    }
    // and sentences before the others)
    for (String layerName : layerNames) {
        List<SpanPosition> positions = aDiff.getPositions().stream().filter(pos -> layerName.equals(pos.getType())).filter(pos -> pos instanceof SpanPosition).map(pos -> (SpanPosition) pos).filter(pos -> pos.getFeature() == null).collect(Collectors.toList());
        if (positions.isEmpty()) {
            continue;
        }
        LOG.debug("Processing {} span positions on layer {}", positions.size(), layerName);
        // Slots are also excluded for the moment
        for (SpanPosition position : positions) {
            LOG.trace(" |   processing {}", position);
            ConfigurationSet cfgs = aDiff.getConfigurationSet(position);
            if (!shouldMerge(aDiff, cfgs)) {
                continue;
            }
            try {
                Map<String, List<CAS>> casMap = new LinkedHashMap<>();
                aCases.forEach((k, v) -> casMap.put(k, asList(v)));
                AnnotationFS sourceFS = (AnnotationFS) cfgs.getConfigurations().get(0).getRepresentative(casMap);
                CasMergeOperationResult result = mergeSpanAnnotation(aTargetDocument, aTargetUsername, type2layer.get(position.getType()), aTargetCas, sourceFS, false);
                LOG.trace(" `-> merged annotation with agreement");
                switch(result.getState()) {
                    case CREATED:
                        created++;
                        break;
                    case UPDATED:
                        updated++;
                        break;
                }
            } catch (AnnotationException e) {
                LOG.trace(" `-> not merged annotation: {}", e.getMessage());
                messages.add(LogMessage.error(this, "%s", e.getMessage()));
            }
        }
    }
    // After the spans are in place, we can merge the slot features
    for (String layerName : layerNames) {
        List<SpanPosition> positions = aDiff.getPositions().stream().filter(pos -> layerName.equals(pos.getType())).filter(pos -> pos instanceof SpanPosition).map(pos -> (SpanPosition) pos).filter(pos -> pos.getFeature() != null).collect(Collectors.toList());
        if (positions.isEmpty()) {
            continue;
        }
        LOG.debug("Processing {} slot positions on layer [{}]", positions.size(), layerName);
        for (SpanPosition position : positions) {
            LOG.trace(" |   processing {}", position);
            ConfigurationSet cfgs = aDiff.getConfigurationSet(position);
            if (!shouldMerge(aDiff, cfgs)) {
                continue;
            }
            try {
                Map<String, List<CAS>> casMap = new LinkedHashMap<>();
                aCases.forEach((k, v) -> casMap.put(k, asList(v)));
                AnnotationFS sourceFS = (AnnotationFS) cfgs.getConfigurations().get(0).getRepresentative(casMap);
                AID sourceFsAid = cfgs.getConfigurations().get(0).getRepresentativeAID();
                mergeSlotFeature(aTargetDocument, aTargetUsername, type2layer.get(position.getType()), aTargetCas, sourceFS, sourceFsAid.feature, sourceFsAid.index);
                LOG.trace(" `-> merged annotation with agreement");
            } catch (AnnotationException e) {
                LOG.trace(" `-> not merged annotation: {}", e.getMessage());
                messages.add(LogMessage.error(this, "%s", e.getMessage()));
            }
        }
    }
    // Finally, we merge the relations
    for (String layerName : layerNames) {
        List<RelationPosition> positions = aDiff.getPositions().stream().filter(pos -> layerName.equals(pos.getType())).filter(pos -> pos instanceof RelationPosition).map(pos -> (RelationPosition) pos).collect(Collectors.toList());
        if (positions.isEmpty()) {
            continue;
        }
        LOG.debug("Processing {} relation positions on layer [{}]", positions.size(), layerName);
        for (RelationPosition position : positions) {
            LOG.trace(" |   processing {}", position);
            ConfigurationSet cfgs = aDiff.getConfigurationSet(position);
            if (!shouldMerge(aDiff, cfgs)) {
                continue;
            }
            try {
                Map<String, List<CAS>> casMap = new LinkedHashMap<>();
                aCases.forEach((k, v) -> casMap.put(k, asList(v)));
                AnnotationFS sourceFS = (AnnotationFS) cfgs.getConfigurations().get(0).getRepresentative(casMap);
                CasMergeOperationResult result = mergeRelationAnnotation(aTargetDocument, aTargetUsername, type2layer.get(position.getType()), aTargetCas, sourceFS, false);
                LOG.trace(" `-> merged annotation with agreement");
                switch(result.getState()) {
                    case CREATED:
                        created++;
                        break;
                    case UPDATED:
                        updated++;
                        break;
                }
            } catch (AnnotationException e) {
                LOG.trace(" `-> not merged annotation: {}", e.getMessage());
                messages.add(LogMessage.error(this, "%s", e.getMessage()));
            }
        }
    }
    if (eventPublisher != null) {
        eventPublisher.publishEvent(new BulkAnnotationEvent(this, aTargetDocument, aTargetUsername, null));
    }
}

