Examples with MemberSearchRequest org.snomed.snowstorm.core.data.services.pojo.MemberSearchRequest used on opensource projects

Example 1 with MemberSearchRequest

use of org.snomed.snowstorm.core.data.services.pojo.MemberSearchRequest in project snowstorm by IHTSDO.

the class MRCMLoader method getDomains.

private List<Domain> getDomains(final String branchPath, final BranchCriteria branchCriteria, final TimerUtil timer) {
    List<ReferenceSetMember> domainMembers = memberService.findMembers(branchPath, branchCriteria, new MemberSearchRequest().referenceSet(Concepts.REFSET_MRCM_DOMAIN_INTERNATIONAL), LARGE_PAGE).getContent();
    List<Domain> domains = new ArrayList<>();
    for (ReferenceSetMember member : domainMembers) {
        // proximalPrimitiveConstraint	proximalPrimitiveRefinement	domainTemplateForPrecoordination	domainTemplateForPostcoordination	guideURL
        if (member.isActive()) {
            domains.add(new Domain(member.getMemberId(), member.getEffectiveTime(), member.isActive(), member.getReferencedComponentId(), getConstraint(member, "domainConstraint"), member.getAdditionalField("parentDomain"), getConstraint(member, "proximalPrimitiveConstraint"), member.getAdditionalField("proximalPrimitiveRefinement"), member.getAdditionalField("domainTemplateForPrecoordination"), member.getAdditionalField("domainTemplateForPostcoordination")));
        }
    }
    timer.checkpoint("Load domains");
    return domains;
}

Example 2 with MemberSearchRequest

use of org.snomed.snowstorm.core.data.services.pojo.MemberSearchRequest in project snowstorm by IHTSDO.

the class MRCMLoader method getAttributeDomains.

private List<AttributeDomain> getAttributeDomains(final String branchPath, final BranchCriteria branchCriteria, final TimerUtil timer) throws ServiceException {
    List<ReferenceSetMember> attributeDomainMembers = memberService.findMembers(branchPath, branchCriteria, new MemberSearchRequest().referenceSet(Concepts.REFSET_MRCM_ATTRIBUTE_DOMAIN_INTERNATIONAL), LARGE_PAGE).getContent();
    List<AttributeDomain> attributeDomains = new ArrayList<>();
    for (ReferenceSetMember member : attributeDomainMembers) {
        // grouped	attributeCardinality	attributeInGroupCardinality	ruleStrengthId	contentTypeId
        if (member.isActive()) {
            attributeDomains.add(new AttributeDomain(member.getMemberId(), member.getEffectiveTime(), member.isActive(), member.getReferencedComponentId(), member.getAdditionalField("domainId"), "1".equals(member.getAdditionalField("grouped")), new Cardinality(member.getAdditionalField("attributeCardinality")), new Cardinality(member.getAdditionalField("attributeInGroupCardinality")), RuleStrength.lookupByConceptId(member.getAdditionalField("ruleStrengthId")), ContentType.lookupByConceptId(member.getAdditionalField("contentTypeId"))));
        }
    }
    timer.checkpoint("Load attribute domains");
    return attributeDomains;
}

Example 3 with MemberSearchRequest

use of org.snomed.snowstorm.core.data.services.pojo.MemberSearchRequest in project snowstorm by IHTSDO.

the class MRCMLoader method getAttributeRanges.

private List<AttributeRange> getAttributeRanges(final String branchPath, final BranchCriteria branchCriteria, final TimerUtil timer) {
    List<ReferenceSetMember> attributeRangeMembers = memberService.findMembers(branchPath, branchCriteria, new MemberSearchRequest().referenceSet(Concepts.REFSET_MRCM_ATTRIBUTE_RANGE_INTERNATIONAL), LARGE_PAGE).getContent();
    List<AttributeRange> attributeRanges = new ArrayList<>();
    for (ReferenceSetMember member : attributeRangeMembers) {
        // id	effectiveTime	active	moduleId	refsetId	referencedComponentId	rangeConstraint	attributeRule	ruleStrengthId	contentTypeId
        if (member.isActive()) {
            String rangeConstraint = member.getAdditionalField("rangeConstraint");
            attributeRanges.add(new AttributeRange(member.getMemberId(), member.getEffectiveTime(), member.isActive(), member.getReferencedComponentId(), rangeConstraint, member.getAdditionalField("attributeRule"), RuleStrength.lookupByConceptId(member.getAdditionalField("ruleStrengthId")), ContentType.lookupByConceptId(member.getAdditionalField("contentTypeId")), getConcreteValueDataType(rangeConstraint)));
        }
    }
    timer.checkpoint("Load attribute ranges");
    return attributeRanges;
}

Example 4 with MemberSearchRequest

use of org.snomed.snowstorm.core.data.services.pojo.MemberSearchRequest in project snowstorm by IHTSDO.

the class UpgradeInactivationServiceTest method testFindAndUpdateInactivationIndicators.

