Expanding ValueSet using hierarchical CodeSystem fails with constraint violation exception (#5461)

* Expanding a ValueSet using hierarchical CodeSystem would fail in different scenarios with a constraint violation exception when codes (term concepts) were being persisted

* Expanding a ValueSet using hierarchical CodeSystem would fail in different scenarios with a constraint violation exception when codes (term concepts) were being persisted

* Small changes after code review. Doing some variable/method renaming and correcting changelog Jira issue number.

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_10_0/5431-version_canonicalizer_fails_capabilitystatement_dstu2.yaml

@@ -1,5 +1,5 @@
 ---
 type: fix
 issue: 5431
-jira: SMILE-5306
+jira: SMILE-7589
 title: "Previously, using VersionCanonicalizer to convert a CapabilityStatement from R5 to DSTU2 would fail. This is now fixed."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5460-failed-to-expand-valueset-with-hierarchical-codesystem.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 5460
+jira: SMILE-7594
+title: "Previously, expanding a ValueSet using hierarchical CodeSystem would fail in different scenarios 
+with a constraint violation exception when codes (term concepts) were being persisted. This is now fixed."

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcImpl.java

@@ -196,14 +196,9 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 	public static final int DEFAULT_MASS_INDEXER_OBJECT_LOADING_THREADS = 2;
 	// doesn't seem to be much gain by using more threads than this value
 	public static final int MAX_MASS_INDEXER_OBJECT_LOADING_THREADS = 6;
-	private static final int SINGLE_FETCH_SIZE = 1;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TermReadSvcImpl.class);
 	private static final ValueSetExpansionOptions DEFAULT_EXPANSION_OPTIONS = new ValueSetExpansionOptions();
 	private static final TermCodeSystemVersionDetails NO_CURRENT_VERSION = new TermCodeSystemVersionDetails(-1L, null);
-	private static final String IDX_PROPERTIES = "myProperties";
-	private static final String IDX_PROP_KEY = IDX_PROPERTIES + ".myKey";
-	private static final String IDX_PROP_VALUE_STRING = IDX_PROPERTIES + ".myValueString";
-	private static final String IDX_PROP_DISPLAY_STRING = IDX_PROPERTIES + ".myDisplayString";
 	private static final String OUR_PIPE_CHARACTER = "|";
 	private static final int SECONDS_IN_MINUTE = 60;
 	private static final int INDEXED_ROOTS_LOGGING_COUNT = 50_000;
@@ -540,6 +535,7 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 			@Nullable ValueSetExpansionOptions theExpansionOptions,
 			ValueSet theValueSetToExpand,
 			ExpansionFilter theFilter) {
+		Set<String> addedCodes = new HashSet<>();
 		ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSetToExpand, "ValueSet to expand can not be null");
 
 		ValueSetExpansionOptions expansionOptions = provideExpansionOptions(theExpansionOptions);
@@ -560,9 +556,8 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 			accumulator.addParameter().setName("count").setValue(new IntegerType(count));
 		}
 
-		myTxTemplate.executeWithoutResult(tx -> {
+		myTxTemplate.executeWithoutResult(tx -> expandValueSetIntoAccumulator(
-			expandValueSetIntoAccumulator(theValueSetToExpand, theExpansionOptions, accumulator, theFilter, true);
+				theValueSetToExpand, theExpansionOptions, accumulator, theFilter, true, addedCodes));
-		});
 
 		if (accumulator.getTotalConcepts() != null) {
 			accumulator.setTotal(accumulator.getTotalConcepts());
@@ -594,7 +589,8 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 			ValueSetExpansionOptions theExpansionOptions,
 			IValueSetConceptAccumulator theAccumulator,
 			ExpansionFilter theFilter,
-			boolean theAdd) {
+			boolean theAdd,
+			Set<String> theAddedCodes) {
 		Optional<TermValueSet> optionalTermValueSet;
 		if (theValueSetToExpand.hasUrl()) {
 			if (theValueSetToExpand.hasVersion()) {
@@ -621,7 +617,7 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 							"valueSetExpandedUsingInMemoryExpansion",
 							getValueSetInfo(theValueSetToExpand));
 			theAccumulator.addMessage(msg);
-			doExpandValueSet(theExpansionOptions, theValueSetToExpand, theAccumulator, theFilter);
+			doExpandValueSet(theExpansionOptions, theValueSetToExpand, theAccumulator, theFilter, theAddedCodes);
 			return;
 		}
 
