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MAINT-2072 Add test cases for toggling state of Concepts & Descriptions
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@dmcgihtsdo
dmcgihtsdo committed Jan 25, 2023
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243 changes: 243 additions & 0 deletions src/test/java/org/snomed/snowstorm/core/data/services/BranchMergeServiceTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3464,6 +3464,233 @@ void testPropertiesWhenRebasingDifferentScenarios() throws ServiceException, Int
);
}

@Test
void testTogglingInactivatingConcept() throws ServiceException {
String intMain = "MAIN";
Map<String, String> intPreferred = Map.of(US_EN_LANG_REFSET, descriptionAcceptabilityNames.get(PREFERRED), GB_EN_LANG_REFSET, descriptionAcceptabilityNames.get(PREFERRED));
Map<String, String> intAcceptable = Map.of(US_EN_LANG_REFSET, descriptionAcceptabilityNames.get(PREFERRED), GB_EN_LANG_REFSET, descriptionAcceptabilityNames.get(ACCEPTABLE));
String ci = "CASE_INSENSITIVE";
Concept concept;
Description description;
CodeSystem codeSystem;
List<ReferenceSetMember> members;
ReferenceSetMember member;

// 1. Create International Concept
concept = new Concept()
.addDescription(new Description("Vehicle (vehicle)").setTypeId(FSN).setCaseSignificance(ci).setAcceptabilityMap(intPreferred))
.addDescription(new Description("Vehicle").setTypeId(SYNONYM).setCaseSignificance(ci).setAcceptabilityMap(intPreferred))
.addAxiom(new Relationship(ISA, SNOMEDCT_ROOT));
concept = conceptService.create(concept, intMain);
String vehicleId = concept.getConceptId();

// 2. Version International
codeSystem = codeSystemService.find("SNOMEDCT");
codeSystemService.createVersion(codeSystem, 20220131, "20220131");

// 3. Assert members
members = memberService.findMembers(MAIN, new MemberSearchRequest().referencedComponentId(vehicleId), PageRequest.of(0, 10)).getContent();
assertEquals(1, members.size()); // Axiom

// 4. Inactivate Concept
concept = conceptService.find(vehicleId, MAIN);
inactivate(concept, "AMBIGUOUS");
conceptService.update(concept, MAIN);

// 5. Version International
codeSystem = codeSystemService.find("SNOMEDCT");
codeSystemService.createVersion(codeSystem, 20220228, "20220228");

// 6. Assert members
members = memberService.findMembers(MAIN, new MemberSearchRequest().referencedComponentId(vehicleId), PageRequest.of(0, 10)).getContent();
assertEquals(2, members.size()); // Axiom & Inactivation indicator

member = getMemberByRefsetId(members, OWL_AXIOM_REFERENCE_SET);
assertNotNull(member);
assertFalse(member.isActive());

member = getMemberByRefsetId(members, CONCEPT_INACTIVATION_INDICATOR_REFERENCE_SET);
assertNotNull(member);
assertTrue(member.isActive());

// 7. Reactivate Concept
concept = conceptService.find(vehicleId, MAIN);
activate(concept, MAIN);

// 8. Version International
codeSystem = codeSystemService.find("SNOMEDCT");
codeSystemService.createVersion(codeSystem, 20220331, "20220331");

// 9. Assert members
members = memberService.findMembers(MAIN, new MemberSearchRequest().referencedComponentId(vehicleId), PageRequest.of(0, 10)).getContent();
assertEquals(2, members.size()); // Axiom & Inactivation indicator

member = getMemberByRefsetId(members, OWL_AXIOM_REFERENCE_SET);
assertNotNull(member);
assertTrue(member.isActive());

member = getMemberByRefsetId(members, CONCEPT_INACTIVATION_INDICATOR_REFERENCE_SET);
assertNotNull(member);
assertFalse(member.isActive());

