Examples with Repair de.tudarmstadt.ukp.clarin.webanno.diag.repairs.Repair used on opensource projects

Example 1 with Repair

use of de.tudarmstadt.ukp.clarin.webanno.diag.repairs.Repair in project webanno by webanno.

the class CasDoctor method scanRepairs.

public static List<Class<? extends Repair>> scanRepairs() {
    long start = currentTimeMillis();
    Reflections reflections = new Reflections(Repair.class.getPackage().getName());
    List<Class<? extends Repair>> repairs = reflections.getSubTypesOf(Repair.class).stream().filter(c -> !Modifier.isAbstract(c.getModifiers())).sorted(Comparator.comparing(Class::getName)).collect(Collectors.toList());
    LOG.info("Found {} repairs in {}ms", repairs.size(), currentTimeMillis() - start);
    return repairs;
}

Example 2 with Repair

use of de.tudarmstadt.ukp.clarin.webanno.diag.repairs.Repair in project webanno by webanno.

the class CasDoctor method repair.

public void repair(Project aProject, CAS aCas, List<LogMessage> aMessages) {
    // If there are no active repairs, don't do anything
    if (repairClasses.isEmpty()) {
        return;
    }
    // APPLY REPAIRS
    long tStart = System.currentTimeMillis();
    for (Class<? extends Repair> repairClass : repairClasses) {
        try {
            long tStartTask = System.currentTimeMillis();
            Repair repair = repairClass.newInstance();
            if (context != null) {
                context.getAutowireCapableBeanFactory().autowireBean(repair);
            }
            LOG.info("CasDoctor repair [" + repairClass.getSimpleName() + "] running...");
            repair.repair(aProject, aCas, aMessages);
            LOG.info("CasDoctor repair [" + repairClass.getSimpleName() + "] completed in " + (System.currentTimeMillis() - tStartTask) + "ms");
        } catch (Exception e) {
            // aMessages.add(new LogMessage(this, LogLevel.ERROR, "Cannot perform repair [%s]:
            // %s",
            // repairClass.getSimpleName(), ExceptionUtils.getRootCauseMessage(e)));
            LOG.error("Cannot perform repair [" + repairClass.getSimpleName() + "]", e);
            throw new IllegalStateException("Repair attempt failed - ask system administrator " + "for details.");
        }
    }
    LOG.info("CasDoctor completed all repairs in " + (System.currentTimeMillis() - tStart) + "ms");
    // POST-CONDITION: CAS must be consistent
    // Ensure that the repairs actually fixed the CAS
    analyze(aProject, aCas, aMessages, true);
}

Example 3 with Repair

use of de.tudarmstadt.ukp.clarin.webanno.diag.repairs.Repair in project webanno by webanno.

the class ProjectCasDoctorPanel method actionRepair.

private void actionRepair(AjaxRequestTarget aTarget, Form<?> aForm) throws IOException, UIMAException, ClassNotFoundException {
    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)) {
        // Repair INITIAL CAS
        {
            LogMessageSet messageSet = new LogMessageSet(sd.getName() + " [INITIAL]");
            try {
                casStorageService.forceActionOnCas(sd, INITIAL_CAS_PSEUDO_USER, (doc, user) -> createOrReadInitialCasWithoutSaving(doc, messageSet), // 
                (cas) -> casDoctor.repair(project, cas, messageSet.messages), true);
            } catch (Exception e) {
                messageSet.messages.add(new LogMessage(getClass(), LogLevel.ERROR, "Error repairing initial CAS for [" + sd.getName() + "]: " + e.getMessage()));
                LOG.error("Error repairing initial CAS for [{}]", sd.getName(), e);
            }
            noticeIfThereAreNoMessages(messageSet);
            formModel.messageSets.add(messageSet);
        }
        // Repair CORRECTION_USER CAS if necessary
        if (PROJECT_TYPE_CORRECTION.equals(project.getMode())) {
            LogMessageSet messageSet = new LogMessageSet(sd.getName() + " [" + CORRECTION_USER + "]");
            try {
                casStorageService.forceActionOnCas(sd, CORRECTION_USER, (doc, user) -> casStorageService.readCas(doc, user, UNMANAGED_NON_INITIALIZING_ACCESS), // 
                (cas) -> casDoctor.repair(project, cas, messageSet.messages), true);
            } catch (FileNotFoundException e) {
                // If there is no CAS for the correction user, then correction has not started
                // yet. This is not a problem, so we can ignore it. (REC: I wonder if this
                // assumption is correct in curation mode...)
                messageSet.messages.add(LogMessage.info(getClass(), "Correction seems to have not yet started."));
            } catch (Exception e) {
                messageSet.messages.add(new LogMessage(getClass(), LogLevel.ERROR, "Error checking annotations for [" + CORRECTION_USER + "] for [" + sd.getName() + "]: " + e.getMessage()));
                LOG.error("Error checking annotations for [{}] for [{}]", CORRECTION_USER, sd.getName(), e);
            }
            noticeIfThereAreNoMessages(messageSet);
            formModel.messageSets.add(messageSet);
        }
        // Repair CURATION_USER CAS
        {
            LogMessageSet messageSet = new LogMessageSet(sd.getName() + " [" + CURATION_USER + "]");
            try {
                casStorageService.forceActionOnCas(sd, CURATION_USER, (doc, user) -> casStorageService.readCas(doc, user, UNMANAGED_NON_INITIALIZING_ACCESS), // 
                (cas) -> casDoctor.repair(project, cas, messageSet.messages), true);
            } catch (FileNotFoundException e) {
                if (asList(CURATION_IN_PROGRESS, CURATION_FINISHED).contains(sd.getState())) {
                    messageSet.messages.add(LogMessage.error(getClass(), "Curation CAS missing."));
                } else {
                    // If there is no CAS for the curation user, then curation has not started
                    // yet. This is not a problem, so we can ignore it.
                    messageSet.messages.add(LogMessage.info(getClass(), "Curation has not started."));
                }
            } catch (Exception e) {
                messageSet.messages.add(new LogMessage(getClass(), LogLevel.ERROR, "Error checking annotations for [" + CURATION_USER + "] for [" + sd.getName() + "]: " + e.getMessage()));
                LOG.error("Error checking annotations for [{}] for [{}]", CURATION_USER, sd.getName(), e);
            }
            noticeIfThereAreNoMessages(messageSet);
            formModel.messageSets.add(messageSet);
        }
        // Repair regular annotator CASes
        for (AnnotationDocument ad : documentService.listAnnotationDocuments(sd)) {
            if (documentService.existsAnnotationCas(ad)) {
                LogMessageSet messageSet = new LogMessageSet(sd.getName() + " [" + ad.getUser() + "]");
                try {
                    casStorageService.forceActionOnCas(sd, ad.getUser(), (doc, user) -> casStorageService.readCas(doc, user, UNMANAGED_NON_INITIALIZING_ACCESS), // 
                    (cas) -> casDoctor.repair(project, cas, messageSet.messages), true);
                } catch (Exception e) {
                    messageSet.messages.add(new LogMessage(getClass(), LogLevel.ERROR, "Error repairing annotations of user [" + ad.getUser() + "] for [" + sd.getName() + "]: " + e.getMessage()));
                    LOG.error("Error repairing annotations of user [{}] for [{}]", ad.getUser(), sd.getName(), e);
                }
                noticeIfThereAreNoMessages(messageSet);
                formModel.messageSets.add(messageSet);
            }
        }
    }
    aTarget.add(this);
}