@@ -639,7 +635,7 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 							termValueSet.getExpansionStatus().name(),
 							termValueSet.getExpansionStatus().getDescription());
 			theAccumulator.addMessage(msg);
-			doExpandValueSet(theExpansionOptions, theValueSetToExpand, theAccumulator, theFilter);
+			doExpandValueSet(theExpansionOptions, theValueSetToExpand, theAccumulator, theFilter, theAddedCodes);
 			return;
 		}
 
@@ -651,7 +647,8 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 				.getLocalizer()
 				.getMessage(TermReadSvcImpl.class, "valueSetExpandedUsingPreExpansion", expansionTimestamp);
 		theAccumulator.addMessage(msg);
-		expandConcepts(theExpansionOptions, theAccumulator, termValueSet, theFilter, theAdd, isOracleDialect());
+		expandConcepts(
+				theExpansionOptions, theAccumulator, termValueSet, theFilter, theAdd, theAddedCodes, isOracleDialect());
 	}
 
 	@Nonnull
@@ -676,6 +673,7 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 			TermValueSet theTermValueSet,
 			ExpansionFilter theFilter,
 			boolean theAdd,
+			Set<String> theAddedCodes,
 			boolean theOracle) {
 		// NOTE: if you modifiy the logic here, look to `expandConceptsOracle` and see if your new code applies to its
 		// copy pasted sibling
@@ -708,10 +706,6 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 			}
 			wasFilteredResult = true;
 		} else {
-			// TODO JA HS: I'm pretty sure we are overfetching here.  test says offset 3, count 4, but we are fetching
-			// index 3 -> 10 here, grabbing 7 concepts.
-			// Specifically this test
-			// testExpandInline_IncludePreExpandedValueSetByUri_FilterOnDisplay_LeftMatch_SelectRange
 			if (theOracle) {
 				conceptViews = myTermValueSetConceptViewOracleDao.findByTermValueSetId(
 						offset, toIndex, theTermValueSet.getId());
@@ -802,26 +796,27 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 
 				Long sourceConceptPid = pidToSourcePid.get(nextPid);
 				String sourceConceptDirectParentPids = pidToSourceDirectParentPids.get(nextPid);
-				theAccumulator.includeConceptWithDesignations(
+				if (theAddedCodes.add(system + OUR_PIPE_CHARACTER + code)) {
-						system,
+					theAccumulator.includeConceptWithDesignations(
-						code,
+							system,
-						display,
+							code,
-						designations,
+							display,
-						sourceConceptPid,
+							designations,
-						sourceConceptDirectParentPids,
+							sourceConceptPid,
-						systemVersion);
+							sourceConceptDirectParentPids,
+							systemVersion);
+					if (wasFilteredResult) {
+						theAccumulator.incrementOrDecrementTotalConcepts(true, 1);
+					}
+				}
 			} else {
-				boolean removed = theAccumulator.excludeConcept(system, code);
+				if (theAddedCodes.remove(system + OUR_PIPE_CHARACTER + code)) {
-				if (removed) {
+					theAccumulator.excludeConcept(system, code);
 					theAccumulator.incrementOrDecrementTotalConcepts(false, 1);
 				}
 			}
 		}
 
-		if (wasFilteredResult && theAdd) {
-			theAccumulator.incrementOrDecrementTotalConcepts(true, pidToConcept.size());
-		}
-
 		logDesignationsExpanded("Finished expanding designations. ", theTermValueSet, designationsExpanded);
 		logConceptsExpanded("Finished expanding concepts. ", theTermValueSet, conceptsExpanded);
 	}
@@ -886,8 +881,13 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 			ValueSetExpansionOptions theExpansionOptions,
 			ValueSet theValueSetToExpand,
 			IValueSetConceptAccumulator theValueSetCodeAccumulator) {
+		Set<String> addedCodes = new HashSet<>();
 		doExpandValueSet(
-				theExpansionOptions, theValueSetToExpand, theValueSetCodeAccumulator, ExpansionFilter.NO_FILTER);
+				theExpansionOptions,
+				theValueSetToExpand,
+				theValueSetCodeAccumulator,
+				ExpansionFilter.NO_FILTER,
+				addedCodes);
 	}
 
