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

Example 11 with CodeSystem

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

the class SnomedComponentEffectiveTimeRestoreTest method restoreInternationalEffectiveTimeOnExtensionUpgrade.

@Test
public void restoreInternationalEffectiveTimeOnExtensionUpgrade() throws Exception {
    // create extension on the base SI VERSION
    CodeSystem extension = createExtension(baseInternationalCodeSystem, branchPath.lastSegment());
    // start the extension upgrade process
    CodeSystem upgradeCodeSystem = createExtensionUpgrade(extension.getResourceURI(), upgradeInternationalCodeSystem);
    // get the first concept from the Base SI version
    SnomedConcept concept = searchConcepts(upgradeInternationalCodeSystem, Map.of("module", Concepts.MODULE_SCT_CORE, "effectiveTime", "20200131"), 1).stream().findFirst().get();
    LocalDate lastReleasedEffectiveTime = concept.getEffectiveTime();
    String conceptId = concept.getId();
    // create a change on the concept, like change the definition status
    updateConcept(upgradeCodeSystem.getResourceURI(), concept.getId(), Map.of("moduleId", Concepts.MODULE_SCT_MODEL_COMPONENT));
    concept = getConcept(upgradeCodeSystem.getResourceURI(), conceptId);
    assertEquals(null, concept.getEffectiveTime());
    // revert the change, so it reverts the effective time to the EXT_VER effective time
    updateConcept(upgradeCodeSystem.getResourceURI(), conceptId, Map.of("moduleId", Concepts.MODULE_SCT_CORE));
    concept = getConcept(upgradeCodeSystem.getResourceURI(), conceptId);
    assertEquals(lastReleasedEffectiveTime, concept.getEffectiveTime());
}

Example 12 with CodeSystem

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

the class SnomedComponentEffectiveTimeRestoreTest method restoreExtensionEffectiveTimeOnExtensionVersionUpgrade.

@Test
public void restoreExtensionEffectiveTimeOnExtensionVersionUpgrade() throws Exception {
    final String codeSystemId = branchPath.lastSegment();
    // create extension on the base SI VERSION
    final CodeSystem extension = createExtension(baseInternationalCodeSystem, codeSystemId);
    // create the module concept to represent the extension
    String moduleId = createModule(extension);
    // create an extension version, concept receives effective time
    LocalDate effectiveTime = getNextAvailableEffectiveDate(codeSystemId);
    createVersion(codeSystemId, effectiveTime).statusCode(201);
    ResourceURI upgradeExtVersion = CodeSystem.uri(codeSystemId, effectiveTime.toString());
    SnomedConcept concept = getConcept(extension.getResourceURI(), moduleId);
    assertEquals(effectiveTime, concept.getEffectiveTime());
    // Update extension concept
    updateConcept(extension.getResourceURI(), concept.getId(), Map.of("moduleId", Concepts.MODULE_SCT_MODEL_COMPONENT));
    // Create second version
    LocalDate effectiveDate2 = getNextAvailableEffectiveDate(codeSystemId);
    createVersion(codeSystemId, effectiveDate2).statusCode(201);
    // start the extension upgrade process
    CodeSystem upgradeCodeSystem = createExtensionUpgrade(upgradeExtVersion, upgradeInternationalCodeSystem);
    // create a change on the concept, like change the definition status
    updateConcept(upgradeCodeSystem.getResourceURI(), concept.getId(), Map.of("definitionStatusId", Concepts.FULLY_DEFINED));
    concept = getConcept(upgradeCodeSystem.getResourceURI(), moduleId);
    assertEquals(null, concept.getEffectiveTime());
    // revert the change, so it reverts the effective time to the 'effectiveDate' effective time
    updateConcept(upgradeCodeSystem.getResourceURI(), moduleId, Map.of("definitionStatusId", Concepts.PRIMITIVE));
    concept = getConcept(upgradeCodeSystem.getResourceURI(), moduleId);
    assertEquals(effectiveTime, concept.getEffectiveTime());
}

Example 13 with CodeSystem

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

the class SnomedComponentEffectiveTimeRestoreTest method restoreExtensionEffectiveTimeOnExtensionUpgrade.

@Test
public void restoreExtensionEffectiveTimeOnExtensionUpgrade() throws Exception {
    // create extension on the base SI VERSION
    final CodeSystem extension = createExtension(baseInternationalCodeSystem, branchPath.lastSegment());
    // create the module concept to represent the extension
    String moduleId = createModule(extension);
    // create an extension version, concept receives effective time
    createVersion(extension.getId(), EXT_VERSION, LocalDate.parse("2019-10-31")).statusCode(201);
    SnomedConcept concept = getConcept(extension.getResourceURI(), moduleId);
    assertEquals(EffectiveTimes.parse(EXT_VERSION), concept.getEffectiveTime());
    // start the extension upgrade process
    CodeSystem upgradeCodeSystem = createExtensionUpgrade(extension.getResourceURI(), upgradeInternationalCodeSystem);
    // create a change on the concept, like change the definition status
    updateConcept(upgradeCodeSystem.getResourceURI(), concept.getId(), Map.of("definitionStatusId", Concepts.FULLY_DEFINED));
    concept = getConcept(upgradeCodeSystem.getResourceURI(), moduleId);
    assertEquals(null, concept.getEffectiveTime());
    // revert the change, so it reverts the effective time to the EXT_VER effective time
    updateConcept(upgradeCodeSystem.getResourceURI(), moduleId, Map.of("definitionStatusId", Concepts.PRIMITIVE));
    concept = getConcept(upgradeCodeSystem.getResourceURI(), moduleId);
    assertEquals(EffectiveTimes.parse(EXT_VERSION), concept.getEffectiveTime());
}

Example 14 with CodeSystem

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

the class SnomedExtensionUpgradeTest method upgrade09DonatedConceptAndDescriptions.

@Test
public void upgrade09DonatedConceptAndDescriptions() {
    // 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, inferredIsa)));
    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
    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(4).contains(extensionStatedIsaId, extensionInferredIsaId);
}

Example 15 with CodeSystem

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

the class SnomedExtensionUpgradeTest method upgrade22UpgradeSychronizeHead.

@Test
public void upgrade22UpgradeSychronizeHead() 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);
    IBranchPath extensionBranch = BranchPathUtils.createPath(extension.getBranchPath());
    IBranchPath upgradeBranch = BranchPathUtils.createPath(upgradeCodeSystem.getBranchPath());
    merge(extensionBranch, upgradeBranch, "Merged new concept from child branch").body("status", equalTo(Merge.Status.COMPLETED.name()));
    Boolean result = CodeSystemRequests.prepareUpgradeSynchronization(upgradeCodeSystem.getResourceURI(), extension.getResourceURI()).buildAsync().execute(getBus()).getSync(1, TimeUnit.MINUTES);
    assertTrue(result);
    CodeSystems expandedCodeSystemsAfterMerge = CodeSystemRestRequests.search(upgradeCodeSystem.getId(), CodeSystem.Expand.UPGRADE_INFO + "()");
    assertThat(expandedCodeSystemsAfterMerge.first().get().getUpgradeInfo().getAvailableVersions()).isEmpty();
}