@Test
void testFindAndUpdateInactivationIndicators() throws Exception {
    // add content
    Concept conceptA = testUtil.createConceptWithPathIdAndTermWithLang("MAIN", "100000", "Inactivation testing", "en");
    // version
    codeSystemService.createVersion(SNOMEDCT, Integer.valueOf("20200131"), "20200131 International Release");
    // inactivate concept
    conceptA = conceptService.find(conceptA.getConceptId(), MAIN);
    Set<Description> descriptions = conceptA.getDescriptions();
    assertNotNull(descriptions);
    assertEquals(1, descriptions.size());
    Description publishedDescription = descriptions.iterator().next();
    Description unpublished = new Description("new term");
    conceptA.addDescription(unpublished);
    conceptA.setActive(false);
    conceptService.update(conceptA, MAIN);
    conceptA = conceptService.find(conceptA.getConceptId(), MAIN);
    descriptions = conceptA.getDescriptions();
    assertNotNull(descriptions);
    assertEquals(2, descriptions.size());
    Page<ReferenceSetMember> members = referenceSetMemberService.findMembers(MAIN, new MemberSearchRequest().referenceSet("900000000000490003"), PageRequest.of(0, 10));
    assertNotNull(members);
    assertEquals(2, members.getContent().size());
    // delete description inactivation indicator members for testing
    referenceSetMemberService.deleteMember(MAIN, members.getContent().get(0).getMemberId());
    referenceSetMemberService.deleteMember(MAIN, members.getContent().get(1).getMemberId());
    members = referenceSetMemberService.findMembers(MAIN, new MemberSearchRequest().referenceSet("900000000000490003").referencedComponentId(publishedDescription.getDescriptionId()), PageRequest.of(0, 10));
    assertEquals(0, members.getContent().size());
    upgradeInactivationService.findAndUpdateDescriptionsInactivation(SNOMEDCT);
    members = referenceSetMemberService.findMembers(MAIN, new MemberSearchRequest().referenceSet("900000000000490003"), PageRequest.of(0, 10));
    assertEquals(2, members.getContent().size());
    // verify inactivation refset member
    ReferenceSetMember inactivationMember = members.getContent().get(0);
    assertNotNull(inactivationMember.getMemberId());
    assertNull(inactivationMember.getEffectiveTime());
    assertFalse(inactivationMember.isReleased());
    assertTrue(inactivationMember.isActive());
    assertEquals(publishedDescription.getModuleId(), inactivationMember.getModuleId());
    assertEquals(Concepts.DESCRIPTION_INACTIVATION_INDICATOR_REFERENCE_SET, inactivationMember.getRefsetId());
    assertEquals(Concepts.CONCEPT_NON_CURRENT, inactivationMember.getAdditionalField("valueId"));
    assertEquals(publishedDescription.getDescriptionId(), inactivationMember.getReferencedComponentId());
    assertEquals(publishedDescription.getConceptId(), inactivationMember.getConceptId());
    // make sure published description is still active and published and unpublished description is deleted.
    conceptA = conceptService.find(conceptA.getConceptId(), SNOMEDCT.getBranchPath());
    List<Description> descriptionList = new ArrayList<>(conceptA.getDescriptions());
    assertEquals(2, descriptionList.size());
    assertTrue(descriptionList.get(0).isActive());
    assertTrue(descriptionList.get(1).isActive());
}

Example 5 with MemberSearchRequest

use of org.snomed.snowstorm.core.data.services.pojo.MemberSearchRequest in project snowstorm by IHTSDO.

the class ExtensionAdditionalLanguageRefsetUpgradeServiceTest method setUp.

