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

Example 41 with SourceDocument

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

the class AutomationUtil method repeateSpanAnnotation.

public static void repeateSpanAnnotation(AnnotatorState aState, DocumentService aDocumentService, CorrectionDocumentService aCorrectionDocumentService, AnnotationSchemaService aAnnotationService, int aStart, int aEnd, AnnotationFeature aFeature, String aValue) throws UIMAException, ClassNotFoundException, IOException, AnnotationException {
    AnnotationDocument annoDoc = aDocumentService.getAnnotationDocument(aState.getDocument(), aState.getUser());
    JCas annoCas = aDocumentService.readAnnotationCas(annoDoc);
    // get selected text, concatenations of tokens
    String selectedText = WebAnnoCasUtil.getSelectedText(annoCas, aStart, aEnd);
    SpanAdapter adapter = (SpanAdapter) aAnnotationService.getAdapter(aFeature.getLayer());
    for (SourceDocument d : aDocumentService.listSourceDocuments(aState.getProject())) {
        loadDocument(d, aAnnotationService, aDocumentService, aCorrectionDocumentService, aState.getUser());
        JCas jCas = aCorrectionDocumentService.readCorrectionCas(d);
        for (Sentence sentence : select(jCas, Sentence.class)) {
            String sentenceText = sentence.getCoveredText().toLowerCase();
            for (int i = -1; (i = sentenceText.indexOf(selectedText.toLowerCase(), i)) != -1; i = i + selectedText.length()) {
                if (selectCovered(jCas, Token.class, sentence.getBegin() + i, sentence.getBegin() + i + selectedText.length()).size() > 0) {
                    int addr = adapter.add(aState, jCas, sentence.getBegin() + i, sentence.getBegin() + i + selectedText.length() - 1);
                    adapter.setFeatureValue(aState, jCas, addr, aFeature, aValue);
                }
            }
        }
        aCorrectionDocumentService.writeCorrectionCas(jCas, d);
    }
}

Example 42 with SourceDocument

use of de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument 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.getAnnotatorState();
    SourceDocument sourceDocument = state.getDocument();
    Map<String, JCas> jCases = new HashMap<>();
    // This is the CAS that the user can actively edit
    JCas annotatorCas = getAnnotatorCas(state, aAnnotationSelectionByUsernameAndAddress, sourceDocument, jCases);
    // We store the CAS that the user will edit as the "CURATION USER"
    jCases.put(CURATION_USER, annotatorCas);
    // get differing feature structures
    Map<String, Map<VID, AnnotationState>> annoStates = calcColors(state, aCurationSegment, annotatorCas, jCases);
    List<String> usernamesSorted = new ArrayList<>(jCases.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))) {
            JCas jCas = jCases.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(annotationService, aCurationContainer));
            seg.setDocumentResponse(render(jCas, state, curationColoringStrategy));
            seg.setSelectionByUsernameAndAddress(aAnnotationSelectionByUsernameAndAddress);
            segments.add(seg);
        }
    }
    sentenceListView.setModelObject(segments);
    if (aTarget != null) {
        aTarget.add(this);
    }
}

Example 43 with SourceDocument

use of de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument 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?
 */
public void updatePanel(AjaxRequestTarget aTarget, CurationContainer aCurationContainer, Map<String, Map<Integer, AnnotationSelection>> aAnnotationSelectionByUsernameAndAddress, SourceListView aCurationSegment) throws UIMAException, ClassNotFoundException, IOException, AnnotationException {
    AnnotatorState state = aCurationContainer.getAnnotatorState();
    SourceDocument sourceDocument = state.getDocument();
    Map<String, JCas> jCases = new HashMap<>();
    // This is the CAS that the user can actively edit
    JCas annotatorCas = getAnnotatorCas(state, aAnnotationSelectionByUsernameAndAddress, sourceDocument, jCases);
    // We store the CAS that the user will edit as the "CURATION USER"
    jCases.put(CURATION_USER, annotatorCas);
    // get differing feature structures
    Map<String, Map<VID, AnnotationState>> annoStates = calcColors(state, aCurationSegment, annotatorCas, jCases);
    sentenceListView.visitChildren(BratSuggestionVisualizer.class, (v, visit) -> {
        BratSuggestionVisualizer vis = (BratSuggestionVisualizer) v;
        UserAnnotationSegment seg = vis.getModelObject();
        JCas jCas = jCases.get(seg.getUsername());
        // Set up coloring strategy
        ColoringStrategy curationColoringStrategy = makeColoringStrategy(annoStates.get(seg.getUsername()));
        // Create curation view for the current user
        try {
            seg.setCollectionData(getCollectionInformation(annotationService, aCurationContainer));
            seg.setDocumentResponse(render(jCas, state, curationColoringStrategy));
            seg.setAnnotatorState(state);
            seg.setSelectionByUsernameAndAddress(aAnnotationSelectionByUsernameAndAddress);
        } catch (IOException e) {
            error("Unable to render: " + e.getMessage());
            LOG.error("Unable to render", e);
        }
        vis.requestRender(aTarget);
    });
}

