Examples with LogMessage de.tudarmstadt.ukp.clarin.webanno.diag.CasDoctor.LogMessage used on opensource projects

Example 6 with LogMessage

use of de.tudarmstadt.ukp.clarin.webanno.diag.CasDoctor.LogMessage in project webanno by webanno.

the class ProjectCasDoctorPanel method actionRepair.

private void actionRepair(AjaxRequestTarget aTarget, Form<?> aForm) throws IOException, UIMAException, ClassNotFoundException {
    casStorageService.disableCache();
    CasDoctor casDoctor = new CasDoctor();
    casDoctor.setApplicationContext(ApplicationContextProvider.getApplicationContext());
    casDoctor.setFatalChecks(false);
    casDoctor.setRepairClasses(formModel.repairs);
    Project project = getModelObject();
    formModel.messageSets = new ArrayList<>();
    for (SourceDocument sd : documentService.listSourceDocuments(project)) {
        {
            LogMessageSet messageSet = new LogMessageSet(sd.getName() + " [INITIAL]");
            JCas initialCas;
            if (documentService.existsInitialCas(sd)) {
                initialCas = documentService.readInitialCas(sd, false);
            } else {
                messageSet.messages.add(new LogMessage(getClass(), LogLevel.INFO, "Created initial CAS for [" + sd.getName() + "]"));
                initialCas = documentService.createInitialCas(sd, false);
            }
            casDoctor.repair(project, initialCas.getCas(), messageSet.messages);
            CasPersistenceUtils.writeSerializedCas(initialCas, documentService.getCasFile(sd, INITIAL_CAS_PSEUDO_USER));
            noticeIfThereAreNoMessages(messageSet);
            formModel.messageSets.add(messageSet);
        }
        for (AnnotationDocument ad : documentService.listAnnotationDocuments(sd)) {
            if (documentService.existsAnnotationCas(ad)) {
                LogMessageSet messageSet = new LogMessageSet(sd.getName() + " [" + ad.getUser() + "]");
                JCas userCas = documentService.readAnnotationCas(ad, false);
                casDoctor.repair(project, userCas.getCas(), messageSet.messages);
                CasPersistenceUtils.writeSerializedCas(userCas, documentService.getCasFile(ad.getDocument(), ad.getUser()));
                noticeIfThereAreNoMessages(messageSet);
                formModel.messageSets.add(messageSet);
            }
        }
    }
    aTarget.add(this);
}

Example 7 with LogMessage

use of de.tudarmstadt.ukp.clarin.webanno.diag.CasDoctor.LogMessage in project webanno by webanno.

the class ProjectCasDoctorPanel method actionCheck.

private void actionCheck(AjaxRequestTarget aTarget, Form<?> aForm) throws IOException, UIMAException, ClassNotFoundException {
    casStorageService.disableCache();
    CasDoctor casDoctor = new CasDoctor();
    casDoctor.setApplicationContext(ApplicationContextProvider.getApplicationContext());
    casDoctor.setFatalChecks(false);
    casDoctor.setCheckClasses(CasDoctor.scanChecks());
    Project project = getModelObject();
    formModel.messageSets = new ArrayList<>();
    for (SourceDocument sd : documentService.listSourceDocuments(project)) {
        {
            LogMessageSet messageSet = new LogMessageSet(sd.getName() + " [INITIAL]");
            JCas initialCas;
            try {
                if (documentService.existsInitialCas(sd)) {
                    initialCas = documentService.readInitialCas(sd, false);
                } else {
                    messageSet.messages.add(new LogMessage(getClass(), LogLevel.INFO, "No initial CAS for [" + sd.getName() + "]"));
                    initialCas = documentService.createInitialCas(sd, false);
                }
                casDoctor.analyze(project, initialCas.getCas(), messageSet.messages);
            } catch (Exception e) {
                messageSet.messages.add(new LogMessage(getClass(), LogLevel.ERROR, "Error reading initial CAS for [" + sd.getName() + "]: " + e.getMessage()));
                LOG.error("Error reading initial CAS for [" + sd.getName() + "]", e);
            }
            noticeIfThereAreNoMessages(messageSet);
            formModel.messageSets.add(messageSet);
        }
        for (AnnotationDocument ad : documentService.listAnnotationDocuments(sd)) {
            if (documentService.existsAnnotationCas(ad)) {
                LogMessageSet messageSet = new LogMessageSet(sd.getName() + " [" + ad.getUser() + "]");
                JCas userCas = documentService.readAnnotationCas(ad, false);
                casDoctor.analyze(project, userCas.getCas(), messageSet.messages);
                noticeIfThereAreNoMessages(messageSet);
                formModel.messageSets.add(messageSet);
            }
        }
    }
    aTarget.add(this);
}

