Skip to content

Commit

Permalink
MAINT-2452 Add tests for invalid axioms
Browse files Browse the repository at this point in the history
  • Loading branch information
@dmcgihtsdo
dmcgihtsdo committed Jul 15, 2024
1 parent 4bbd860 commit d84f7d7
Showing 1 changed file with 177 additions and 1 deletion.
178 changes: 177 additions & 1 deletion src/test/java/org/snomed/snowstorm/core/data/services/ConceptServiceTest.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@
import org.springframework.data.elasticsearch.client.elc.NativeQuery;
import org.springframework.data.elasticsearch.client.elc.NativeQueryBuilder;
import org.springframework.security.core.context.SecurityContextHolder;
import static org.snomed.snowstorm.core.data.services.CodeSystemService.SNOMEDCT;

import java.io.IOException;
import java.util.*;
Expand Down Expand Up @@ -2835,6 +2836,181 @@ void testAddingTranslationDoesNotReactivateDuplicateLangMember() throws ServiceE
assertEquals(PREFERRED, active.iterator().next().getAdditionalField(ReferenceSetMember.LanguageFields.ACCEPTABILITY_ID));
}

@Test
void testInvalidInactiveAxiomNotReactivated() 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;
CodeSystem codeSystem;

// Create 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();

// Version
codeSystem = codeSystemService.find("SNOMEDCT");
codeSystemService.createVersion(codeSystem, 20240101, "20240101");

// Create type of Vehicle (purposely without Axiom)
concept = new Concept()
.addDescription(new Description("Car (vehicle)").setTypeId(FSN).setCaseSignificance(ci).setAcceptabilityMap(intPreferred))
.addDescription(new Description("Car").setTypeId(SYNONYM).setCaseSignificance(ci).setAcceptabilityMap(intPreferred))
.addRelationship(new Relationship(ISA, vehicleId));
concept = conceptService.create(concept, intMain);
String carId = concept.getConceptId();

// Manually create Axiom incorrectly (formatted back to front)
ReferenceSetMember axiom = new ReferenceSetMember(CORE_MODULE, OWL_AXIOM_REFERENCE_SET, concept.getConceptId());
String backToFront = String.format("SubClassOf(:%s :%s)", vehicleId, carId); // Note: vehicleId -> carId
axiom.setAdditionalField("owlExpression", backToFront);
axiom = referenceSetMemberService.createMember(intMain, axiom);
String invalidAxiomId = axiom.getId();

// Assert formatted incorrectly
axiom = referenceSetMemberService.findMember(intMain, axiom.getMemberId());
String owlExpression = axiom.getAdditionalField("owlExpression");
assertEquals(backToFront, owlExpression);

// Version error
codeSystem = codeSystemService.find("SNOMEDCT");
codeSystemService.createVersion(codeSystem, 20240201, "20240201");

// Fix mistake (replace invalid with valid)
axiom = referenceSetMemberService.findMember(intMain, invalidAxiomId);
axiom.setActive(false);
axiom.updateEffectiveTime();
referenceSetMemberService.updateMember(intMain, axiom);

axiom = new ReferenceSetMember(CORE_MODULE, OWL_AXIOM_REFERENCE_SET, concept.getConceptId());
String frontToBack = String.format("SubClassOf(:%s :%s)", carId, vehicleId); // Note: carId -> vehicleId
axiom.setAdditionalField("owlExpression", frontToBack);
axiom = referenceSetMemberService.createMember(intMain, axiom);
String validAxiomId = axiom.getId();

// Version correction
codeSystem = codeSystemService.find("SNOMEDCT");
codeSystemService.createVersion(codeSystem, 20240301, "20240301");

// Add synonym
concept = conceptService.find(carId, intMain);
concept.addDescription(new Description("Motorised vehicle").setTypeId(SYNONYM).setCaseSignificance(ci).setAcceptabilityMap(intPreferred));
conceptService.update(concept, intMain);

// Assert inactive axiom hasn't changed
Axiom invalidAxiom = concept.getClassAxioms().stream().filter(cA -> cA.getAxiomId().equals(invalidAxiomId)).collect(Collectors.toList()).get(0);
assertEquals(20240301, invalidAxiom.getEffectiveTimeI());
assertEquals(backToFront, invalidAxiom.getReferenceSetMember().getAdditionalField("owlExpression"));
}

