Merge branch 'master' into 2849_add_new_mdm_param

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2837-search-with-not-modifier-on-multiple-codes.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 2837
+title: "The :not modifier does not currently work for observations with multiple codes for the search. This is fixed."

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java

@@ -989,8 +989,11 @@ public class QueryStack {
 													  SearchFilterParser.CompareOperation theOperation, RequestPartitionId theRequestPartitionId) {
 
 		List<IQueryParameterType> tokens = new ArrayList<>(); 
-		for (IQueryParameterType nextOr : theList) {
 		
+		boolean paramInverted = false;
+		TokenParamModifier modifier = null;
+		
+		for (IQueryParameterType nextOr : theList) {
 			if (nextOr instanceof TokenParam) {
 				if (!((TokenParam) nextOr).isEmpty()) {
 					TokenParam id = (TokenParam) nextOr;
@@ -1011,15 +1014,18 @@ public class QueryStack {
 						return createPredicateString(theSourceJoinColumn, theResourceName, theSpnamePrefix, theSearchParam, theList, null, theRequestPartitionId);
 					} 
 					
-					tokens.add(nextOr);
+					modifier = id.getModifier();
-
+					// for :not modifier, create a token and remove the :not modifier
-				}
+					if (modifier != null && modifier == TokenParamModifier.NOT) {
-
+						tokens.add(new TokenParam(((TokenParam) nextOr).getSystem(), ((TokenParam) nextOr).getValue()));
+						paramInverted = true;
+					} else {
+						tokens.add(nextOr);
+					}
+				}
 			} else {
-
 				tokens.add(nextOr);
 			}
-
 		}
 
 		if (tokens.isEmpty()) {
@@ -1027,14 +1033,37 @@ public class QueryStack {
 		}
 
 		String paramName = getParamNameWithPrefix(theSpnamePrefix, theSearchParam.getName());
+		Condition predicate;
+		BaseJoiningPredicateBuilder join;
 		
-		TokenPredicateBuilder join = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.TOKEN, theSourceJoinColumn, paramName, () -> mySqlBuilder.addTokenPredicateBuilder(theSourceJoinColumn)).getResult();
+		if (paramInverted) {
+			SearchQueryBuilder sqlBuilder = mySqlBuilder.newChildSqlBuilder();
+			TokenPredicateBuilder tokenSelector = sqlBuilder.addTokenPredicateBuilder(null);
+			sqlBuilder.addPredicate(tokenSelector.createPredicateToken(tokens, theResourceName, theSpnamePrefix, theSearchParam, theRequestPartitionId));
+			SelectQuery sql = sqlBuilder.getSelect();
+			Expression subSelect = new Subquery(sql);
 			
-		if (theList.get(0).getMissing() != null) {
+			join = mySqlBuilder.getOrCreateFirstPredicateBuilder();
-			return join.createPredicateParamMissingForNonReference(theResourceName, paramName, theList.get(0).getMissing(), theRequestPartitionId);
+			
+			if (theSourceJoinColumn == null) {
+				predicate = new InCondition(join.getResourceIdColumn(), subSelect).setNegate(true);
+			} else {
+				//-- for the resource link, need join with target_resource_id
+			    predicate = new InCondition(theSourceJoinColumn, subSelect).setNegate(true);
+			}
+						
+		} else {
+		
+			TokenPredicateBuilder tokenJoin = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.TOKEN, theSourceJoinColumn, paramName, () -> mySqlBuilder.addTokenPredicateBuilder(theSourceJoinColumn)).getResult();
+
+			if (theList.get(0).getMissing() != null) {
+				return tokenJoin.createPredicateParamMissingForNonReference(theResourceName, paramName, theList.get(0).getMissing(), theRequestPartitionId);
+			}
+
+			predicate = tokenJoin.createPredicateToken(tokens, theResourceName, theSpnamePrefix, theSearchParam, theOperation, theRequestPartitionId);
+			join = tokenJoin; 
 		} 
 		
-		Condition predicate = join.createPredicateToken(tokens, theResourceName, theSpnamePrefix, theSearchParam, theOperation, theRequestPartitionId);
 		return join.combineWithRequestPartitionIdPredicate(theRequestPartitionId, predicate);
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java

@@ -221,11 +221,15 @@ public class SearchBuilder implements ISearchBuilder {
 
 		SearchContainedModeEnum searchContainedMode = theParams.getSearchContainedMode();
 
