Examples with ResourceURI com.b2international.snowowl.core.ResourceURI used on opensource projects

Example 41 with ResourceURI

use of com.b2international.snowowl.core.ResourceURI in project snow-owl by b2ihealthcare.

the class SnomedExtensionUpgradeTest method upgrade17UpgradeFromCodeSystemVersionWithPublishedChanges.

@Test
public void upgrade17UpgradeFromCodeSystemVersionWithPublishedChanges() {
    // create extension on the latest SI VERSION
    CodeSystem extension = createExtension(latestInternationalVersion, branchPath.lastSegment());
    // new SI concept
    String newConceptId = createConcept(SnomedContentRule.SNOMEDCT, createConceptRequestBody(Concepts.ROOT_CONCEPT, Concepts.MODULE_SCT_CORE));
    // create a new INT version
    LocalDate effectiveDate = getNextAvailableEffectiveDate(SNOMEDCT);
    createVersion(SNOMEDCT, effectiveDate).statusCode(201);
    ResourceURI upgradeVersion = CodeSystem.uri(SNOMEDCT, effectiveDate.toString());
    // new SE concept
    String extensionModuleId = createModule(extension);
    String newConceptId2 = createConcept(extension.getResourceURI(), createConceptRequestBody(Concepts.ROOT_CONCEPT, extensionModuleId));
    // version extension
    LocalDate effectiveDate2 = getNextAvailableEffectiveDate(extension.getId());
    createVersion(extension.getId(), effectiveDate2).statusCode(201);
    ResourceURI extensionVersion = CodeSystem.uri(extension.getId(), effectiveDate2.toString());
    // start upgrade to the new available upgrade version
    CodeSystem upgradeCodeSystem = createExtensionUpgrade(extensionVersion, upgradeVersion);
    assertEquals(upgradeVersion, upgradeCodeSystem.getExtensionOf());
    getComponent(upgradeCodeSystem.getResourceURI(), SnomedComponentType.CONCEPT, newConceptId).statusCode(200);
    getComponent(upgradeCodeSystem.getResourceURI(), SnomedComponentType.CONCEPT, newConceptId2).statusCode(200);
}

Example 42 with ResourceURI

use of com.b2international.snowowl.core.ResourceURI in project snow-owl by b2ihealthcare.

the class SnomedExtensionUpgradeTest method upgrade20ExpandUpgradeInfo.

@Test
public void upgrade20ExpandUpgradeInfo() throws Exception {
    // create extension on the latest SI VERSION
    CodeSystem extension = createExtension(latestInternationalVersion, branchPath.lastSegment());
    // new SI concept
    createConcept(SnomedContentRule.SNOMEDCT, createConceptRequestBody(Concepts.ROOT_CONCEPT, Concepts.MODULE_SCT_CORE));
    // create a new INT version
    LocalDate effectiveDate = getNextAvailableEffectiveDate(SNOMEDCT);
    createVersion(SNOMEDCT, effectiveDate).statusCode(201);
    ResourceURI upgradeVersion = CodeSystem.uri(SNOMEDCT, effectiveDate.toString());
    // new SE concept
    String extensionModuleId = createModule(extension);
    createConcept(extension.getResourceURI(), createConceptRequestBody(Concepts.ROOT_CONCEPT, extensionModuleId));
    // version extension
    LocalDate effectiveDate2 = LocalDate.now();
    createVersion(extension.getId(), effectiveDate2).statusCode(201);
    ResourceURI extensionVersion = CodeSystem.uri(extension.getId(), effectiveDate2.toString());
    // new SE concept
    createConcept(extension.getResourceURI(), createConceptRequestBody(Concepts.ROOT_CONCEPT, extensionModuleId));
    // version extension
    LocalDate effectiveDate3 = getNextAvailableEffectiveDate(extension.getId());
    createVersion(extension.getId(), effectiveDate3).statusCode(201);
    ResourceURI extensionVersion2 = CodeSystem.uri(extension.getId(), effectiveDate3.toString());
    // start upgrade to the new available upgrade version
    CodeSystem upgradeCodeSystem = createExtensionUpgrade(extensionVersion, upgradeVersion);
    CodeSystems expandedCodeSystems = CodeSystemRestRequests.search(upgradeCodeSystem.getId(), CodeSystem.Expand.UPGRADE_INFO + "()");
    assertEquals(upgradeVersion, upgradeCodeSystem.getExtensionOf());
    assertThat(expandedCodeSystems.first().get().getUpgradeInfo().getAvailableVersions()).doesNotContainSequence(extensionVersion);
    assertThat(expandedCodeSystems.first().get().getUpgradeInfo().getAvailableVersions()).contains(extensionVersion2);
}

