Examples with ImportDefectAcceptor com.b2international.snowowl.core.request.io.ImportDefectAcceptor used on opensource projects

Example 1 with ImportDefectAcceptor

use of com.b2international.snowowl.core.request.io.ImportDefectAcceptor in project snow-owl by b2ihealthcare.

the class SnomedRf2ImportRequest method readFile.

private void readFile(ZipEntry entry, final InputStream in, final ObjectReader oReader, Rf2EffectiveTimeSlices effectiveTimeSlices, Rf2ValidationIssueReporter reporter) throws IOException, JsonProcessingException {
    final String entryName = entry.getName();
    final ImportDefectAcceptor defectAcceptor = reporter.getDefectAcceptor(entryName);
    boolean header = true;
    Rf2ContentType<?> resolver = null;
    int lineNumber = 1;
    MappingIterator<String[]> mi = oReader.readValues(in);
    while (mi.hasNext()) {
        String[] line = mi.next();
        if (header) {
            for (Rf2ContentType<?> contentType : Rf2Format.getContentTypes()) {
                if (contentType.canResolve(line)) {
                    resolver = contentType;
                    break;
                }
            }
            if (resolver == null) {
                log.warn("Unrecognized RF2 file: {}", entryName);
                break;
            }
            header = false;
        } else {
            final String effectiveTimeKey = getEffectiveTimeKey(line[1]);
            final ImportDefectBuilder defectBuilder = defectAcceptor.on(Integer.toString(lineNumber));
            resolver.register(line, effectiveTimeSlices.getOrCreate(effectiveTimeKey), defectBuilder);
        }
        lineNumber++;
    }
}

Example 2 with ImportDefectAcceptor

use of com.b2international.snowowl.core.request.io.ImportDefectAcceptor in project snow-owl by b2ihealthcare.

the class SnomedRf2ImportRequest method doImport.

ImportResponse doImport(final BranchContext context, final File rf2Archive, final Rf2ImportConfiguration importconfig) throws Exception {
    final ResourceURI codeSystemUri = context.service(ResourceURI.class);
    final Rf2ValidationIssueReporter reporter = new Rf2ValidationIssueReporter();
    String latestVersionEffectiveTime = EffectiveTimes.format(ResourceRequests.prepareSearchVersion().one().filterByResource(codeSystemUri.withoutPath()).sortBy("effectiveTime:desc").buildAsync().execute(context).first().map(Version::getEffectiveTime).orElse(LocalDate.EPOCH), DateFormats.SHORT);
    try (final DB db = createDb()) {
        // Read effective time slices from import files
        final Rf2EffectiveTimeSlices effectiveTimeSlices = new Rf2EffectiveTimeSlices(db, isLoadOnDemandEnabled(), latestVersionEffectiveTime, importUntil == null ? null : EffectiveTimes.format(importUntil, DateFormats.SHORT));
        Stopwatch w = Stopwatch.createStarted();
        read(rf2Archive, effectiveTimeSlices, reporter);
        log.info("Preparing RF2 import took: {}", w);
        w.reset().start();
        // Log issues with rows from the import files
        logValidationIssues(reporter);
        if (reporter.hasErrors()) {
            return ImportResponse.defects(reporter.getDefects());
        }
        // Run validation that takes current terminology content into account
        final List<Rf2EffectiveTimeSlice> orderedEffectiveTimeSlices = effectiveTimeSlices.consumeInOrder();
        final Rf2GlobalValidator globalValidator = new Rf2GlobalValidator(log, ignoreMissingReferencesIn);
        /* 
			 * TODO: Use Attachment to get the release file name and/or track file and line number sources for each row 
			 * so that they can be referenced in this stage as well
			 */
        final ImportDefectAcceptor globalDefectAcceptor = reporter.getDefectAcceptor("RF2 release");
        globalValidator.validateTerminologyComponents(orderedEffectiveTimeSlices, globalDefectAcceptor, context);
        // globalValidator.validateMembers(orderedEffectiveTimeSlices, globalDefectAcceptor, context);
        // Log validation issues (but just the ones found during global validation)
        logValidationIssues(globalDefectAcceptor);
        if (reporter.hasErrors()) {
            return ImportResponse.defects(reporter.getDefects());
        }
        // Import effective time slices in chronological order
        final ImmutableSet.Builder<ComponentURI> visitedComponents = ImmutableSet.builder();
        // if not a dryRun, perform import
        if (!dryRun) {
            // Import effective time slices in chronological order
            for (Rf2EffectiveTimeSlice slice : orderedEffectiveTimeSlices) {
                slice.doImport(context, codeSystemUri, importconfig, visitedComponents);
            }
            // Update locales registered on the code system
            updateCodeSystemSettings(context, codeSystemUri);
        }
        return ImportResponse.success(visitedComponents.build(), reporter.getDefects());
    }
}