-		// Handle _id last, since it can typically be tacked onto a different parameter
+		// Handle _id and _tag last, since they can typically be tacked onto a different parameter
-		List<String> paramNames = myParams.keySet().stream().filter(t -> !t.equals(IAnyResource.SP_RES_ID)).collect(Collectors.toList());
+		List<String> paramNames = myParams.keySet().stream().filter(t -> !t.equals(IAnyResource.SP_RES_ID))
+			.filter(t -> !t.equals(Constants.PARAM_TAG)).collect(Collectors.toList());
 		if (myParams.containsKey(IAnyResource.SP_RES_ID)) {
 			paramNames.add(IAnyResource.SP_RES_ID);
 		}
+		if (myParams.containsKey(Constants.PARAM_TAG)) {
+			paramNames.add(Constants.PARAM_TAG);
+		}
 
 		// Handle each parameter
 		for (String nextParamName : paramNames) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceLinkPredicateBuilder.java

@@ -62,6 +62,7 @@ import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.param.SpecialParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.param.TokenParamModifier;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
@@ -338,6 +339,7 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
 		boolean foundChainMatch = false;
 		List<String> candidateTargetTypes = new ArrayList<>();
 		List<Condition> orPredicates = new ArrayList<>();
+		boolean paramInverted = false;
 		QueryStack childQueryFactory = myQueryStack.newChildQueryFactoryWithFullBuilderReuse();
 		for (String nextType : resourceTypes) {
 			String chain = theReferenceParam.getChain();
@@ -383,6 +385,13 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
 				if (chainValue == null) {
 					continue;
 				}
+
+				// For the token param, if it's a :not modifier, need switch OR to AND
+				if (!paramInverted && chainValue instanceof TokenParam) {
+					if (((TokenParam) chainValue).getModifier() == TokenParamModifier.NOT) {
+						paramInverted = true;
+					}
+				}
 				foundChainMatch = true;
 				orValues.add(chainValue);
 			}
@@ -410,10 +419,17 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
 			warnAboutPerformanceOnUnqualifiedResources(theParamName, theRequest, candidateTargetTypes);
 		}
 
-		Condition multiTypeOrPredicate = toOrPredicate(orPredicates);
+		// If :not modifier for a token, switch OR with AND in the multi-type case
+		Condition multiTypePredicate;
+		if (paramInverted) {
+			multiTypePredicate = toAndPredicate(orPredicates);
+		} else {
+			multiTypePredicate = toOrPredicate(orPredicates);
+		}
+		
 		List<String> pathsToMatch = createResourceLinkPaths(theResourceName, theParamName);
 		Condition pathPredicate = createPredicateSourcePaths(pathsToMatch);
-		return toAndPredicate(pathPredicate, multiTypeOrPredicate);
+		return toAndPredicate(pathPredicate, multiTypePredicate);
 	}
 
 	@Nonnull

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/TestUtil.java

@@ -96,7 +96,7 @@ public class TestUtil {
 				.collect(Collectors.toSet());
 		}
 
-		ImmutableSet<ClassInfo> classes = ClassPath.from(TestUtil.class.getClassLoader()).getTopLevelClasses(packageName);
+		ImmutableSet<ClassInfo> classes = ClassPath.from(TestUtil.class.getClassLoader()).getTopLevelClassesRecursive(packageName);
 		Set<String> names = new HashSet<String>();
 
 		if (classes.size() <= 1) {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java

@@ -63,6 +63,7 @@ import org.hl7.fhir.dstu3.model.AllergyIntolerance;
 import org.hl7.fhir.dstu3.model.Appointment;
 import org.hl7.fhir.dstu3.model.AuditEvent;
 import org.hl7.fhir.dstu3.model.Binary;
+import org.hl7.fhir.dstu3.model.BodySite;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.CarePlan;
 import org.hl7.fhir.dstu3.model.CodeSystem;
@@ -95,6 +96,7 @@ import org.hl7.fhir.dstu3.model.Organization;
 import org.hl7.fhir.dstu3.model.Patient;
 import org.hl7.fhir.dstu3.model.Practitioner;
 import org.hl7.fhir.dstu3.model.PractitionerRole;
+import org.hl7.fhir.dstu3.model.Procedure;
 import org.hl7.fhir.dstu3.model.ProcedureRequest;
 import org.hl7.fhir.dstu3.model.Questionnaire;
 import org.hl7.fhir.dstu3.model.QuestionnaireResponse;
@@ -317,6 +319,12 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	@Qualifier("myTaskDaoDstu3")
 	protected IFhirResourceDao<Task> myTaskDao;
 	@Autowired
+	@Qualifier("myBodySiteDaoDstu3")
+	protected IFhirResourceDao<BodySite> myBodySiteDao;
+	@Autowired
+	@Qualifier("myProcedureDaoDstu3")
+	protected IFhirResourceDao<Procedure> myProcedureDao;
+	@Autowired
 	protected ITermConceptDao myTermConceptDao;
 	@Autowired
 	protected ITermCodeSystemDao myTermCodeSystemDao;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchOptimizedTest.java