Example 44 with SourceDocument

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

the class SuggestionBuilder method buildCurationContainer.

public CurationContainer buildCurationContainer(AnnotatorState aBModel) throws UIMAException, ClassNotFoundException, IOException, AnnotationException {
    CurationContainer curationContainer = new CurationContainer();
    // initialize Variables
    SourceDocument sourceDocument = aBModel.getDocument();
    Map<Integer, Integer> segmentBeginEnd = new HashMap<>();
    Map<Integer, Integer> segmentNumber = new HashMap<>();
    Map<String, Map<Integer, Integer>> segmentAdress = new HashMap<>();
    // get annotation documents
    List<AnnotationDocument> finishedAnnotationDocuments = new ArrayList<>();
    for (AnnotationDocument annotationDocument : documentService.listAnnotationDocuments(aBModel.getDocument())) {
        if (annotationDocument.getState().equals(AnnotationDocumentState.FINISHED)) {
            finishedAnnotationDocuments.add(annotationDocument);
        }
    }
    Map<String, JCas> jCases = new HashMap<>();
    AnnotationDocument randomAnnotationDocument = null;
    JCas mergeJCas;
    // get the correction/automation JCas for the logged in user
    if (aBModel.getMode().equals(Mode.AUTOMATION) || aBModel.getMode().equals(Mode.CORRECTION)) {
        jCases = listJcasesforCorrection(randomAnnotationDocument, sourceDocument, aBModel.getMode());
        mergeJCas = getMergeCas(aBModel, sourceDocument, jCases, randomAnnotationDocument, false);
        String username = jCases.keySet().iterator().next();
        updateSegment(aBModel, segmentBeginEnd, segmentNumber, segmentAdress, jCases.get(username), username, aBModel.getWindowBeginOffset(), aBModel.getWindowEndOffset());
    } else {
        jCases = listJcasesforCuration(finishedAnnotationDocuments, randomAnnotationDocument, aBModel.getMode());
        mergeJCas = getMergeCas(aBModel, sourceDocument, jCases, randomAnnotationDocument, false);
        updateSegment(aBModel, segmentBeginEnd, segmentNumber, segmentAdress, mergeJCas, WebAnnoConst.CURATION_USER, WebAnnoCasUtil.getFirstSentence(mergeJCas).getBegin(), mergeJCas.getDocumentText().length());
    }
    List<Type> entryTypes = null;
    segmentAdress.put(WebAnnoConst.CURATION_USER, new HashMap<>());
    for (Sentence sentence : selectCovered(mergeJCas, Sentence.class, diffRangeBegin, diffRangeEnd)) {
        segmentAdress.get(WebAnnoConst.CURATION_USER).put(sentence.getBegin(), getAddr(sentence));
    }
    if (entryTypes == null) {
        entryTypes = getEntryTypes(mergeJCas, aBModel.getAnnotationLayers(), annotationService);
    }
    // for cross-sentences annotation, update the end of the segment
    if (firstload) {
        long start = System.currentTimeMillis();
        log.debug("Updating cross sentence annotation list...");
        updateCrossSentAnnoList(segmentBeginEnd, segmentNumber, jCases, entryTypes);
        firstload = false;
        log.debug("Cross sentence annotation list complete in {}ms", (System.currentTimeMillis() - start));
    }
    long diffStart = System.currentTimeMillis();
    log.debug("Calculating differences...");
    int count = 0;
    for (Integer begin : segmentBeginEnd.keySet()) {
        Integer end = segmentBeginEnd.get(begin);
        count++;
        if (count % 100 == 0) {
            log.debug("Processing differences: {} of {} sentences...", count, segmentBeginEnd.size());
        }
        DiffResult diff = CasDiff2.doDiffSingle(annotationService, aBModel.getProject(), entryTypes, LinkCompareBehavior.LINK_ROLE_AS_LABEL, jCases, begin, end);
        SourceListView curationSegment = new SourceListView();
        curationSegment.setBegin(begin);
        curationSegment.setEnd(end);
        curationSegment.setSentenceNumber(segmentNumber.get(begin));
        if (diff.hasDifferences() || !diff.getIncompleteConfigurationSets().isEmpty()) {
            // Is this confSet a diff due to stacked annotations (with same configuration)?
            boolean stackedDiff = false;
            stackedDiffSet: for (ConfigurationSet d : diff.getDifferingConfigurationSets().values()) {
                for (Configuration c : d.getConfigurations()) {
                    if (c.getCasGroupIds().size() != d.getCasGroupIds().size()) {
                        stackedDiff = true;
                        break stackedDiffSet;
                    }
                }
            }
            if (stackedDiff) {
                curationSegment.setSentenceState(SentenceState.DISAGREE);
            } else if (!diff.getIncompleteConfigurationSets().isEmpty()) {
                curationSegment.setSentenceState(SentenceState.DISAGREE);
            } else {
                curationSegment.setSentenceState(SentenceState.AGREE);
            }
        } else {
            curationSegment.setSentenceState(SentenceState.AGREE);
        }
        for (String username : segmentAdress.keySet()) {
            curationSegment.getSentenceAddress().put(username, segmentAdress.get(username).get(begin));
        }
        curationContainer.getCurationViewByBegin().put(begin, curationSegment);
    }
    log.debug("Difference calculation completed in {}ms", (System.currentTimeMillis() - diffStart));
    return curationContainer;
}

