Examples with CodeSystem com.b2international.snowowl.core.codesystem.CodeSystem used on opensource projects

Example 41 with CodeSystem

use of com.b2international.snowowl.core.codesystem.CodeSystem 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 42 with CodeSystem

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

the class SnomedExtensionUpgradeTest method upgrade10DonatedConceptAndDescriptionsAndRelationships.

@Test
public void upgrade10DonatedConceptAndDescriptionsAndRelationships() {
    // create extension on the latest SI VERSION
    CodeSystem extension = createExtension(latestInternationalVersion, branchPath.lastSegment());
    String extensionModuleId = createModule(extension);
    String extensionFsnTerm = "FSN of concept";
    String extensionPtTerm = "PT of concept";
    String extensionSynonymTerm = "Synonym of extension concept";
    Json fsnRequestBody = Json.object("typeId", Concepts.FULLY_SPECIFIED_NAME, "term", extensionFsnTerm, "languageCode", DEFAULT_LANGUAGE_CODE, "acceptability", SnomedApiTestConstants.UK_PREFERRED_MAP);
    Json ptRequestBody = Json.object("typeId", Concepts.SYNONYM, "term", extensionPtTerm, "languageCode", DEFAULT_LANGUAGE_CODE, "acceptability", SnomedApiTestConstants.UK_PREFERRED_MAP);
    Json synonymRequestBody = Json.object("typeId", Concepts.SYNONYM, "term", extensionSynonymTerm, "languageCode", DEFAULT_LANGUAGE_CODE, "acceptability", SnomedApiTestConstants.UK_ACCEPTABLE_MAP);
    Json statedIsa = Json.object("typeId", Concepts.IS_A, "destinationId", Concepts.ROOT_CONCEPT, "characteristicTypeId", Concepts.STATED_RELATIONSHIP);
    Json inferredIsa = Json.object("typeId", Concepts.IS_A, "destinationId", Concepts.ROOT_CONCEPT, "characteristicTypeId", Concepts.INFERRED_RELATIONSHIP);
    Json extensionConceptRequestBody = Json.object("namespaceId", Concepts.B2I_NAMESPACE, "moduleId", extensionModuleId, "descriptions", Json.array(fsnRequestBody, ptRequestBody, synonymRequestBody), "relationships", Json.array(statedIsa, inferredIsa));
    String extensionConceptId = createConcept(extension.getResourceURI(), extensionConceptRequestBody);
    // create new extension version
    createVersion(extension.getId(), "v1", LocalDate.now()).statusCode(201);
    SnomedConcept extensionConcept = getConcept(extension.getResourceURI(), extensionConceptId, "descriptions()", "relationships()");
    String extensionFsnId = getFirstMatchingDescription(extensionConcept, extensionFsnTerm).getId();
    String extensionPtId = getFirstMatchingDescription(extensionConcept, extensionPtTerm).getId();
    String extensionSynonymId = getFirstMatchingDescription(extensionConcept, extensionSynonymTerm).getId();
    String extensionStatedIsaId = getFirstRelationshipId(extensionConcept, Concepts.STATED_RELATIONSHIP);
    String extensionInferredIsaId = getFirstRelationshipId(extensionConcept, Concepts.INFERRED_RELATIONSHIP);
    // simulate donation via concept create and versioning
    // create INT concept with same ID and with same description and relationship IDs
    String intConceptId = createConcept(SnomedContentRule.SNOMEDCT, Json.object("id", extensionConceptId, "moduleId", Concepts.MODULE_SCT_CORE, "descriptions", Json.array(fsnRequestBody.with("id", extensionFsnId), ptRequestBody.with("id", extensionPtId)), "relationships", Json.array(statedIsa.with("id", extensionStatedIsaId), inferredIsa.with("id", extensionInferredIsaId))));
    LocalDate effectiveTime = getNextAvailableEffectiveDate(SNOMEDCT);
    createVersion(SNOMEDCT, effectiveTime).statusCode(201);
    // start upgrade to the new available upgrade version
    CodeSystem upgradeCodeSystem = createExtensionUpgrade(extension.getResourceURI(), CodeSystem.uri(SNOMEDCT, effectiveTime.toString()));
    SnomedConcept donatedConceptInExtension = getConcept(upgradeCodeSystem.getResourceURI(), intConceptId, "descriptions()", "relationships()");
    // validate components of donated concept on extension branch
    // same ID, different module
    assertEquals(donatedConceptInExtension.getId(), extensionConcept.getId());
    assertNotEquals(donatedConceptInExtension.getModuleId(), extensionConcept.getModuleId());
    SnomedDescription donatedFsn = getFirstMatchingDescription(donatedConceptInExtension, extensionFsnTerm);
    assertEquals(extensionFsnId, donatedFsn.getId());
    assertEquals(Concepts.MODULE_SCT_CORE, donatedFsn.getModuleId());
    SnomedDescription donatedPt = getFirstMatchingDescription(donatedConceptInExtension, extensionPtTerm);
    assertEquals(extensionPtId, donatedPt.getId());
    assertEquals(Concepts.MODULE_SCT_CORE, donatedPt.getModuleId());
    Set<String> descriptionIds = donatedConceptInExtension.getDescriptions().getItems().stream().map(SnomedDescription::getId).collect(Collectors.toSet());
    assertThat(descriptionIds).hasSize(3).contains(extensionSynonymId);
    Set<String> relationshipIds = donatedConceptInExtension.getRelationships().getItems().stream().map(SnomedRelationship::getId).collect(Collectors.toSet());
    assertThat(relationshipIds).hasSize(2).contains(extensionStatedIsaId, extensionInferredIsaId);
}

Example 43 with CodeSystem

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

the class SnomedComponentRevisionConflictProcessor method filterConflicts.