@@ -21,18 +21,29 @@ import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.param.TokenOrListParam;
 import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.param.TokenParamModifier;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.exception.ExceptionUtils;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.BodyStructure;
+import org.hl7.fhir.r4.model.CodeableConcept;
+import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.DateTimeType;
+import org.hl7.fhir.r4.model.Device;
 import org.hl7.fhir.r4.model.Enumerations;
+import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Organization;
 import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.Procedure;
+import org.hl7.fhir.r4.model.Provenance;
 import org.hl7.fhir.r4.model.Reference;
+import org.hl7.fhir.r4.model.SearchParameter;
+import org.hl7.fhir.r4.model.StringType;
+import org.hl7.fhir.r4.model.UriType;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -906,6 +917,117 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testSearchOnUnderscoreParams_AvoidHFJResourceJoins() {
+		// This Issue: https://github.com/hapifhir/hapi-fhir/issues/2942
+		// See this PR for a similar type of Fix: https://github.com/hapifhir/hapi-fhir/pull/2909
+		SearchParameter searchParameter = new SearchParameter();
+		searchParameter.addBase("BodySite").addBase("Procedure");
+		searchParameter.setCode("focalAccess");
+		searchParameter.setType(Enumerations.SearchParamType.REFERENCE);
+		searchParameter.setExpression("Procedure.extension('Procedure#focalAccess')");
+		searchParameter.setXpathUsage(SearchParameter.XPathUsageType.NORMAL);
+		searchParameter.setStatus(Enumerations.PublicationStatus.ACTIVE);
+		IIdType spId = mySearchParameterDao.create(searchParameter).getId().toUnqualifiedVersionless();
+		mySearchParamRegistry.forceRefresh();
+
+		BodyStructure bs = new BodyStructure();
+		bs.setDescription("BodyStructure in R4 replaced BodySite from DSTU4");
+		IIdType bsId = myBodyStructureDao.create(bs, mySrd).getId().toUnqualifiedVersionless();
+
+		Patient patient = new Patient();
+		patient.setId("P1");
+		patient.setActive(true);
+		patient.addName().setFamily("FamilyName");
+		Extension extParent = patient
+			.addExtension()
+			.setUrl("http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity");
+		extParent
+			.addExtension()
+			.setUrl("ombCategory")
+			.setValue(new CodeableConcept().addCoding(new Coding().setSystem("urn:oid:2.16.840.1.113883.5.50")
+			.setCode("2186-5")
+			.setDisplay("Not Hispanic or Latino")));
+		extParent
+			.addExtension()
+			.setUrl("text")
+			.setValue(new StringType("Not Hispanic or Latino"));
+		myPatientDao.update(patient);
+		CodeableConcept categoryCodeableConcept1 = new CodeableConcept().addCoding(new Coding().setSystem("acc_proccat_fkc")
+			.setCode("CANN")
+			.setDisplay("Cannulation"));
+		Procedure procedure = new Procedure();
+		procedure.setSubject(new Reference("Patient/P1"));
+		procedure.setStatus(Procedure.ProcedureStatus.COMPLETED);
+		procedure.setCategory(categoryCodeableConcept1);
+		Extension extProcedure = procedure
+			.addExtension()
+			.setUrl("Procedure#focalAccess")
+			.setValue(new UriType("BodyStructure/" + bsId.getIdPartAsLong()));
+		procedure.getMeta()
+			.addTag("acc_procext_fkc", "1STCANN2NDL", "First Successful Cannulation with 2 Needles");
+		IIdType procedureId = myProcedureDao.create(procedure).getId().toUnqualifiedVersionless();
+
+		logAllResources();