Example 43 with ResourceURI

use of com.b2international.snowowl.core.ResourceURI in project snow-owl by b2ihealthcare.

the class SnomedVersioningApiTest method forceCreateVersionShouldUpdateEffectiveTime.

@Test
public void forceCreateVersionShouldUpdateEffectiveTime() {
    final String versionName = "forceCreateVersionShouldUpdateEffectiveTime";
    ResourceURI codeSystemVersionURI = SnomedContentRule.SNOMEDCT.withPath(versionName);
    LocalDate versionEffectiveDate = getNextAvailableEffectiveDate(INT_CODESYSTEM);
    createVersion(INT_CODESYSTEM, versionName, versionEffectiveDate).statusCode(201);
    String conceptId = createConcept(SnomedContentRule.SNOMEDCT, SnomedRestFixtures.childUnderRootWithDefaults());
    SnomedConcept afterFailedVersioning = getConcept(SnomedContentRule.SNOMEDCT, conceptId);
    assertEquals(null, afterFailedVersioning.getEffectiveTime());
    // Should succeed to recreate version with the force flag set
    createVersion(INT_CODESYSTEM, versionName, versionEffectiveDate, true).statusCode(201);
    SnomedConcept afterForceVersioning = getConcept(codeSystemVersionURI, conceptId);
    assertEquals(versionEffectiveDate, afterForceVersioning.getEffectiveTime());
}

Example 44 with ResourceURI

use of com.b2international.snowowl.core.ResourceURI in project snow-owl by b2ihealthcare.

the class SnomedRf2ExportRequest method collectExportableCodeSystemVersions.

private void collectExportableCodeSystemVersions(final RepositoryContext context, final Set<Version> versionsToExport, final TerminologyResource codeSystem, final String referenceBranch) {
    final List<Version> candidateVersions = newArrayList(getCodeSystemVersions(context, codeSystem.getResourceURI()));
    if (candidateVersions.isEmpty()) {
        return;
    }
    final Set<String> versionPaths = candidateVersions.stream().map(Version::getBranchPath).collect(Collectors.toSet());
    final Branches versionBranches = getBranches(context, versionPaths);
    final Map<String, Branch> versionBranchesByPath = Maps.uniqueIndex(versionBranches, Branch::path);
    // cutoff timestamp represents the timestamp on the current referenceBranch segments, cutting off any versions created after this timestamp
    final Branch cutoffBranch = getBranch(context, referenceBranch);
    final String latestVersionParentBranch = candidateVersions.stream().findFirst().map(v -> BranchPathUtils.createPath(v.getBranchPath()).getParentPath()).get();
    final long cutoffBaseTimestamp = getCutoffBaseTimestamp(context, cutoffBranch, latestVersionParentBranch);
    // Remove all code system versions which were created after the cut-off date, or don't have a corresponding branch
    candidateVersions.removeIf(v -> false || !versionBranchesByPath.containsKey(v.getBranchPath()) || versionBranchesByPath.get(v.getBranchPath()).baseTimestamp() > cutoffBaseTimestamp);
    versionsToExport.addAll(candidateVersions);
    // Exit early if only an extension code system should be exported, or we are already at the "base" code system
    final ResourceURI extensionOfUri = codeSystem.getExtensionOf();
    if (extensionOnly || extensionOfUri == null) {
        return;
    }
    // Otherwise, collect applicable versions using this code system's working path
    final CodeSystem extensionOfCodeSystem = CodeSystemRequests.prepareGetCodeSystem(extensionOfUri.getResourceId()).buildAsync().execute(context);
    collectExportableCodeSystemVersions(context, versionsToExport, extensionOfCodeSystem, codeSystem.getBranchPath());
}

Example 45 with ResourceURI

use of com.b2international.snowowl.core.ResourceURI 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());
    }
}