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

Example 26 with SourceDocument

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

the class TwoPairedKappaTest method init.

@Before
public void init() throws Exception {
    user1 = new User();
    user1.setUsername("user1");
    user2 = new User();
    user2.setUsername("user2");
    user3 = new User();
    user3.setUsername("user3");
    document = new SourceDocument();
    kappatestCas = JCasFactory.createJCas().getCas();
    CollectionReader reader1 = createReader(WebannoTsv2Reader.class, WebannoTsv2Reader.PARAM_SOURCE_LOCATION, "src/test/resources/", WebannoTsv2Reader.PARAM_PATTERNS, "kappatest.tsv");
    reader1.getNext(kappatestCas);
    kappaspandiff = JCasFactory.createJCas().getCas();
    CollectionReader reader2 = createReader(WebannoTsv2Reader.class, WebannoTsv2Reader.PARAM_SOURCE_LOCATION, "src/test/resources/", WebannoTsv2Reader.PARAM_PATTERNS, "kappaspandiff.tsv");
    reader2.getNext(kappaspandiff);
    kappaarcdiff = JCasFactory.createJCas().getCas();
    CollectionReader reader3 = createReader(WebannoTsv2Reader.class, WebannoTsv2Reader.PARAM_SOURCE_LOCATION, "src/test/resources/", WebannoTsv2Reader.PARAM_PATTERNS, "kappaarcdiff.tsv");
    reader3.getNext(kappaarcdiff);
    kappaspanarcdiff = JCasFactory.createJCas().getCas();
    CollectionReader reader4 = createReader(WebannoTsv2Reader.class, WebannoTsv2Reader.PARAM_SOURCE_LOCATION, "src/test/resources/", WebannoTsv2Reader.PARAM_PATTERNS, "kappaspanarcdiff.tsv");
    reader4.getNext(kappaspanarcdiff);
}

Example 27 with SourceDocument

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

the class TwoPairedKappaTest method testTwoUserDiffSpanAnnotation.

@Test
public void testTwoUserDiffSpanAnnotation() throws Exception {
    Map<User, List<SourceDocument>> userDocs = new HashMap<>();
    userDocs.put(user1, asList(document));
    userDocs.put(user2, asList(document));
    Map<User, JCas> userCases = new HashMap<>();
    userCases.put(user1, kappatestCas.getJCas());
    userCases.put(user2, kappaspandiff.getJCas());
    Map<SourceDocument, Map<User, JCas>> documentJCases = new HashMap<>();
    documentJCases.put(document, userCases);
    // Check against new impl
    DiffResult diff = CasDiff2.doDiff(POS.class, new SpanDiffAdapter(POS.class, "PosValue"), LinkCompareBehavior.LINK_TARGET_AS_LABEL, convert(userCases));
    AgreementResult agreement = AgreementUtils.getCohenKappaAgreement(diff, POS.class.getName(), "PosValue", convert(userCases));
    // Asserts
    System.out.printf("Agreement: %s%n", agreement.toString());
    diff.print(System.out);
    assertEquals(0.86153d, agreement.getAgreement(), 0.00001d);
    assertEquals(9, diff.size());
    assertEquals(1, diff.getDifferingConfigurationSets().size());
    assertEquals(0, diff.getIncompleteConfigurationSets().size());
}

Example 28 with SourceDocument

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

the class DocumentListPanel method actionDelete.

private void actionDelete(AjaxRequestTarget aTarget, Form<Void> aForm) {
    if (selectedDocuments.getObject() == null || selectedDocuments.getObject().isEmpty()) {
        error("No documents selected");
        aTarget.addChildren(getPage(), IFeedback.class);
        return;
    }
    confirmationDialog.setContentModel(new StringResourceModel("DeleteDialog.text", this).setParameters(selectedDocuments.getObject().size()));
    confirmationDialog.show(aTarget);
    confirmationDialog.setConfirmAction((_target) -> {
        for (SourceDocument sourceDocument : selectedDocuments.getObject()) {
            try {
                documentService.removeSourceDocument(sourceDocument);
            } catch (IOException e) {
                LOG.error("Unable to delete document", e);
                error("Unable to delete document: " + e.getMessage());
                _target.addChildren(getPage(), IFeedback.class);
            }
        }
        selectedDocuments.getObject().clear();
        _target.add(getPage());
    });
}

Example 29 with SourceDocument

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

the class AutomationUtil method predict.