/**
 * Detects SNOMED CT specific donation patterns reported as conflicts during merge/upgrade. This works between any two branches, not just during upgrades so custom branch management is also supported (although not recommended).
 * <p>
 * {@inheritDoc}
 * </p>
 */
@Override
public List<Conflict> filterConflicts(StagingArea staging, List<Conflict> conflicts) {
    // skip if not merging content and if there is no conflicts
    if (!staging.isMerge() || CompareUtils.isEmpty(conflicts)) {
        return conflicts;
    }
    RepositoryContext context = (RepositoryContext) staging.getContext();
    // detect if we are merging content between two CodeSystems, if not skip donation check
    // get the two CodeSystems
    String extensionBranch = staging.getMergeFromBranchPath();
    String donationBranch = staging.getBranchPath();
    CodeSystem extensionCodeSystem = context.service(PathTerminologyResourceResolver.class).resolve(context, context.info().id(), extensionBranch);
    CodeSystem donationCodeSystem = context.service(PathTerminologyResourceResolver.class).resolve(context, context.info().id(), donationBranch);
    // extensionOf is a required property for Code Systems that would like to participate in content donation
    if (extensionCodeSystem.getExtensionOf() == null || !extensionCodeSystem.getExtensionOf().getResourceId().equals(donationCodeSystem.getId())) {
        return conflicts;
    }
    final Multimap<Class<?>, String> donatedComponentsByType = HashMultimap.create();
    // collect components from known donation conflicts
    for (Conflict conflict : conflicts) {
        ObjectId objectId = conflict.getObjectId();
        // - components that have been added on both paths are potential donation candidates (due to centralized ID management (CIS), ID collision should not happen under normal circumstances, so this is certainly a donated content)
        if (conflict instanceof AddedInSourceAndTargetConflict) {
            donatedComponentsByType.put(staging.mappings().getClass(objectId.type()), objectId.id());
        } else if (conflict instanceof ChangedInSourceAndTargetConflict) {
            // always ignore effective time and module differences
            ChangedInSourceAndTargetConflict changedInSourceAndTarget = (ChangedInSourceAndTargetConflict) conflict;
            if (SnomedRf2Headers.FIELD_EFFECTIVE_TIME.equals(changedInSourceAndTarget.getSourceChange().getProperty()) || SnomedRf2Headers.FIELD_MODULE_ID.equals(changedInSourceAndTarget.getSourceChange().getProperty())) {
                donatedComponentsByType.put(staging.mappings().getClass(objectId.type()), objectId.id());
            }
        }
    }
    // collect donations
    final Set<String> donatedComponentIds = Sets.newHashSet();
    donatedComponentIds.addAll(collectDonatedComponents(staging, donatedComponentsByType, SnomedConceptDocument.class, CONCEPT_FIELDS_TO_LOAD));
    donatedComponentIds.addAll(collectDonatedComponents(staging, donatedComponentsByType, SnomedDescriptionIndexEntry.class, DESCRIPTION_FIELDS_TO_LOAD));
    donatedComponentIds.addAll(collectDonatedComponents(staging, donatedComponentsByType, SnomedRelationshipIndexEntry.class, RELATIONSHIP_FIELDS_TO_LOAD));
    donatedComponentIds.addAll(collectDonatedComponents(staging, donatedComponentsByType, SnomedRefSetMemberIndexEntry.class, MEMBER_FIELDS_TO_LOAD));
    return conflicts.stream().filter(conflict -> {
        ObjectId objectId = conflict.getObjectId();
        if (donatedComponentIds.contains(objectId.id())) {
            // filter out all conflicts reported around donated content
            // revise all donated content on merge source, so new parent revision will take place instead
            staging.reviseOnMergeSource(staging.mappings().getClass(objectId.type()), objectId.id());
            return false;
        } else {
            return true;
        }
    }).collect(Collectors.toList());
}

Example 44 with CodeSystem

use of com.b2international.snowowl.core.codesystem.CodeSystem 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 CodeSystem

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

the class ResourceApiTest method createdAtAndUpdatedAt.

@Test
public void createdAtAndUpdatedAt() throws Exception {
    createDefaultCodeSystem(DEFAULT_CODE_SYSTEM_SHORT_NAME, DEFAULT_CODE_SYSTEM_OID);
    // assert that createdAt and updatedAt values are the same after create
    CodeSystem createdCodeSystem = assertResourceGet(DEFAULT_CODE_SYSTEM_SHORT_NAME).statusCode(200).extract().as(CodeSystem.class);
    assertEquals(createdCodeSystem.getCreatedAt(), createdCodeSystem.getUpdatedAt());
    CommitResult updateResult = CodeSystemRequests.prepareUpdateCodeSystem(DEFAULT_CODE_SYSTEM_SHORT_NAME).setCopyright("Updated copyright").build(RestExtensions.USER, String.format("Updated copyright %s", DEFAULT_CODE_SYSTEM_SHORT_NAME)).execute(bus).getSync();
    // assert that createdAt and updatedAt values are the same after create
    CodeSystem updatedCodeSystem = assertResourceGet(DEFAULT_CODE_SYSTEM_SHORT_NAME).statusCode(200).extract().as(CodeSystem.class);
    // createdAt stays as is, but updatedAt got updated to a time after the marked value
    assertEquals(createdCodeSystem.getCreatedAt(), updatedCodeSystem.getCreatedAt());
    assertEquals((Long) updateResult.getCommitTimestamp(), updatedCodeSystem.getUpdatedAt());
}