+		logAllResourceTags();
+		logAllResourceVersions();
+
+		// Search example 1:
+		// http://FHIR_SERVER/fhir_request/Procedure
+		// ?status%3Anot=entered-in-error&subject=B
+		// &category=CANN&focalAccess=BodySite%2F3530342921&_tag=TagValue
+		// NOTE: This gets sorted once so the order is different once it gets executed!
+		{
+			// IMPORTANT: Keep the query param order exactly as shown below!
+			SearchParameterMap map = SearchParameterMap.newSynchronous();
+			// _tag, category, status, subject, focalAccess
+			map.add("_tag", new TokenParam("TagValue"));
+			map.add("category", new TokenParam("CANN"));
+			map.add("status", new TokenParam("entered-in-error").setModifier(TokenParamModifier.NOT));
+			map.add("subject", new ReferenceParam("Patient/P1"));
+			map.add("focalAccess", new ReferenceParam("BodyStructure/" + bsId.getIdPart()));
+			myCaptureQueriesListener.clear();
+			IBundleProvider outcome = myProcedureDao.search(map, new SystemRequestDetails());
+			ourLog.info("Search returned {} resources.", outcome.getResources(0, 999).size());
+			myCaptureQueriesListener.logSelectQueriesForCurrentThread();
+
+			String selectQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
+			// Check for a particular WHERE CLAUSE in the generated SQL to make sure we are verifying the correct query
+			assertEquals(2, StringUtils.countMatches(selectQuery.toLowerCase(), " join hfj_res_link "), selectQuery);
+
+			// Ensure that we do NOT see a couple of particular WHERE clauses
+			assertEquals(0, StringUtils.countMatches(selectQuery.toLowerCase(), ".res_type = 'procedure'"), selectQuery);
+			assertEquals(0, StringUtils.countMatches(selectQuery.toLowerCase(), ".res_deleted_at is null"), selectQuery);
+		}
+
+		// Search example 2:
+		// http://FHIR_SERVER/fhir_request/Procedure
+		// ?status%3Anot=entered-in-error&category=CANN&focalAccess=3692871435
+		// &_tag=1STCANN1NDL%2C1STCANN2NDL&outcome=SUCCESS&_count=1&_requestTrace=True
+		// NOTE: This gets sorted once so the order is different once it gets executed!
+		{
+			// IMPORTANT: Keep the query param order exactly as shown below!
+			// NOTE: The "outcome" SearchParameter is not being used below, but it doesn't affect the test.
+			SearchParameterMap map = SearchParameterMap.newSynchronous();
+			// _tag, category, status, focalAccess
+			map.add("_tag", new TokenParam("TagValue"));
+			map.add("category", new TokenParam("CANN"));
+			map.add("status", new TokenParam("entered-in-error").setModifier(TokenParamModifier.NOT));
+			map.add("focalAccess", new ReferenceParam("BodyStructure/" + bsId.getIdPart()));
+			myCaptureQueriesListener.clear();
+			IBundleProvider outcome = myProcedureDao.search(map, new SystemRequestDetails());
+			ourLog.info("Search returned {} resources.", outcome.getResources(0, 999).size());
+			myCaptureQueriesListener.logSelectQueriesForCurrentThread();
+
+			String selectQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
+			// Check for a particular WHERE CLAUSE in the generated SQL to make sure we are verifying the correct query
+			assertEquals(1, StringUtils.countMatches(selectQuery.toLowerCase(), " join hfj_res_link "), selectQuery);
+
+			// Ensure that we do NOT see a couple of particular WHERE clauses
+			assertEquals(0, StringUtils.countMatches(selectQuery.toLowerCase(), ".res_type = 'procedure'"), selectQuery);
+			assertEquals(0, StringUtils.countMatches(selectQuery.toLowerCase(), ".res_deleted_at is null"), selectQuery);
+		}
+	}
 