Example 3 with ConfigurationSet

use of de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.CasDiff.ConfigurationSet in project webanno by webanno.

the class SuggestionViewPanel method addSuggestionColor.

/**
 * For each {@link ConfigurationSet}, where there are some differences in users annotation and
 * the curation annotation.
 */
private void addSuggestionColor(Project aProject, Mode aMode, Map<String, CAS> aCasMap, Map<String, Map<VID, AnnotationState>> aSuggestionColors, Collection<ConfigurationSet> aCfgSet, boolean aDisagree, boolean aAgree) {
    for (ConfigurationSet cs : aCfgSet) {
        boolean use = false;
        for (String u : cs.getCasGroupIds()) {
            Map<VID, AnnotationState> colors = aSuggestionColors.computeIfAbsent(u, k -> new HashMap<>());
            for (Configuration c : cs.getConfigurations(u)) {
                FeatureStructure fs = c.getFs(u, aCasMap);
                AnnotationLayer layer = schemaService.findLayer(aProject, fs.getType().getName());
                TypeAdapter typeAdapter = schemaService.getAdapter(layer);
                VID vid;
                // link FS
                if (c.getPosition().getFeature() != null) {
                    int fi = 0;
                    for (AnnotationFeature f : typeAdapter.listFeatures()) {
                        if (f.getName().equals(c.getPosition().getFeature())) {
                            break;
                        }
                        fi++;
                    }
                    vid = new VID(WebAnnoCasUtil.getAddr(fs), fi, c.getAID(u).index);
                } else {
                    vid = new VID(WebAnnoCasUtil.getAddr(fs));
                }
                if (aAgree) {
                    colors.put(vid, AGREE);
                    continue;
                }
                // automation and correction projects
                if (!aMode.equals(CURATION) && !aAgree) {
                    if (cs.getCasGroupIds().size() == 2) {
                        colors.put(vid, DO_NOT_USE);
                    } else {
                        colors.put(vid, DISAGREE);
                    }
                    continue;
                }
                // this set agree with the curation annotation
                if (c.getCasGroupIds().contains(CURATION_USER)) {
                    use = true;
                } else {
                    use = false;
                }
                // this curation view
                if (u.equals(CURATION_USER)) {
                    continue;
                }
                if (aAgree) {
                    colors.put(vid, AGREE);
                } else if (use) {
                    colors.put(vid, USE);
                } else if (aDisagree) {
                    colors.put(vid, DISAGREE);
                } else if (!cs.getCasGroupIds().contains(CURATION_USER)) {
                    colors.put(vid, DISAGREE);
                } else {
                    colors.put(vid, DO_NOT_USE);
                }
            }
        }
    }
}

Example 4 with ConfigurationSet

use of de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.CasDiff.ConfigurationSet in project webanno by webanno.

the class SuggestionViewPanel method init.

