Examples with Rf2GlobalValidator com.b2international.snowowl.snomed.datastore.request.rf2.validation.Rf2GlobalValidator used on opensource projects

Example 1 with Rf2GlobalValidator

use of com.b2international.snowowl.snomed.datastore.request.rf2.validation.Rf2GlobalValidator 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());
    }
}