 	/**
@@ -898,8 +898,8 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 			ValueSetExpansionOptions theExpansionOptions,
 			ValueSet theValueSetToExpand,
 			IValueSetConceptAccumulator theValueSetCodeAccumulator,
-			@Nonnull ExpansionFilter theExpansionFilter) {
+			@Nonnull ExpansionFilter theExpansionFilter,
-		Set<String> addedCodes = new HashSet<>();
+			Set<String> theAddedCodes) {
 
 		StopWatch sw = new StopWatch();
 		String valueSetInfo = getValueSetInfo(theValueSetToExpand);
@@ -908,7 +908,7 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 		// Offset can't be combined with excludes
 		Integer skipCountRemaining = theValueSetCodeAccumulator.getSkipCountRemaining();
 		if (skipCountRemaining != null && skipCountRemaining > 0) {
-			if (theValueSetToExpand.getCompose().getExclude().size() > 0) {
+			if (!theValueSetToExpand.getCompose().getExclude().isEmpty()) {
 				String msg = myContext
 						.getLocalizer()
 						.getMessage(TermReadSvcImpl.class, "valueSetNotYetExpanded_OffsetNotAllowed", valueSetInfo);
@@ -921,7 +921,7 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 		for (ValueSet.ConceptSetComponent include :
 				theValueSetToExpand.getCompose().getInclude()) {
 			myTxTemplate.executeWithoutResult(tx -> expandValueSetHandleIncludeOrExclude(
-					theExpansionOptions, theValueSetCodeAccumulator, addedCodes, include, true, theExpansionFilter));
+					theExpansionOptions, theValueSetCodeAccumulator, theAddedCodes, include, true, theExpansionFilter));
 		}
 
 		// Handle excludes
@@ -931,7 +931,7 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 			myTxTemplate.executeWithoutResult(tx -> expandValueSetHandleIncludeOrExclude(
 					theExpansionOptions,
 					theValueSetCodeAccumulator,
-					addedCodes,
+					theAddedCodes,
 					exclude,
 					false,
 					ExpansionFilter.NO_FILTER));
@@ -976,7 +976,7 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 
 		String system = theIncludeOrExclude.getSystem();
 		boolean hasSystem = isNotBlank(system);
-		boolean hasValueSet = theIncludeOrExclude.getValueSet().size() > 0;
+		boolean hasValueSet = !theIncludeOrExclude.getValueSet().isEmpty();
 
 		if (hasSystem) {
 
@@ -1004,7 +1004,7 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 
 			} else {
 
-				if (theIncludeOrExclude.getConcept().size() > 0 && theExpansionFilter.hasCode()) {
+				if (!theIncludeOrExclude.getConcept().isEmpty() && theExpansionFilter.hasCode()) {
 					if (defaultString(theIncludeOrExclude.getSystem()).equals(theExpansionFilter.getSystem())) {
 						if (theIncludeOrExclude.getConcept().stream()
 								.noneMatch(t -> t.getCode().equals(theExpansionFilter.getCode()))) {
@@ -1065,7 +1065,12 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 				}
 
 				expandValueSetIntoAccumulator(
-						valueSet, theExpansionOptions, theValueSetCodeAccumulator, subExpansionFilter, theAdd);
+						valueSet,
+						theExpansionOptions,
+						theValueSetCodeAccumulator,
+						subExpansionFilter,
+						theAdd,
+						theAddedCodes);
 			}
 
 		} else {
@@ -1855,12 +1860,11 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 			if (!handled) {
 				throwInvalidFilter(
 						nextFilter,
-						" - Note that Hibernate Search is disabled on this server so not all ValueSet expansion funtionality is available.");
+						" - Note that Hibernate Search is disabled on this server so not all ValueSet expansion functionality is available.");
 			}
 		}
 
-		if (theInclude.getConcept().isEmpty()) {
+		if (theInclude.getFilter().isEmpty() && theInclude.getConcept().isEmpty()) {
-
 			Collection<TermConcept> concepts =
 					myConceptDao.fetchConceptsAndDesignationsByVersionPid(theVersion.getPid());
 			for (TermConcept next : concepts) {
@@ -2392,7 +2396,8 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
 						sw);
 