/**
 * Initializes the user annotation segments later to be filled with content.
 */
public void init(AjaxRequestTarget aTarget, CurationContainer aCurationContainer, Map<String, Map<Integer, AnnotationSelection>> aAnnotationSelectionByUsernameAndAddress, SourceListView aCurationSegment) throws UIMAException, ClassNotFoundException, IOException {
    AnnotatorState state = aCurationContainer.getState();
    SourceDocument sourceDocument = state.getDocument();
    Map<String, CAS> casses = new HashMap<>();
    // This is the CAS that the user can actively edit
    CAS annotatorCas = getAnnotatorCas(state, aAnnotationSelectionByUsernameAndAddress, sourceDocument, casses);
    // We store the CAS that the user will edit as the "CURATION USER"
    casses.put(CURATION_USER, annotatorCas);
    List<DiffAdapter> adapters = getDiffAdapters(schemaService, state.getAnnotationLayers());
    Map<String, Map<VID, AnnotationState>> annoStates1 = new HashMap<>();
    Project project = state.getProject();
    Mode mode1 = state.getMode();
    DiffResult diff;
    if (mode1.equals(CURATION)) {
        diff = doDiffSingle(adapters, LINK_ROLE_AS_LABEL, casses, aCurationSegment.getCurationBegin(), aCurationSegment.getCurationEnd()).toResult();
    } else {
        diff = doDiffSingle(adapters, LINK_ROLE_AS_LABEL, casses, aCurationSegment.getBegin(), aCurationSegment.getEnd()).toResult();
    }
    Collection<ConfigurationSet> d = diff.getDifferingConfigurationSets().values();
    Collection<ConfigurationSet> i = diff.getIncompleteConfigurationSets().values();
    for (ConfigurationSet cfgSet : d) {
        if (i.contains(cfgSet)) {
            i.remove(cfgSet);
        }
    }
    addSuggestionColor(project, mode1, casses, annoStates1, d, false, false);
    addSuggestionColor(project, mode1, casses, annoStates1, i, true, false);
    List<ConfigurationSet> all = new ArrayList<>();
    all.addAll(diff.getConfigurationSets());
    all.removeAll(d);
    all.removeAll(i);
    addSuggestionColor(project, mode1, casses, annoStates1, all, false, true);
    // get differing feature structures
    Map<String, Map<VID, AnnotationState>> annoStates = annoStates1;
    List<String> usernamesSorted = new ArrayList<>(casses.keySet());
    Collections.sort(usernamesSorted);
    final Mode mode = state.getMode();
    boolean isAutomationMode = mode.equals(Mode.AUTOMATION);
    boolean isCorrectionMode = mode.equals(Mode.CORRECTION);
    boolean isCurationMode = mode.equals(Mode.CURATION);
    List<UserAnnotationSegment> segments = new ArrayList<>();
    for (String username : usernamesSorted) {
        if ((!username.equals(CURATION_USER) && isCurationMode) || (username.equals(CURATION_USER) && (isAutomationMode || isCorrectionMode))) {
            CAS cas = casses.get(username);
            // Set up coloring strategy
            ColoringStrategy curationColoringStrategy = makeColoringStrategy(annoStates.get(username));
            // Create curation view for the current user
            UserAnnotationSegment seg = new UserAnnotationSegment();
            seg.setUsername(username);
            seg.setAnnotatorState(state);
            seg.setCollectionData(getCollectionInformation(schemaService, aCurationContainer));
            seg.setDocumentResponse(render(cas, state, curationColoringStrategy));
            seg.setSelectionByUsernameAndAddress(aAnnotationSelectionByUsernameAndAddress);
            segments.add(seg);
        }
    }
    sentenceListView.setModelObject(segments);
    if (aTarget != null) {
        aTarget.add(this);
    }
}

Example 5 with ConfigurationSet

use of de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.CasDiff.ConfigurationSet in project webanno by webanno.

the class SuggestionViewPanel method updatePanel.