 	@AfterEach
 	public void afterResetDao() {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/PartitioningSqlR4Test.java

@@ -2272,7 +2272,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
 		ourLog.info("Search SQL:\n{}", searchSql);
 		assertEquals(0, StringUtils.countMatches(searchSql, "PARTITION_ID"), searchSql);
 		assertEquals(1, StringUtils.countMatches(searchSql, "TAG_SYSTEM = 'http://system'"), searchSql);
-		assertEquals(1, StringUtils.countMatches(searchSql, "t1.HASH_SYS_AND_VALUE ="), searchSql);
+		assertEquals(1, StringUtils.countMatches(searchSql, ".HASH_SYS_AND_VALUE ="), searchSql);
 
 
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderSearchModifierDstu3Test.java

@@ -0,0 +1,77 @@
+package ca.uhn.fhir.jpa.provider.dstu3;
+
+import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
+import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
+import ca.uhn.fhir.jpa.searchparam.ResourceSearch;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import org.hl7.fhir.dstu3.model.BodySite;
+import org.hl7.fhir.dstu3.model.CodeableConcept;
+import org.hl7.fhir.dstu3.model.Coding;
+import org.hl7.fhir.dstu3.model.Encounter;
+import org.hl7.fhir.dstu3.model.Observation;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.dstu3.model.Procedure;
+import org.hl7.fhir.dstu3.model.Reference;
+import org.hl7.fhir.dstu3.model.SearchParameter;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.Collections;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.equalTo;
+import static org.hamcrest.Matchers.is;
+
+public class ResourceProviderSearchModifierDstu3Test extends BaseResourceProviderDstu3Test{
+	@Autowired
+	MatchUrlService myMatchUrlService;
+
+	@Test
+	public void testReplicateBugWithNotDuringChain() {
+		Encounter enc = new Encounter();
+		enc.setType(Collections.singletonList(new CodeableConcept().addCoding(new Coding("system", "value", "display"))));
+		IIdType encId = myEncounterDao.create(enc).getId();
+
+		Observation obs = new Observation();
+		obs.setContext(new Reference(encId));
+		myObservationDao.create(obs).getId();
+
+		{
+			//Works when not chained:
+			String encounterSearchString = "Encounter?type:not=system|value";
+			ResourceSearch resourceSearch = myMatchUrlService.getResourceSearch(encounterSearchString);
+			SearchParameterMap searchParameterMap = resourceSearch.getSearchParameterMap();
+			IBundleProvider search = myEncounterDao.search(searchParameterMap);
+			assertThat(search.size(), is(equalTo(0)));
+		}
+		{
+			//Works without the NOT qualifier.
+			String resultSearchString = "Observation?context.type=system|value";
+			ResourceSearch resourceSearch = myMatchUrlService.getResourceSearch(resultSearchString);
+			SearchParameterMap searchParameterMap = resourceSearch.getSearchParameterMap();
+			IBundleProvider search = myObservationDao.search(searchParameterMap);
+			assertThat(search.size(), is(equalTo(1)));
+		}
+
+		{
+			//Works in a chain
+			String noResultSearchString = "Observation?context.type:not=system|value";
+			ResourceSearch resourceSearch = myMatchUrlService.getResourceSearch(noResultSearchString);
+			SearchParameterMap searchParameterMap = resourceSearch.getSearchParameterMap();
+			IBundleProvider search = myObservationDao.search(searchParameterMap);
+			assertThat(search.size(), is(equalTo(0)));
+		}
+		{
+			//Works in a chain with only value
+			String noResultSearchString = "Observation?context.type:not=value";
+			ResourceSearch resourceSearch = myMatchUrlService.getResourceSearch(noResultSearchString);
+			SearchParameterMap searchParameterMap = resourceSearch.getSearchParameterMap();
+			IBundleProvider search = myObservationDao.search(searchParameterMap);
+			assertThat(search.size(), is(equalTo(0)));
+
+		}
+
+	}
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderSearchModifierR4Test.java