 			} catch (Exception e) {
-				ourLog.error("Failed to pre-expand ValueSet: " + e.getMessage(), e);
+				ourLog.error(
+						"Failed to pre-expand ValueSet with URL[{}]: {}", valueSetToExpand.getUrl(), e.getMessage(), e);
 				txTemplate.executeWithoutResult(t -> {
 					valueSetToExpand.setExpansionStatus(TermValueSetPreExpansionStatusEnum.FAILED_TO_EXPAND);
 					myTermValueSetDao.saveAndFlush(valueSetToExpand);

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4Test.java

@@ -36,7 +36,6 @@ import org.hl7.fhir.r4.model.codesystems.HttpVerb;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
-import org.mockito.Mock;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.data.domain.Pageable;
@@ -73,9 +72,6 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test {
 
 	private final ValueSetTestUtil myValueSetTestUtil = new ValueSetTestUtil(FhirVersionEnum.R4);
 
-	@Mock
-	private IValueSetConceptAccumulator myValueSetCodeAccumulator;
-
 	@AfterEach
 	public void afterEach() {
 		SearchBuilder.setMaxPageSize50ForTest(false);
@@ -280,8 +276,9 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test {
 
 		//Ensure that the subsequent expansion with offset returns the same slice we are anticipating.
 		assertThat(myValueSetTestUtil.toCodes(expandedValueSet).toString(), myValueSetTestUtil.toCodes(expandedValueSet), is(equalTo(expandedConceptCodes.subList(offset, offset + count))));
-		Assertions.assertEquals(4, expandedValueSet.getExpansion().getContains().size(), myValueSetTestUtil.toCodes(expandedValueSet).toString());
+		Assertions.assertEquals(count, expandedValueSet.getExpansion().getContains().size(), myValueSetTestUtil.toCodes(expandedValueSet).toString());
-		assertEquals(11, expandedValueSet.getExpansion().getTotal());
+		assertEquals(offset + count, expandedValueSet.getExpansion().getTotal());
+		assertEquals(count, expandedValueSet.getExpansion().getContains().size());
 
 		// Make sure we used the pre-expanded version
 		List<SqlQuery> selectQueries = myCaptureQueriesListener.getSelectQueries();

