Examples with LogMessage de.tudarmstadt.ukp.clarin.webanno.support.logging.LogMessage used on opensource projects

Example 16 with LogMessage

use of de.tudarmstadt.ukp.clarin.webanno.support.logging.LogMessage in project webanno by webanno.

the class RemoveDanglingChainLinksRepair method repair.

@Override
public void repair(Project aProject, CAS aCas, List<LogMessage> aMessages) {
    for (AnnotationLayer layer : annotationService.listAnnotationLayer(aProject)) {
        if (!WebAnnoConst.CHAIN_TYPE.equals(layer.getType())) {
            continue;
        }
        List<FeatureStructure> chains = new ArrayList<>(selectFS(aCas, getType(aCas, layer.getName() + "Chain")));
        List<AnnotationFS> links = new ArrayList<>(select(aCas, getType(aCas, layer.getName() + "Link")));
        for (FeatureStructure chain : chains) {
            AnnotationFS link = FSUtil.getFeature(chain, "first", AnnotationFS.class);
            while (link != null) {
                links.remove(link);
                link = FSUtil.getFeature(link, "next", AnnotationFS.class);
            }
        }
        // Delete those relations that pointed to deleted spans
        if (!links.isEmpty()) {
            links.forEach(aCas::removeFsFromIndexes);
            aMessages.add(new LogMessage(this, LogLevel.INFO, "Removed [%d] dangling links in layer [" + layer.getName() + "].", links.size()));
        }
    }
}

Example 17 with LogMessage

use of de.tudarmstadt.ukp.clarin.webanno.support.logging.LogMessage in project webanno by webanno.

the class RemoveDanglingRelationsRepair method repair.

@Override
public void repair(Project aProject, CAS aCas, List<LogMessage> aMessages) {
    Set<FeatureStructure> nonIndexed = getNonIndexedFSes(aCas);
    Set<FeatureStructure> toDelete = new LinkedHashSet<>();
    for (AnnotationFS fs : aCas.getAnnotationIndex()) {
        Type t = fs.getType();
        Feature sourceFeat = t.getFeatureByBaseName(FEAT_REL_SOURCE);
        Feature targetFeat = t.getFeatureByBaseName(FEAT_REL_TARGET);
        // Is this a relation?
        if (!(sourceFeat != null && targetFeat != null)) {
            continue;
        }
        FeatureStructure source = fs.getFeatureValue(sourceFeat);
        FeatureStructure target = fs.getFeatureValue(targetFeat);
        // Are there null end-points or does it point to deleted spans?
        if (source == null || target == null || nonIndexed.contains(source) || nonIndexed.contains(target)) {
            toDelete.add(fs);
            continue;
        }
        RelationAdapter relationAdapter = (RelationAdapter) annotationService.findAdapter(aProject, fs);
        Feature relationSourceAttachFeature = null;
        Feature relationTargetAttachFeature = null;
        if (relationAdapter.getAttachFeatureName() != null) {
            relationSourceAttachFeature = sourceFeat.getRange().getFeatureByBaseName(relationAdapter.getAttachFeatureName());
            relationTargetAttachFeature = targetFeat.getRange().getFeatureByBaseName(relationAdapter.getAttachFeatureName());
        }
        // Here we get the annotations that the relation is pointing to in the UI
        if (relationSourceAttachFeature != null) {
            source = (AnnotationFS) source.getFeatureValue(relationSourceAttachFeature);
        }
        if (relationTargetAttachFeature != null) {
            target = (AnnotationFS) target.getFeatureValue(relationTargetAttachFeature);
        }
        // annotations linked to in the UI?
        if (source == null || target == null || nonIndexed.contains(source) || nonIndexed.contains(target)) {
            toDelete.add(fs);
            continue;
        }
    }
    // Delete those relations that pointed to deleted spans
    if (!toDelete.isEmpty()) {
        toDelete.forEach(aCas::removeFsFromIndexes);
        aMessages.add(new LogMessage(this, INFO, "Removed [%d] dangling relations.", toDelete.size()));
    }
}

Example 18 with LogMessage

use of de.tudarmstadt.ukp.clarin.webanno.support.logging.LogMessage in project webanno by webanno.

the class RemoveDanglingRelationsRepairTest method test.

