Examples with SnomedReferenceSetMember com.b2international.snowowl.snomed.core.domain.refset.SnomedReferenceSetMember used on opensource projects

Example 31 with SnomedReferenceSetMember

use of com.b2international.snowowl.snomed.core.domain.refset.SnomedReferenceSetMember in project snow-owl by b2ihealthcare.

the class SnomedRf2ExportRequest method getLatestModuleEffectiveTime.

private Optional<LocalDate> getLatestModuleEffectiveTime(final RepositoryContext context, final Version version, String field) {
    SnomedRefSetMemberSearchRequestBuilder requestBuilder = SnomedRequests.prepareSearchMember().filterByRefSet(Concepts.REFSET_MODULE_DEPENDENCY_TYPE).filterByActive(true).sortBy(Sort.fieldDesc(field)).setLimit(1);
    // See the comment in setModules; a value of "null" means that all modules should be exported
    if (modules != null) {
        requestBuilder.filterByModules(modules);
    }
    final Optional<SnomedReferenceSetMember> moduleDependencyMember = requestBuilder.build(version.getVersionResourceURI()).execute(context.service(IEventBus.class)).getSync(1, TimeUnit.MINUTES).first();
    return moduleDependencyMember.map(m -> {
        return (LocalDate) m.getProperties().get(field);
    });
}

Example 32 with SnomedReferenceSetMember

use of com.b2international.snowowl.snomed.core.domain.refset.SnomedReferenceSetMember in project snow-owl by b2ihealthcare.

the class SnomedDescriptionApiTest method updateInactivationIndicatorOnActiveReleasedDescription.

@Test
public void updateInactivationIndicatorOnActiveReleasedDescription() throws Exception {
    String descriptionToInactivate = createNewDescription(branchPath);
    assertInactivation(branchPath, descriptionToInactivate, new InactivationProperties(Concepts.PENDING_MOVE, Collections.emptyList()));
    // release component
    createCodeSystemAndVersion(branchPath, "SNOMEDCT-RELDESC-INACTIVATIONINDICATOR", "v1", LocalDate.parse("2018-07-01"));
    SnomedDescription description = assertInactivation(branchPath, descriptionToInactivate, new InactivationProperties(Concepts.CONCEPT_NON_CURRENT, Collections.emptyList())).extract().as(SnomedDescription.class);
    List<SnomedReferenceSetMember> inactivationIndicators = description.getMembers().stream().filter(member -> Concepts.REFSET_DESCRIPTION_INACTIVITY_INDICATOR.equals(member.getRefsetId())).collect(Collectors.toList());
    final SnomedReferenceSetMember inactivationIndicator = Iterables.getOnlyElement(inactivationIndicators);
    assertEquals(Concepts.CONCEPT_NON_CURRENT, inactivationIndicator.getProperties().get(SnomedRf2Headers.FIELD_VALUE_ID));
    assertNull(inactivationIndicator.getEffectiveTime());
}

Example 33 with SnomedReferenceSetMember

use of com.b2international.snowowl.snomed.core.domain.refset.SnomedReferenceSetMember in project snow-owl by b2ihealthcare.

the class SnomedDescriptionApiTest method testDuplicateMemberCleanupEmptiesAcceptabilityMap.

@Test
public void testDuplicateMemberCleanupEmptiesAcceptabilityMap() throws Exception {
    String descriptionId = createNewDescription(branchPath);
    // Inject inactive language member with different acceptability (API won't allow it)
    String memberIdToUpdate = UUID.randomUUID().toString();
    SnomedRefSetMemberIndexEntry member = SnomedRefSetMemberIndexEntry.builder().id(memberIdToUpdate).active(false).released(false).moduleId(Concepts.MODULE_SCT_CORE).refsetId(Concepts.REFSET_LANGUAGE_TYPE_UK).referencedComponentId(descriptionId).referenceSetType(SnomedRefSetType.LANGUAGE).field(SnomedRf2Headers.FIELD_ACCEPTABILITY_ID, Concepts.REFSET_DESCRIPTION_ACCEPTABILITY_PREFERRED).build();
    new RepositoryRequest<>(SnomedTerminologyComponentConstants.TOOLING_ID, context -> {
        ApplicationContext.getServiceForClass(RepositoryManager.class).get(SnomedTerminologyComponentConstants.TOOLING_ID).service(RevisionIndex.class).prepareCommit(branchPath.getPath()).stageNew(member).withContext(context.inject().bind(ModuleIdProvider.class, c -> c.getModuleId()).build()).commit(ApplicationContext.getServiceForClass(TimestampProvider.class).getTimestamp(), "test", "Added duplicate language reference set member to " + descriptionId);
        return null;
    }).execute(ApplicationContext.getServiceForClass(Environment.class));
    // Check the acceptability map; the description should be acceptable in the UK reference set
    SnomedDescription description = getComponent(branchPath, SnomedComponentType.DESCRIPTION, descriptionId, "members()").statusCode(200).extract().as(SnomedDescription.class);
    assertEquals(Acceptability.ACCEPTABLE, description.getAcceptabilityMap().get(Concepts.REFSET_LANGUAGE_TYPE_UK));
    assertEquals(2, description.getMembers().getTotal());
    String memberIdToDelete = null;
    for (SnomedReferenceSetMember descriptionMember : description.getMembers()) {
        if (Concepts.REFSET_DESCRIPTION_ACCEPTABILITY_ACCEPTABLE.equals(descriptionMember.getProperties().get(SnomedRf2Headers.FIELD_ACCEPTABILITY_ID))) {
            memberIdToDelete = descriptionMember.getId();
            break;
        }
    }
    assertNotNull(memberIdToDelete);
    // Using bulk update, remove the currently active member and activate the inactive one, also changing its acceptability
    Json bulkRequest = Json.object("requests", Json.array(Json.object("action", "delete", "memberId", memberIdToDelete), Json.object("action", "update", "memberId", memberIdToUpdate, "active", true, "acceptabilityId", Concepts.REFSET_DESCRIPTION_ACCEPTABILITY_ACCEPTABLE)), "commitComment", "Consolidated language reference set members");
    bulkUpdateMembers(branchPath, Concepts.REFSET_LANGUAGE_TYPE_UK, bulkRequest).statusCode(204);
    // Verify that description acceptability is still acceptable, but only one member remains
    SnomedDescription newDescription = getComponent(branchPath, SnomedComponentType.DESCRIPTION, descriptionId, "members()").statusCode(200).extract().as(SnomedDescription.class);
    assertEquals(Acceptability.ACCEPTABLE, newDescription.getAcceptabilityMap().get(Concepts.REFSET_LANGUAGE_TYPE_UK));
    assertEquals(1, newDescription.getMembers().getTotal());
    SnomedReferenceSetMember languageMember = Iterables.getOnlyElement(newDescription.getMembers());
    assertEquals(memberIdToUpdate, languageMember.getId());
    assertEquals(true, languageMember.isActive());
}