// 10. Inactivate Concept (again)
concept = conceptService.find(vehicleId, MAIN);
// If we re-use AMBIGUOUS, the test will pass. Using a different inactivation reason will cause the test to fail.
inactivate(concept, "DUPLICATE");
conceptService.update(concept, MAIN);

// 11. Activate Concept (change mind)
concept = conceptService.find(vehicleId, MAIN);
activate(concept, MAIN);

members = memberService.findMembers(MAIN, new MemberSearchRequest().referencedComponentId(vehicleId), PageRequest.of(0, 10)).getContent();
member = getMemberByRefsetId(members, OWL_AXIOM_REFERENCE_SET);
assertNotNull(member);
assertTrue(member.isActive());

member = getMemberByRefsetId(members, CONCEPT_INACTIVATION_INDICATOR_REFERENCE_SET);
assertNotNull(member);
assertFalse(member.isActive());
assertEquals(member.getReleaseHash(), member.buildReleaseHash());
}

@Test
void testTogglingInactivatingDescription() throws ServiceException {
String intMain = "MAIN";
Map<String, String> intPreferred = Map.of(US_EN_LANG_REFSET, descriptionAcceptabilityNames.get(PREFERRED), GB_EN_LANG_REFSET, descriptionAcceptabilityNames.get(PREFERRED));
Map<String, String> intAcceptable = Map.of(US_EN_LANG_REFSET, descriptionAcceptabilityNames.get(PREFERRED), GB_EN_LANG_REFSET, descriptionAcceptabilityNames.get(ACCEPTABLE));
String ci = "CASE_INSENSITIVE";
Concept concept;
Description description;
CodeSystem codeSystem;
List<ReferenceSetMember> members;
ReferenceSetMember member;

// 1. Create International Concept
concept = new Concept()
.addDescription(new Description("Vehicle (vehicle)").setTypeId(FSN).setCaseSignificance(ci).setAcceptabilityMap(intPreferred))
.addDescription(new Description("Vehicle").setTypeId(SYNONYM).setCaseSignificance(ci).setAcceptabilityMap(intPreferred))
.addDescription(new Description("Motorvehicle").setTypeId(SYNONYM).setCaseSignificance(ci).setAcceptabilityMap(intPreferred))
.addAxiom(new Relationship(ISA, SNOMEDCT_ROOT));
concept = conceptService.create(concept, intMain);
String vehicleId = concept.getConceptId();
String motorVehicleId = getDescription(concept, "Motorvehicle").getDescriptionId();

// 2. Version International
codeSystem = codeSystemService.find("SNOMEDCT");
codeSystemService.createVersion(codeSystem, 20220131, "20220131");

// 3. Inactivate Description
concept = conceptService.find(vehicleId, MAIN);
description = getDescriptionById(concept, motorVehicleId);
inactivate(description, "OUTDATED");
conceptService.update(concept, MAIN);

// 5. Version International
codeSystem = codeSystemService.find("SNOMEDCT");
codeSystemService.createVersion(codeSystem, 20220228, "20220228");

// 6. Assert members
members = memberService.findMembers(MAIN, new MemberSearchRequest().referencedComponentId(motorVehicleId), PageRequest.of(0, 10)).getContent();
assertEquals(3, members.size()); // GB, US & Inactivation indicator

member = getMemberByRefsetId(members, DESCRIPTION_INACTIVATION_INDICATOR_REFERENCE_SET);
assertNotNull(member);
assertTrue(member.isActive());

// 7. Reactivate Description
concept = conceptService.find(vehicleId, MAIN);
activateDescription(concept, motorVehicleId, MAIN);

// 8. Version International
codeSystem = codeSystemService.find("SNOMEDCT");
codeSystemService.createVersion(codeSystem, 20220331, "20220331");

// 9. Assert members
members = memberService.findMembers(MAIN, new MemberSearchRequest().referencedComponentId(motorVehicleId), PageRequest.of(0, 10)).getContent();
assertEquals(3, members.size()); // GB, US & Inactivation indicator

member = getMemberByRefsetId(members, DESCRIPTION_INACTIVATION_INDICATOR_REFERENCE_SET);
assertNotNull(member);
assertFalse(member.isActive());