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionWithHierarchyR4Test.java

@@ -0,0 +1,109 @@
+package ca.uhn.fhir.jpa.term;
+
+import ca.uhn.fhir.jpa.entity.TermValueSet;
+import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.ValueSet;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
+
+import java.util.Optional;
+import java.util.stream.Stream;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.params.provider.Arguments.arguments;
+
+public class ValueSetExpansionWithHierarchyR4Test extends BaseTermR4Test {
+   private static final String ourCodeSystemId = "CodeSystem-WithHierarchy", ourCodeSystemUrl = "http://example/" + ourCodeSystemId;
+   private static final String ourCodeA = "CodeA", ourCodeB = "CodeB", ourCodeC = "CodeC", ourCodeD = "CodeD";
+   private static final String ourValueSetAUrl = "http://example/ValueSetA", ourValueSetBUrl = "http://example/ValueSetB", ourValueSetUrl = "http://example/ValueSet";
+   private static final int ourChildConceptCount = 10;
+
+   @BeforeAll
+   public static void setup() {
+      TermReadSvcImpl.setForceDisableHibernateSearchForUnitTest(true);
+   }
+   @AfterAll
+   public static void tearDown() {
+      TermReadSvcImpl.setForceDisableHibernateSearchForUnitTest(false);
+   }
+   @BeforeEach
+   public void setupHierarchicalCodeSystemWithValueSets() {
+      myStorageSettings.setPreExpandValueSets(true);
+
+      CodeSystem codeSystem = new CodeSystem();
+      codeSystem.setId(ourCodeSystemId);
+      codeSystem.setUrl(ourCodeSystemUrl);
+      CodeSystem.ConceptDefinitionComponent concept1 = codeSystem.addConcept().setCode(ourCodeA);
+      CodeSystem.ConceptDefinitionComponent concept2 = codeSystem.addConcept().setCode(ourCodeB);
+      for (int i = 0; i < ourChildConceptCount; i++) {
+         concept1.addConcept().setCode(concept1.getCode() + i);
+         concept2.addConcept().setCode(concept2.getCode() + i);
+      }
+      codeSystem.addConcept().setCode(ourCodeC);
+      codeSystem.addConcept().setCode(ourCodeD);
+      myCodeSystemDao.create(codeSystem, mySrd);
+
+      ValueSet valueSetA = new ValueSet();
+      valueSetA.setUrl(ourValueSetAUrl);
+      valueSetA.getCompose().addInclude().setSystem(ourCodeSystemUrl)
+            .addFilter().setProperty("concept").setOp(ValueSet.FilterOperator.ISA).setValue(ourCodeA);
+      myValueSetDao.create(valueSetA, mySrd);
+
+      ValueSet valueSetB = new ValueSet();
+      valueSetB.setUrl(ourValueSetBUrl);
+      valueSetA.getCompose().addInclude().setSystem(ourCodeSystemUrl)
+            .addFilter().setProperty("concept").setOp(ValueSet.FilterOperator.ISA).setValue(ourCodeB);
+      myValueSetDao.create(valueSetB, mySrd);
+   }
+
+   static Stream<Arguments> parametersValueSets() {
+      ValueSet valueSet0 = new ValueSet();
+      valueSet0.setUrl(ourValueSetUrl + "-WithIncludeChildValueSet");
+      valueSet0.getCompose().addInclude().addValueSet(ourValueSetAUrl);
+
+      ValueSet valueSet1 = new ValueSet();
+      valueSet1.setUrl(ourValueSetUrl + "-WithIncludeChildValueSetAndCodeSystem");
+      valueSet1.getCompose().addInclude().addValueSet(ourValueSetAUrl);
+      valueSet1.getCompose().addInclude().addValueSet(ourValueSetBUrl);
+      valueSet1.getCompose().addInclude().setSystem(ourCodeSystemUrl);
+
+      ValueSet valueSet2 = new ValueSet();
+      valueSet2.setUrl(ourValueSetUrl + "-WithIncludeChildValueSetAndCodeSystemConceptSet-NoIntersectionCodes");
+      valueSet2.getCompose().addInclude().addValueSet(ourValueSetAUrl);
+      ValueSet.ConceptSetComponent conceptSetWithCodeSystem = valueSet2.getCompose().addInclude().setSystem(ourCodeSystemUrl);
+      conceptSetWithCodeSystem.addConcept().setCode(ourCodeC);
+      conceptSetWithCodeSystem.addConcept().setCode(ourCodeD);
+
+      ValueSet valueSet3 = new ValueSet();
+      valueSet3.setUrl(ourValueSetUrl + "-WithIncludeChildValueSetAndCodeSystemConceptSet-WithIntersectionCodes");
+      valueSet3.getCompose().addInclude().addValueSet(ourValueSetAUrl);
+      conceptSetWithCodeSystem = valueSet3.getCompose().addInclude().setSystem(ourCodeSystemUrl);
+      conceptSetWithCodeSystem.addConcept().setCode(ourCodeA + "1");
+      conceptSetWithCodeSystem.addConcept().setCode(ourCodeA + "2");
+
+      return Stream.of(
+            arguments(valueSet0, ourChildConceptCount),
+            arguments(valueSet1, 4 + ourChildConceptCount * 2),
+            arguments(valueSet2, 2 + ourChildConceptCount),
+            arguments(valueSet3, ourChildConceptCount)
+      );
+   }
+
+   @ParameterizedTest
+   @MethodSource(value = "parametersValueSets")
+   public void testExpandValueSet_whenUsingHierarchicalCodeSystem_willExpandSuccessfully(ValueSet theValueSet, int theExpectedConceptExpensionCount) {
+      myValueSetDao.create(theValueSet, mySrd);
+      myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
+      Optional<TermValueSet> optionalTermValueSet = runInTransaction(() -> myTermValueSetDao.findTermValueSetByUrlAndNullVersion(theValueSet.getUrl()));
+      assertTrue(optionalTermValueSet.isPresent());
+      TermValueSet expandedTermValueSet = optionalTermValueSet.get();
+      assertEquals(TermValueSetPreExpansionStatusEnum.EXPANDED, expandedTermValueSet.getExpansionStatus());
+      assertEquals(theExpectedConceptExpensionCount, expandedTermValueSet.getTotalConcepts());
+   }
+}