/**
 * @param aTarget
 *            the AJAX target.
 * @param aCurationContainer
 *            the container.
 * @param aAnnotationSelectionByUsernameAndAddress
 *            selections by user.
 * @param aCurationSegment
 *            the segment.
 * @throws UIMAException
 *             hum?
 * @throws ClassNotFoundException
 *             hum?
 * @throws IOException
 *             hum?
 * @throws AnnotationException
 *             hum?
 */
private void updatePanel(AjaxRequestTarget aTarget, CurationContainer aCurationContainer, Map<String, Map<Integer, AnnotationSelection>> aAnnotationSelectionByUsernameAndAddress, SourceListView aCurationSegment) throws UIMAException, ClassNotFoundException, IOException, AnnotationException {
    LOG.trace("call update");
    AnnotatorState state = aCurationContainer.getState();
    if (state.getDocument() == null) {
        return;
    }
    SourceDocument sourceDocument = state.getDocument();
    Map<String, CAS> casses = new HashMap<>();
    // This is the CAS that the user can actively edit
    CAS annotatorCas = getAnnotatorCas(state, aAnnotationSelectionByUsernameAndAddress, sourceDocument, casses);
    // We store the CAS that the user will edit as the "CURATION USER"
    casses.put(CURATION_USER, annotatorCas);
    List<DiffAdapter> adapters = getDiffAdapters(schemaService, state.getAnnotationLayers());
    Map<String, Map<VID, AnnotationState>> annoStates = new HashMap<>();
    Project project = state.getProject();
    Mode mode = state.getMode();
    DiffResult diff;
    if (mode.equals(CURATION)) {
        diff = doDiffSingle(adapters, LINK_ROLE_AS_LABEL, casses, aCurationSegment.getCurationBegin(), aCurationSegment.getCurationEnd()).toResult();
    } else {
        diff = doDiffSingle(adapters, LINK_ROLE_AS_LABEL, casses, aCurationSegment.getBegin(), aCurationSegment.getEnd()).toResult();
    }
    Collection<ConfigurationSet> d = diff.getDifferingConfigurationSets().values();
    Collection<ConfigurationSet> i = diff.getIncompleteConfigurationSets().values();
    for (ConfigurationSet cfgSet : d) {
        if (i.contains(cfgSet)) {
            i.remove(cfgSet);
        }
    }
    addSuggestionColor(project, mode, casses, annoStates, d, false, false);
    addSuggestionColor(project, mode, casses, annoStates, i, true, false);
    List<ConfigurationSet> all = new ArrayList<>();
    all.addAll(diff.getConfigurationSets());
    all.removeAll(d);
    all.removeAll(i);
    addSuggestionColor(project, mode, casses, annoStates, all, false, true);
    // get differing feature structures
    sentenceListView.visitChildren(BratSuggestionVisualizer.class, (v, visit) -> {
        BratSuggestionVisualizer vis = (BratSuggestionVisualizer) v;
        UserAnnotationSegment seg = vis.getModelObject();
        CAS cas = casses.get(seg.getUsername());
        if (cas == null) {
            // This may happen if a user has not yet finished document
            return;
        }
        // Set up coloring strategy
        ColoringStrategy curationColoringStrategy = makeColoringStrategy(annoStates.get(seg.getUsername()));
        // Create curation view for the current user
        try {
            seg.setCollectionData(getCollectionInformation(schemaService, aCurationContainer));
            seg.setDocumentResponse(render(cas, state, curationColoringStrategy));
            seg.setAnnotatorState(state);
            seg.setSelectionByUsernameAndAddress(aAnnotationSelectionByUsernameAndAddress);
        } catch (IOException e) {
            error("Unable to render: " + e.getMessage());
            LOG.error("Unable to render", e);
        }
        if (isBlank(vis.getDocumentData())) {
            return;
        }
        vis.render(aTarget);
    });
}