Example 45 with SourceDocument

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

the class TwoPairedKappaTest method testThreeUserDiffArcAndSpanAnnotation.

@Test
public void testThreeUserDiffArcAndSpanAnnotation() throws Exception {
    Map<User, List<SourceDocument>> userDocs = new HashMap<>();
    userDocs.put(user1, asList(document));
    userDocs.put(user2, asList(document));
    userDocs.put(user3, asList(document));
    Map<User, JCas> userCases = new HashMap<>();
    userCases.put(user1, kappatestCas.getJCas());
    userCases.put(user2, kappaspandiff.getJCas());
    userCases.put(user3, kappaspanarcdiff.getJCas());
    Map<SourceDocument, Map<User, JCas>> documentJCases = new HashMap<>();
    documentJCases.put(document, userCases);
    // Check against new impl
    DiffResult diff = CasDiff2.doDiff(asList(POS.class.getName(), Dependency.class.getName()), asList(SpanDiffAdapter.POS, ArcDiffAdapter.DEPENDENCY), LinkCompareBehavior.LINK_TARGET_AS_LABEL, convert(userCases));
    Map<String, List<JCas>> user1and2 = convert(userCases);
    user1and2.remove("user3");
    AgreementResult agreement12 = AgreementUtils.getCohenKappaAgreement(diff, Dependency.class.getName(), "DependencyType", user1and2);
    Map<String, List<JCas>> user2and3 = convert(userCases);
    user2and3.remove("user1");
    AgreementResult agreement23 = AgreementUtils.getCohenKappaAgreement(diff, Dependency.class.getName(), "DependencyType", user2and3);
    Map<String, List<JCas>> user1and3 = convert(userCases);
    user1and3.remove("user2");
    AgreementResult agreement13 = AgreementUtils.getCohenKappaAgreement(diff, Dependency.class.getName(), "DependencyType", user1and3);
    // Asserts
    diff.print(System.out);
    System.out.printf("New agreement 1/2: %s%n", agreement12.toString());
    System.out.printf("New agreement 2/3: %s%n", agreement23.toString());
    System.out.printf("New agreement 1/3: %s%n", agreement13.toString());
}