Example 34 with SnomedReferenceSetMember

use of com.b2international.snowowl.snomed.core.domain.refset.SnomedReferenceSetMember in project snow-owl by b2ihealthcare.

the class SnomedDescriptionApiTest method updateAcceptabilityWithRemove.

@Test
public void updateAcceptabilityWithRemove() throws Exception {
    changeToAcceptable(branchPath, Concepts.ROOT_CONCEPT, Concepts.REFSET_LANGUAGE_TYPE_US);
    String descriptionId = createNewDescription(branchPath, Concepts.ROOT_CONCEPT, Concepts.SYNONYM, Map.<String, Acceptability>of(Concepts.REFSET_LANGUAGE_TYPE_UK, Acceptability.ACCEPTABLE, Concepts.REFSET_LANGUAGE_TYPE_US, Acceptability.PREFERRED));
    Json requestBody = Json.object("acceptability", Json.object(Concepts.REFSET_LANGUAGE_TYPE_UK, Acceptability.ACCEPTABLE), "commitComment", "Removed US preferred acceptability from description");
    updateComponent(branchPath, SnomedComponentType.DESCRIPTION, descriptionId, requestBody).statusCode(204);
    SnomedReferenceSetMembers members = getComponent(branchPath, SnomedComponentType.DESCRIPTION, descriptionId, "members()").statusCode(200).extract().as(SnomedDescription.class).getMembers();
    assertEquals(1, members.getTotal());
    SnomedReferenceSetMember member = Iterables.getOnlyElement(members);
    assertEquals(Concepts.REFSET_LANGUAGE_TYPE_UK, member.getRefsetId());
    assertEquals(Concepts.REFSET_DESCRIPTION_ACCEPTABILITY_ACCEPTABLE, member.getProperties().get(SnomedRf2Headers.FIELD_ACCEPTABILITY_ID));
}

Example 35 with SnomedReferenceSetMember

use of com.b2international.snowowl.snomed.core.domain.refset.SnomedReferenceSetMember in project snow-owl by b2ihealthcare.

the class SnomedConceptApiTest method addMemberViaConceptUpdate.

@Test
public void addMemberViaConceptUpdate() throws Exception {
    final String refSetId = createNewRefSet(branchPath);
    final String conceptId = createNewConcept(branchPath);
    SnomedConcept concept = getComponent(branchPath, SnomedComponentType.CONCEPT, conceptId, "members()").statusCode(200).extract().as(SnomedConcept.class);
    assertEquals(0, concept.getMembers().getTotal());
    // Add a reference set member
    SnomedReferenceSetMember newMember = new SnomedReferenceSetMember();
    newMember.setId(UUID.randomUUID().toString());
    newMember.setActive(true);
    newMember.setRefsetId(refSetId);
    newMember.setModuleId(Concepts.MODULE_SCT_CORE);
    final List<SnomedReferenceSetMember> changedMembers = ImmutableList.<SnomedReferenceSetMember>builder().addAll(concept.getMembers()).add(newMember).build();
    final Map<?, ?> updateRequestBody = Json.object("members", SnomedReferenceSetMembers.of(changedMembers), "commitComment", "Add new reference set member via concept update");
    updateComponent(branchPath, SnomedComponentType.CONCEPT, conceptId, updateRequestBody).statusCode(204);
    final SnomedConcept updatedConcept = getComponent(branchPath, SnomedComponentType.CONCEPT, conceptId, "members()").statusCode(200).extract().as(SnomedConcept.class);
    assertEquals(1, updatedConcept.getMembers().getTotal());
}