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

Example 11 with SnomedConcepts

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

the class SnomedSimpleTypeRefSetDSVExporter method writeValues.

private void writeValues(IProgressMonitor monitor, BufferedWriter writer) throws IOException {
    SearchResourceRequestIterator<SnomedConceptSearchRequestBuilder, SnomedConcepts> conceptIterator = getMemberConceptIterator(DATA_EXPAND);
    while (conceptIterator.hasNext()) {
        SnomedConcepts chunk = conceptIterator.next();
        writeValues(writer, chunk);
        monitor.worked(chunk.getItems().size());
    }
}

Example 12 with SnomedConcepts

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

the class SnomedQueryMemberCreateDelegate method createWithNewRefSet.

private String createWithNewRefSet(SnomedReferenceSet refSet, TransactionContext context) {
    checkNonEmptyProperty(REFERENCED_COMPONENT);
    checkComponentExists(refSet, context, SnomedRf2Headers.FIELD_MODULE_ID, getModuleId());
    // create new simple type reference set
    final SnomedConcept referencedComponent = getProperty(REFERENCED_COMPONENT, SnomedConcept.class);
    final String referencedComponentId = new IdRequest<>(referencedComponent.toCreateRequest()).execute(context);
    // write the generated ID back to the request
    setReferencedComponentId(referencedComponentId);
    // add all matching members
    final SnomedConcepts queryResults = SnomedRequests.prepareSearchConcept().all().filterByEcl(getProperty(SnomedRf2Headers.FIELD_QUERY)).build().execute(context);
    for (SnomedConcept queryResult : queryResults) {
        SnomedComponents.newSimpleMember().withActive(isActive()).withReferencedComponent(queryResult.getId()).withModuleId(getModuleId()).withRefSet(referencedComponentId).addTo(context);
    }
    return createWithExistingRefSet(refSet, context);
}

Example 13 with SnomedConcepts

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

the class SnomedClassificationApiTest method issue_SO_1830_testInferredEquivalentConceptParents.

@Test
public void issue_SO_1830_testInferredEquivalentConceptParents() throws Exception {
    String parentConceptId = createNewConcept(branchPath);
    String childConceptId = createNewConcept(branchPath, parentConceptId);
    String equivalentConceptId = createNewConcept(branchPath, parentConceptId);
    changeToDefining(branchPath, equivalentConceptId);
    String classificationId = getClassificationJobId(beginClassification(branchPath));
    waitForClassificationJob(branchPath, classificationId).statusCode(200).body("status", equalTo(ClassificationStatus.COMPLETED.name()));
    /* 
		 * Expecting that childConceptId will get two inferred IS A-s pointing to parentConceptId and equivalentConceptId, respectively, 
		 * while parentConceptId and equivalentConceptId each will get a single inferred IS A pointing to the root concept.
		 */
    RelationshipChanges changes = MAPPER.readValue(getRelationshipChanges(branchPath, classificationId).statusCode(200).extract().asInputStream(), RelationshipChanges.class);
    FluentIterable<RelationshipChange> changesIterable = FluentIterable.from(changes.getItems());
    assertEquals(4, changes.getTotal());
    assertTrue("All changes should be inferred.", changesIterable.allMatch(relationshipChange -> ChangeNature.NEW.equals(relationshipChange.getChangeNature())));
    assertInferredIsAExists(changesIterable, childConceptId, parentConceptId);
    assertInferredIsAExists(changesIterable, childConceptId, equivalentConceptId);
    assertInferredIsAExists(changesIterable, parentConceptId, Concepts.ROOT_CONCEPT);
    assertInferredIsAExists(changesIterable, equivalentConceptId, Concepts.ROOT_CONCEPT);
    EquivalentConceptSets equivalentConceptSets = MAPPER.readValue(getEquivalentConceptSets(branchPath, classificationId).statusCode(200).extract().asInputStream(), EquivalentConceptSets.class);
    assertEquals(1, equivalentConceptSets.getItems().size());
    SnomedConcepts equivalentConceptsInFirstSet = equivalentConceptSets.first().get().getEquivalentConcepts();
    FluentIterable<SnomedConcept> equivalentConceptsIterable = FluentIterable.from(equivalentConceptsInFirstSet);
    assertEquals(2, equivalentConceptsInFirstSet.getTotal());
    assertEquivalentConceptPresent(equivalentConceptsIterable, parentConceptId);
    assertEquivalentConceptPresent(equivalentConceptsIterable, equivalentConceptId);
}

Example 14 with SnomedConcepts

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

the class SnomedConceptSearchApiTest method searchByMembership.

@Test
public void searchByMembership() throws Exception {
    String conceptId1 = createNewConcept(branchPath, Concepts.ROOT_CONCEPT);
    String conceptId2 = createNewConcept(branchPath, Concepts.ROOT_CONCEPT);
    String refSetId = createNewRefSet(branchPath, SnomedRefSetType.SIMPLE);
    String memberId1 = createNewRefSetMember(branchPath, conceptId1, refSetId);
    createNewRefSetMember(branchPath, conceptId2, refSetId);
    updateComponent(branchPath, SnomedComponentType.MEMBER, memberId1, Json.object("active", false, "commitComment", "Inactivated reference set member")).statusCode(204);
    SnomedConcepts hits = givenAuthenticatedRequest(getApiBaseUrl()).accept(JSON_UTF8).queryParams(Map.of("isActiveMemberOf", List.of(refSetId))).get("/{path}/concepts/", branchPath.getPath()).then().assertThat().statusCode(200).extract().as(SnomedConcepts.class);
    assertThat(hits.getTotal()).isEqualTo(1);
}

Example 15 with SnomedConcepts

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

the class SnomedConceptSearchApiTest method searchByNamespace.

@Test
public void searchByNamespace() throws Exception {
    String conceptId = createNewConcept(branchPath, createConceptRequestBody(Concepts.ROOT_CONCEPT).with("namespaceId", "1000001").with("commitComment", "Create new concept"));
    SnomedConcepts hits = givenAuthenticatedRequest(getApiBaseUrl()).accept(JSON_UTF8).queryParams(Map.of("namespace", List.of("1000001"))).get("/{path}/concepts/", branchPath.getPath()).then().assertThat().statusCode(200).extract().as(SnomedConcepts.class);
    assertThat(hits.getTotal()).isEqualTo(1);
    assertThat(hits.getItems()).allMatch(c -> conceptId.equals(c.getId()));
}