// 10. Inactivate Description (again)
concept = conceptService.find(vehicleId, MAIN);
description = getDescriptionById(concept, motorVehicleId);
inactivate(description, "GRAMMATICAL_DESCRIPTION_ERROR");
conceptService.update(concept, MAIN);

members = memberService.findMembers(MAIN, new MemberSearchRequest().referencedComponentId(motorVehicleId), PageRequest.of(0, 10)).getContent();
assertEquals(3, members.size()); // GB, US & Inactivation indicator

member = getMemberByRefsetId(members, DESCRIPTION_INACTIVATION_INDICATOR_REFERENCE_SET);
assertNotNull(member);
assertTrue(member.isActive());

// 11. Activate Description (change mind)
concept = conceptService.find(vehicleId, MAIN);
activateDescription(concept, motorVehicleId, MAIN);

members = memberService.findMembers(MAIN, new MemberSearchRequest().referencedComponentId(motorVehicleId), PageRequest.of(0, 10)).getContent();
member = getMemberByRefsetId(members, DESCRIPTION_INACTIVATION_INDICATOR_REFERENCE_SET);
assertNotNull(member);
assertFalse(member.isActive());
assertEquals(member.getReleaseHash(), member.buildReleaseHash());
}

private void activateDescription(Concept concept, String descriptionId, String branchPath) throws ServiceException {
Description description = getDescriptionById(concept, descriptionId);
description.setActive(true);
description.setInactivationIndicator(null);
description.updateEffectiveTime();

conceptService.update(concept, branchPath);
}

private ReferenceSetMember getMemberByRefsetId(List<ReferenceSetMember> members, String refsetId) {
for (ReferenceSetMember member : members) {
if (refsetId.equals(member.getRefsetId())) {
return member;
}
}

return null;
}

private void inactivate(Concept concept, String inactivationIndicator) {
concept.setActive(false);
concept.setInactivationIndicator(inactivationIndicator);
concept.updateEffectiveTime();
}

private void inactivate(Description description, String inactivationIndicator) {
description.setActive(false);
description.setInactivationIndicator(inactivationIndicator);
description.updateEffectiveTime();
}

private void activate(Concept concept, String branchPath) throws ServiceException {
Concept newState = new Concept();

newState.setConceptId(concept.getConceptId());
newState.setEffectiveTimeI(null);
newState.setActive(true);
newState.setModuleId(concept.getModuleId());
newState.setDefinitionStatusId(concept.getDefinitionStatusId());
newState.setReleased(concept.isReleased());
newState.setReleaseHash(concept.getReleaseHash());
newState.setClassAxioms(concept.getClassAxioms());
newState.getClassAxioms().forEach(m -> {
m.setActive(true);
ReferenceSetMember referenceSetMember = m.getReferenceSetMember();
referenceSetMember.setActive(true);
referenceSetMember.updateEffectiveTime();
memberService.updateMember(branchPath, referenceSetMember);
});

conceptService.update(newState, branchPath);
}

void assertReleaseProperties(
String initialReleaseEffectiveTime,
String projectReleaseEffectiveTime,
Expand Down Expand Up @@ -4097,6 +4324,22 @@ private Description getDescription(Concept concept, String term) {
return null;
}

private Description getDescriptionById(Concept concept, String descriptionId) {
if (concept == null || concept.getDescriptions() == null || concept.getDescriptions().isEmpty()) {
return null;
}


Set<Description> descriptions = concept.getDescriptions();
for (Description description : descriptions) {
if (descriptionId.equals(description.getDescriptionId())) {
return description;
}
}

return null;
}

private ReferenceSetMember getMember(Page<ReferenceSetMember> page){
return page.getContent().iterator().next();
}
Expand Down

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