@BeforeEach
void setUp() throws Exception {
    snomedct = new CodeSystem("SNOMEDCT", "MAIN");
    codeSystemService.createCodeSystem(snomedct);
    ReferenceSetMember enGbLanguageMember = new ReferenceSetMember(null, null, true, "900000000000207008", "900000000000508004", "675173018");
    enGbLanguageMember.setAdditionalField(ReferenceSetMember.LanguageFields.ACCEPTABILITY_ID, "900000000000548007");
    ReferenceSetMember enUsLanguageMember = new ReferenceSetMember(null, null, true, "900000000000207008", "900000000000509007", "675173018");
    enUsLanguageMember.setAdditionalField(ReferenceSetMember.LanguageFields.ACCEPTABILITY_ID, "900000000000549004");
    Concept concept = new Concept("123456");
    Description description = new Description("675173018", "testing");
    description.addLanguageRefsetMember(enGbLanguageMember);
    description.addLanguageRefsetMember(enUsLanguageMember);
    concept.addDescription(description);
    conceptService.create(concept, snomedct.getBranchPath());
    codeSystemService.createVersion(snomedct, 20190731, "2019-07-31 release");
    ReferenceSetMember enGbLanguageMemberLatest = new ReferenceSetMember(null, null, true, "900000000000207008", "900000000000508004", "675173019");
    enGbLanguageMemberLatest.setAdditionalField(ReferenceSetMember.LanguageFields.ACCEPTABILITY_ID, "900000000000548007");
    ReferenceSetMember enUsLanguageMemberLatest = new ReferenceSetMember(null, null, true, "900000000000207008", "900000000000509007", "675173019");
    enUsLanguageMemberLatest.setAdditionalField(ReferenceSetMember.LanguageFields.ACCEPTABILITY_ID, "900000000000549004");
    Description latestDescription = new Description("675173019", "new term testing");
    latestDescription.addLanguageRefsetMember(enGbLanguageMemberLatest);
    latestDescription.addLanguageRefsetMember(enUsLanguageMemberLatest);
    concept = conceptService.find("123456", snomedct.getBranchPath());
    concept.addDescription(latestDescription);
    concept = conceptService.update(concept, snomedct.getBranchPath());
    // this is for testing complete copy as only active ones are copied.
    Description existing = concept.getDescription("675173018");
    ReferenceSetMember existingGbMember = existing.getLangRefsetMembersFirstValuesMap().get("900000000000508004");
    existingGbMember.setActive(false);
    referenceSetMemberService.updateMember("MAIN", existingGbMember);
    assertEquals(1, concept.getDescription("675173018").getAcceptabilityMap().keySet().size());
    MemberSearchRequest searchRequest = new MemberSearchRequest();
    searchRequest.referenceSet("900000000000508004");
    Page<ReferenceSetMember> updatedResult = referenceSetMemberService.findMembers(snomedct.getBranchPath(), searchRequest, PageRequest.of(0, 10));
    assertNotNull(updatedResult);
    assertEquals(2, updatedResult.getContent().size());
    codeSystemService.createVersion(snomedct, 20200131, "2020-01-31 release");
    snomedctNZ = new CodeSystem("SNOMEDCT-NZ", "MAIN/SNOMEDCT-NZ");
    snomedctNZ.setDependantVersionEffectiveTime(20200131);
    codeSystemService.createCodeSystem(snomedctNZ);
    Map<String, Object> metaData = new HashMap<>();
    metaData.put(BranchMetadataKeys.DEPENDENCY_PACKAGE, "International_Release.zip");
    metaData.put(BranchMetadataKeys.PREVIOUS_PACKAGE, "NZExtension_Release.zip");
    metaData.put("defaultModuleId", "21000210109");
    metaData.put("defaultNamespace", "1000210");
    metaData.put("shortname", "NZ");
    final TypeReference<List<Map<String, String>>> listTypeReference = new TypeReference<>() {
    };
    List<Map<String, String>> requiredLanguageRefsets = objectMapper.readValue("[{\n" + "        \"default\": \"false\",\n" + "        \"en\": \"900000000000508004\",\n" + "        \"readOnly\": \"true\",\n" + "        \"dialectName\": \"en-gb\"\n" + "      },\n" + "      {\n" + "        \"default\": \"true\",\n" + "        \"en\": \"271000210107\",\n" + "        \"dialectName\": \"en-nz\"\n" + "      },\n" + "      {\n" + "        \"default\": \"false\",\n" + "        \"mi\": \"291000210106\"\n" + "      },\n" + "      {\n" + "        \"default\": \"false\",\n" + "        \"en\": \"900000000000509007\",\n" + "        \"dialectName\": \"en-us\"\n" + "      }\n" + "    ]", listTypeReference);
    metaData.put("requiredLanguageRefsets", requiredLanguageRefsets);
    branchService.updateMetadata("MAIN/SNOMEDCT-NZ", metaData);
}