@Test
void testActivatingInvalidAxiomThrowsException() 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;
CodeSystem codeSystem;

// Create 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();

// Version
codeSystem = codeSystemService.find("SNOMEDCT");
codeSystemService.createVersion(codeSystem, 20240101, "20240101");

// Create type of Vehicle (purposely without Axiom)
concept = new Concept()
.addDescription(new Description("Car (vehicle)").setTypeId(FSN).setCaseSignificance(ci).setAcceptabilityMap(intPreferred))
.addDescription(new Description("Car").setTypeId(SYNONYM).setCaseSignificance(ci).setAcceptabilityMap(intPreferred))
.addRelationship(new Relationship(ISA, vehicleId));
concept = conceptService.create(concept, intMain);
String carId = concept.getConceptId();

// Manually create Axiom incorrectly (formatted back to front)
ReferenceSetMember axiom = new ReferenceSetMember(CORE_MODULE, OWL_AXIOM_REFERENCE_SET, concept.getConceptId());
String backToFront = String.format("SubClassOf(:%s :%s)", vehicleId, carId); // Note: vehicleId -> carId
axiom.setAdditionalField("owlExpression", backToFront);
axiom = referenceSetMemberService.createMember(intMain, axiom);
String invalidAxiomId = axiom.getId();

// Assert formatted incorrectly
axiom = referenceSetMemberService.findMember(intMain, axiom.getMemberId());
String owlExpression = axiom.getAdditionalField("owlExpression");
assertEquals(backToFront, owlExpression);

// Version error
codeSystem = codeSystemService.find("SNOMEDCT");
codeSystemService.createVersion(codeSystem, 20240201, "20240201");

// Fix mistake (replace invalid with valid)
axiom = referenceSetMemberService.findMember(intMain, invalidAxiomId);
axiom.setActive(false);
axiom.updateEffectiveTime();
referenceSetMemberService.updateMember(intMain, axiom);

axiom = new ReferenceSetMember(CORE_MODULE, OWL_AXIOM_REFERENCE_SET, concept.getConceptId());
String frontToBack = String.format("SubClassOf(:%s :%s)", carId, vehicleId); // Note: carId -> vehicleId
axiom.setAdditionalField("owlExpression", frontToBack);
axiom = referenceSetMemberService.createMember(intMain, axiom);
String validAxiomId = axiom.getId();

// Version correction
codeSystem = codeSystemService.find("SNOMEDCT");
codeSystemService.createVersion(codeSystem, 20240301, "20240301");

// Inactivate concept
concept = conceptService.find(carId, intMain);
concept.setActive(false);
concept.updateEffectiveTime();
conceptService.update(concept, intMain);

// Version inactivation
codeSystem = codeSystemService.find("SNOMEDCT");
codeSystemService.createVersion(codeSystem, 20240401, "20240401");

// Assert inactive
concept = conceptService.find(carId, intMain);
assertFalse(concept.isActive());
assertNotNull(concept.getEffectiveTime());

// Reactivate concept
concept = conceptService.find(carId, intMain);
concept.setActive(true);
concept.updateEffectiveTime();
concept = conceptService.update(concept, intMain);

// Reactivate valid axiom (allowed)
for (Axiom classAxiom : concept.getClassAxioms()) {
if (validAxiomId.equals(classAxiom.getAxiomId())) {
classAxiom.setActive(true);
}
}
concept = conceptService.update(concept, intMain);

// Reactivate invalid axiom (not allowed)
for (Axiom classAxiom : concept.getClassAxioms()) {
if (invalidAxiomId.equals(classAxiom.getAxiomId())) {
classAxiom.setActive(true);
}
}

Concept finalConcept = concept;
assertThrows(IllegalStateException.class, () -> {
conceptService.update(finalConcept, intMain);
});
}

private Description getDescriptionByTerm(Concept concept, String term) {
if (concept == null) {
return null;
Expand Down Expand Up @@ -2883,4 +3059,4 @@ private Description fsn(String term) {
return description;
}

}
}

0 comments on commit d84f7d7

Please sign in to comment.