@@ -0,0 +1,249 @@
+package ca.uhn.fhir.jpa.provider.r4;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.CodeableConcept;
+import org.hl7.fhir.r4.model.DateTimeType;
+import org.hl7.fhir.r4.model.Observation;
+import org.hl7.fhir.r4.model.Observation.ObservationStatus;
+import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.Quantity;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.parser.StrictErrorHandler;
+import ca.uhn.fhir.rest.client.interceptor.CapturingInterceptor;
+
+
+public class ResourceProviderSearchModifierR4Test extends BaseResourceProviderR4Test {
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderSearchModifierR4Test.class);
+	private CapturingInterceptor myCapturingInterceptor = new CapturingInterceptor();
+
+	@Override
+	@AfterEach
+	public void after() throws Exception {
+		super.after();
+
+		myDaoConfig.setAllowMultipleDelete(new DaoConfig().isAllowMultipleDelete());
+		myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
+		myDaoConfig.setReuseCachedSearchResultsForMillis(new DaoConfig().getReuseCachedSearchResultsForMillis());
+		myDaoConfig.setCountSearchResultsUpTo(new DaoConfig().getCountSearchResultsUpTo());
+		myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
+		myDaoConfig.setAllowContainsSearches(new DaoConfig().isAllowContainsSearches());
+		myDaoConfig.setIndexMissingFields(new DaoConfig().getIndexMissingFields());
+		
+		myClient.unregisterInterceptor(myCapturingInterceptor);
+	}
+
+	@BeforeEach
+	@Override
+	public void before() throws Exception {
+		super.before();
+		myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
+
+		myDaoConfig.setAllowMultipleDelete(true);
+		myClient.registerInterceptor(myCapturingInterceptor);
+		myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
+	}
+
+	@BeforeEach
+	public void beforeDisableResultReuse() {
+		myDaoConfig.setReuseCachedSearchResultsForMillis(null);
+	}
+
+	@Test
+	public void testSearch_SingleCode_not_modifier() throws Exception {
+
+		List<IIdType> obsList = createObs(10, false);
+		
+		String uri = ourServerBase + "/Observation?code:not=2345-3";
+		List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+		
+		assertEquals(9, ids.size());
+		assertEquals(obsList.get(0).toString(), ids.get(0));
+		assertEquals(obsList.get(1).toString(), ids.get(1));
+		assertEquals(obsList.get(2).toString(), ids.get(2));
+		assertEquals(obsList.get(4).toString(), ids.get(3));
+		assertEquals(obsList.get(5).toString(), ids.get(4));
+		assertEquals(obsList.get(6).toString(), ids.get(5));
+		assertEquals(obsList.get(7).toString(), ids.get(6));
+		assertEquals(obsList.get(8).toString(), ids.get(7));
+		assertEquals(obsList.get(9).toString(), ids.get(8));
+	}
+
+	@Test
+	public void testSearch_SingleCode_multiple_not_modifier() throws Exception {
+
+		List<IIdType> obsList = createObs(10, false);
+		
+		String uri = ourServerBase + "/Observation?code:not=2345-3&code:not=2345-7&code:not=2345-9";
+		List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+		
+		assertEquals(7, ids.size());
+		assertEquals(obsList.get(0).toString(), ids.get(0));
+		assertEquals(obsList.get(1).toString(), ids.get(1));
+		assertEquals(obsList.get(2).toString(), ids.get(2));
+		assertEquals(obsList.get(4).toString(), ids.get(3));
+		assertEquals(obsList.get(5).toString(), ids.get(4));
+		assertEquals(obsList.get(6).toString(), ids.get(5));
+		assertEquals(obsList.get(8).toString(), ids.get(6));
+	}
+	
+	@Test
+	public void testSearch_SingleCode_mix_modifier() throws Exception {
+
+		List<IIdType> obsList = createObs(10, false);
+		
+		// Observation?code:not=2345-3&code:not=2345-7&code:not=2345-9
+		// slower than Observation?code:not=2345-3&code=2345-7&code:not=2345-9
+		String uri = ourServerBase + "/Observation?code:not=2345-3&code=2345-7&code:not=2345-9";
+		List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+		
+		assertEquals(1, ids.size());
+		assertEquals(obsList.get(7).toString(), ids.get(0));
+	}
+	
+	@Test
+	public void testSearch_SingleCode_or_not_modifier() throws Exception {
+
+		List<IIdType> obsList = createObs(10, false);
+		
+		String uri = ourServerBase + "/Observation?code:not=2345-3,2345-7,2345-9";
+		List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+		
+		assertEquals(7, ids.size());
+		assertEquals(obsList.get(0).toString(), ids.get(0));
+		assertEquals(obsList.get(1).toString(), ids.get(1));