@Test
public void test() throws Exception {
    JCas jcas = JCasFactory.createJCas();
    jcas.setDocumentText("This is a test.");
    Token span1 = new Token(jcas, 0, 4);
    span1.addToIndexes();
    Token span2 = new Token(jcas, 6, 8);
    Dependency dep = new Dependency(jcas, 0, 8);
    dep.setGovernor(span1);
    dep.setDependent(span2);
    dep.addToIndexes();
    List<LogMessage> messages = new ArrayList<>();
    CasDoctor cd = new CasDoctor(RemoveDanglingRelationsRepair.class, AllFeatureStructuresIndexedCheck.class);
    // A project is not required for this check
    boolean result = cd.analyze(null, jcas.getCas(), messages);
    // A project is not required for this repair
    cd.repair(null, jcas.getCas(), messages);
    assertFalse(result);
    messages.forEach(System.out::println);
}

Example 19 with LogMessage

use of de.tudarmstadt.ukp.clarin.webanno.support.logging.LogMessage in project webanno by webanno.

the class NoMultipleIncomingRelationsCheckTest method testOK.

@Test
public void testOK() throws Exception {
    AnnotationLayer relationLayer = new AnnotationLayer();
    relationLayer.setName(Dependency.class.getName());
    relationLayer.setType(WebAnnoConst.RELATION_TYPE);
    Mockito.when(annotationService.listAnnotationLayer(Mockito.isNull())).thenReturn(Arrays.asList(relationLayer));
    JCas jcas = JCasFactory.createJCas();
    jcas.setDocumentText("This is a test.");
    Token spanThis = new Token(jcas, 0, 4);
    spanThis.addToIndexes();
    Token spanIs = new Token(jcas, 6, 8);
    spanIs.addToIndexes();
    Token spanA = new Token(jcas, 9, 10);
    spanA.addToIndexes();
    Dependency dep1 = new Dependency(jcas, 0, 8);
    dep1.setGovernor(spanThis);
    dep1.setDependent(spanIs);
    dep1.addToIndexes();
    Dependency dep2 = new Dependency(jcas, 6, 10);
    dep2.setGovernor(spanIs);
    dep2.setDependent(spanA);
    dep2.addToIndexes();
    List<LogMessage> messages = new ArrayList<>();
    boolean result = check.check(null, jcas.getCas(), messages);
    messages.forEach(System.out::println);
    assertTrue(result);
}

Example 20 with LogMessage

use of de.tudarmstadt.ukp.clarin.webanno.support.logging.LogMessage in project webanno by webanno.

the class NoMultipleIncomingRelationsCheck method check.

@Override
public boolean check(Project aProject, CAS aCas, List<LogMessage> aMessages) {
    boolean ok = true;
    if (annotationService == null) {
        return ok;
    }
    List<AnnotationLayer> allAnnoLayers = annotationService.listAnnotationLayer(aProject);
    if (allAnnoLayers != null) {
        for (AnnotationLayer layer : allAnnoLayers) {
            if (!WebAnnoConst.RELATION_TYPE.equals(layer.getType())) {
                continue;
            }
            if (!Dependency.class.getName().equals(layer.getName())) {
                continue;
            }
            Type type;
            try {
                type = getType(aCas, layer.getName());
            } catch (IllegalArgumentException e) {
                // can skip checking the layer because there will be no annotations anyway.
                continue;
            }
            // Remember all nodes that already have a known incoming relation.
            // Map from the target to the existing source, so the source can be used
            // to provide a better debugging output.
            Map<AnnotationFS, AnnotationFS> incoming = new HashMap<>();
            for (AnnotationFS rel : select(aCas, type)) {
                AnnotationFS source = getFeature(rel, FEAT_REL_SOURCE, AnnotationFS.class);
                AnnotationFS target = getFeature(rel, FEAT_REL_TARGET, AnnotationFS.class);
                AnnotationFS existingSource = incoming.get(target);
                if (existingSource != null) {
                    // Debug output should include sentence number to make the orientation
                    // easier
                    Optional<Integer> sentenceNumber = Optional.empty();
                    try {
                        sentenceNumber = Optional.of(WebAnnoCasUtil.getSentenceNumber(target.getCAS(), target.getBegin()));
                    } catch (IndexOutOfBoundsException e) {
                        // ignore this error and don't output sentence number
                        sentenceNumber = Optional.empty();
                    }
                    if (sentenceNumber.isPresent()) {
                        aMessages.add(new LogMessage(this, LogLevel.WARN, "Sentence %d: Relation [%s] -> [%s] points to span that already has an " + "incoming relation [%s] -> [%s].", sentenceNumber.get(), source.getCoveredText(), target.getCoveredText(), existingSource.getCoveredText(), target.getCoveredText()));
                    } else {
                        aMessages.add(new LogMessage(this, LogLevel.WARN, "Relation [%s] -> [%s] points to span that already has an " + "incoming relation [%s] -> [%s].", source.getCoveredText(), target.getCoveredText(), existingSource.getCoveredText(), target.getCoveredText()));
                    }
                // This check only logs warnings - it should not fail. Having multiple
                // incoming edges is not a serious problem.
                // ok = false;
                } else {
                    incoming.put(target, source);
                }
            }
        }
    }
    return ok;
}