Example 8 with LogMessage

use of de.tudarmstadt.ukp.clarin.webanno.diag.CasDoctor.LogMessage in project webanno by webanno.

the class LinksReachableThroughChainsCheck method check.

@Override
public boolean check(Project aProject, CAS aCas, List<LogMessage> aMessages) {
    boolean ok = true;
    for (AnnotationLayer layer : annotationService.listAnnotationLayer(aProject)) {
        if (!WebAnnoConst.CHAIN_TYPE.equals(layer.getType())) {
            continue;
        }
        Type chainType;
        Type linkType;
        try {
            chainType = getType(aCas, layer.getName() + "Chain");
            linkType = getType(aCas, layer.getName() + "Link");
        } catch (IllegalArgumentException e) {
            // check
            continue;
        }
        List<FeatureStructure> chains = new ArrayList<>(selectFS(aCas, chainType));
        List<AnnotationFS> links = new ArrayList<>(select(aCas, linkType));
        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);
            }
        }
        if (!links.isEmpty()) {
            ok = false;
            aMessages.add(new LogMessage(this, LogLevel.ERROR, "CoreferenceLinks not reachable through chains: %d", links.size()));
            for (AnnotationFS link : links) {
                aMessages.add(new LogMessage(this, LogLevel.ERROR, "Unreachable CoreferenceLink [%s]", link));
            }
        }
    }
    return ok;
}

Example 9 with LogMessage

use of de.tudarmstadt.ukp.clarin.webanno.diag.CasDoctor.LogMessage in project webanno by webanno.

the class RelationOffsetsCheck method check.

@Override
public boolean check(Project aProject, CAS aCas, List<LogMessage> aMessages) {
    boolean ok = true;
    for (AnnotationLayer layer : annotationService.listAnnotationLayer(aProject)) {
        if (!WebAnnoConst.RELATION_TYPE.equals(layer.getType())) {
            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;
        }
        for (AnnotationFS rel : select(aCas, type)) {
            AnnotationFS target = getFeature(rel, WebAnnoConst.FEAT_REL_TARGET, AnnotationFS.class);
            if ((rel.getBegin() != target.getBegin()) || (rel.getEnd() != target.getEnd())) {
                aMessages.add(new LogMessage(this, LogLevel.ERROR, "Relation offsets [%d,%d] to not match target offsets [%d,%d]", rel.getBegin(), rel.getEnd(), target.getBegin(), target.getEnd()));
                ok = false;
            }
        }
    }
    return ok;
}

Example 10 with LogMessage

use of de.tudarmstadt.ukp.clarin.webanno.diag.CasDoctor.LogMessage in project webanno by webanno.

the class ReindexFeatureAttachedSpanAnnotationsRepair method repair.

@Override
public void repair(Project aProject, CAS aCas, List<LogMessage> aMessages) {
    Map<FeatureStructure, FeatureStructure> nonIndexed = getNonIndexedFSesWithOwner(aCas);
    for (AnnotationLayer layer : annotationService.listAnnotationLayer(aProject)) {
        if (!(WebAnnoConst.SPAN_TYPE.equals(layer.getType()) && layer.getAttachFeature() != null)) {
            continue;
        }
        int count = 0;
        // anno -> e.g. Lemma
        for (AnnotationFS attach : select(aCas, getType(aCas, layer.getAttachType().getName()))) {
            AnnotationFS anno = getFeature(attach, layer.getAttachFeature().getName(), AnnotationFS.class);
            if (anno != null && nonIndexed.containsKey(anno)) {
                aCas.addFsToIndexes(anno);
                count++;
            }
        }
        if (count > 0) {
            aMessages.add(new LogMessage(this, LogLevel.INFO, "Reindexed [%d] unindexed spans in layer [" + layer.getName() + "].", count));
        }
    }
}