+		assertEquals(obsList.get(2).toString(), ids.get(2));
+		assertEquals(obsList.get(4).toString(), ids.get(3));
+		assertEquals(obsList.get(5).toString(), ids.get(4));
+		assertEquals(obsList.get(6).toString(), ids.get(5));
+		assertEquals(obsList.get(8).toString(), ids.get(6));
+	}
+	
+	@Test
+	public void testSearch_MultiCode_not_modifier() throws Exception {
+
+		List<IIdType> obsList = createObs(10, true);
+		
+		String uri = ourServerBase + "/Observation?code:not=2345-3";
+		List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+		
+		assertEquals(8, ids.size());
+		assertEquals(obsList.get(0).toString(), ids.get(0));
+		assertEquals(obsList.get(1).toString(), ids.get(1));
+		assertEquals(obsList.get(4).toString(), ids.get(2));
+		assertEquals(obsList.get(5).toString(), ids.get(3));
+		assertEquals(obsList.get(6).toString(), ids.get(4));
+		assertEquals(obsList.get(7).toString(), ids.get(5));
+		assertEquals(obsList.get(8).toString(), ids.get(6));
+		assertEquals(obsList.get(9).toString(), ids.get(7));
+	}
+	
+	@Test
+	public void testSearch_MultiCode_multiple_not_modifier() throws Exception {
+
+		List<IIdType> obsList = createObs(10, true);
+		
+		String uri = ourServerBase + "/Observation?code:not=2345-3&code:not=2345-4";
+		List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+		
+		assertEquals(7, ids.size());
+		assertEquals(obsList.get(0).toString(), ids.get(0));
+		assertEquals(obsList.get(1).toString(), ids.get(1));
+		assertEquals(obsList.get(5).toString(), ids.get(2));
+		assertEquals(obsList.get(6).toString(), ids.get(3));
+		assertEquals(obsList.get(7).toString(), ids.get(4));
+		assertEquals(obsList.get(8).toString(), ids.get(5));
+		assertEquals(obsList.get(9).toString(), ids.get(6));
+	}
+	
+	@Test
+	public void testSearch_MultiCode_mix_modifier() throws Exception {
+
+		List<IIdType> obsList = createObs(10, true);
+		
+		String uri = ourServerBase + "/Observation?code:not=2345-3&code=2345-7&code:not=2345-9";
+		List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+		
+		assertEquals(2, ids.size());
+		assertEquals(obsList.get(6).toString(), ids.get(0));
+		assertEquals(obsList.get(7).toString(), ids.get(1));
+	}
+	
+	@Test
+	public void testSearch_MultiCode_or_not_modifier() throws Exception {
+
+		List<IIdType> obsList = createObs(10, true);
+		
+		String uri = ourServerBase + "/Observation?code:not=2345-3,2345-7,2345-9";
+		List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
+		
+		assertEquals(4, ids.size());
+		assertEquals(obsList.get(0).toString(), ids.get(0));
+		assertEquals(obsList.get(1).toString(), ids.get(1));
+		assertEquals(obsList.get(4).toString(), ids.get(2));
+		assertEquals(obsList.get(5).toString(), ids.get(3));
+	}
+
+
+	
+	private List<String> searchAndReturnUnqualifiedVersionlessIdValues(String uri) throws IOException {
+		List<String> ids;
+		HttpGet get = new HttpGet(uri);
+
+		try (CloseableHttpResponse response = ourHttpClient.execute(get)) {
+			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info("Response was: {}", resp);
+			Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, resp);
+			ourLog.info("Bundle: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
+			ids = toUnqualifiedVersionlessIdValues(bundle);
+		}
+		return ids;
+	}
+
+	private List<IIdType> createObs(int obsNum, boolean isMultiple) {
+		
+		Patient patient = new Patient();
+		patient.addIdentifier().setSystem("urn:system").setValue("001");
+		patient.addName().setFamily("Tester").addGiven("Joe");
+		IIdType pid = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+		
+		List<IIdType> obsIds = new ArrayList<>();
+		IIdType obsId = null;
+		for (int i=0; i<obsNum; i++) {
+			Observation obs = new Observation();
+			obs.setStatus(ObservationStatus.FINAL);
+			obs.getSubject().setReferenceElement(pid);
+			obs.setEffective(new DateTimeType("2001-02-01"));
+		
+			CodeableConcept cc = obs.getCode();
+			cc.addCoding().setCode("2345-"+i).setSystem("http://loinc.org");
+			obs.setValue(new Quantity().setValue(200));	
+
+			if (isMultiple) {
+				cc = obs.getCode();
+				cc.addCoding().setCode("2345-"+(i+1)).setSystem("http://loinc.org");
+				obs.setValue(new Quantity().setValue(300));	
+			}
+
+			obsId = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
+			obsIds.add(obsId);
+		}
+		
+		return obsIds;
+	}
+}