public static void predict(MiraTemplate aTemplate, DocumentService aRepository, CorrectionDocumentService aCorrectionDocumentService, AutomationService aAutomationService, UserDao aUserDao) throws UIMAException, ClassNotFoundException, IOException, AnnotationException {
    AnnotationFeature layerFeature = aTemplate.getTrainFeature();
    File miraDir = aAutomationService.getMiraDir(layerFeature);
    AutomationStatus status = aAutomationService.getAutomationStatus(aTemplate);
    for (SourceDocument document : aRepository.listSourceDocuments(layerFeature.getProject())) {
        File predFile = new File(miraDir, document.getId() + ".pred");
        Mira mira = new Mira();
        int shiftColumns = 0;
        int nbest = 1;
        int beamSize = 0;
        boolean maxPosteriors = false;
        String modelName = aAutomationService.getMiraModel(layerFeature, false, null).getAbsolutePath();
        String testName = predFile.getAbsolutePath();
        File predcitedFile = new File(predFile.getAbsolutePath() + "-pred");
        PrintStream stream = new PrintStream(predcitedFile);
        BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
        if (testName != null) {
            input = new BufferedReader(new FileReader(testName));
        }
        mira.loadModel(modelName);
        mira.setShiftColumns(shiftColumns);
        mira.nbest = nbest;
        mira.beamSize = beamSize;
        mira.maxPosteriors = maxPosteriors;
        mira.test(input, stream);
        LOG.info("Prediction is wrtten to a MIRA File. To be done is writing back to the CAS");
        LineIterator it = IOUtils.lineIterator(new FileReader(predcitedFile));
        List<String> annotations = new ArrayList<>();
        while (it.hasNext()) {
            String line = it.next();
            if (line.trim().equals("")) {
                continue;
            }
            StringTokenizer st = new StringTokenizer(line, " ");
            String tag = "";
            while (st.hasMoreTokens()) {
                tag = st.nextToken();
            }
            annotations.add(tag);
        }
        LOG.info(annotations.size() + " Predictions found to be written to the CAS");
        JCas jCas = null;
        User user = aUserDao.getCurrentUser();
        try {
            AnnotationDocument annoDocument = aRepository.getAnnotationDocument(document, user);
            jCas = aRepository.readAnnotationCas(annoDocument);
            automate(jCas, layerFeature, annotations);
        } catch (DataRetrievalFailureException e) {
            automate(jCas, layerFeature, annotations);
            LOG.info("Predictions found are written to the CAS");
            aCorrectionDocumentService.writeCorrectionCas(jCas, document);
            status.setAnnoDocs(status.getAnnoDocs() - 1);
        }
        automate(jCas, layerFeature, annotations);
        LOG.info("Predictions found are written to the CAS");
        aCorrectionDocumentService.writeCorrectionCas(jCas, document);
        status.setAnnoDocs(status.getAnnoDocs() - 1);
    }
}

Example 30 with SourceDocument

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

the class AutomationUtil method repeateRelationAnnotation.

public static void repeateRelationAnnotation(AnnotatorState aState, DocumentService aDocumentService, CorrectionDocumentService aCorrectionDocumentService, AnnotationSchemaService aAnnotationService, AnnotationFS fs, AnnotationFeature aFeature, String aValue) throws UIMAException, ClassNotFoundException, IOException, AnnotationException {
    for (SourceDocument d : aDocumentService.listSourceDocuments(aState.getProject())) {
        loadDocument(d, aAnnotationService, aDocumentService, aCorrectionDocumentService, aState.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);
        }
        if (adapter.isCrossMultipleSentence()) {
            List<AnnotationFS> mSpanAnnos = new ArrayList<>(getAllAnnoFss(jCas, governorFs.getType()));
            repeatRelation(aState, 0, jCas.getDocumentText().length() - 1, aFeature, aValue, jCas, adapter, dependentFs, governorFs, mSpanAnnos);
        } else {
            for (Sentence sent : select(jCas, Sentence.class)) {
                List<AnnotationFS> spanAnnos = selectCovered(governorFs.getType(), sent);
                repeatRelation(aState, sent.getBegin(), sent.getEnd(), aFeature, aValue, jCas, adapter, dependentFs, governorFs, spanAnnos);
            }
        }
        aCorrectionDocumentService.writeCorrectionCas(jCas, d);
    }
}