Merge pull request #2950 from hapifhir/ft-search-with-not-modifier
Fixed :not modifier issue for the resourceLink
This commit is contained in:
Tadgh
GitHub
commit
4d1de25a36
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@ -0,0 +1,4 @@
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---
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type: fix
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issue: 2837
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title: "The :not modifier does not currently work for observations with multiple codes for the search. This is fixed."
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@ -988,9 +988,12 @@ public class QueryStack {
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String theSpnamePrefix, RuntimeSearchParam theSearchParam, List<? extends IQueryParameterType> theList,
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SearchFilterParser.CompareOperation theOperation, RequestPartitionId theRequestPartitionId) {
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List<IQueryParameterType> tokens = new ArrayList<>();
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List<IQueryParameterType> tokens = new ArrayList<>();
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boolean paramInverted = false;
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TokenParamModifier modifier = null;
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for (IQueryParameterType nextOr : theList) {
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if (nextOr instanceof TokenParam) {
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if (!((TokenParam) nextOr).isEmpty()) {
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TokenParam id = (TokenParam) nextOr;
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@ -1009,17 +1012,20 @@ public class QueryStack {
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}
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return createPredicateString(theSourceJoinColumn, theResourceName, theSpnamePrefix, theSearchParam, theList, null, theRequestPartitionId);
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}
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modifier = id.getModifier();
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// for :not modifier, create a token and remove the :not modifier
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if (modifier != null && modifier == TokenParamModifier.NOT) {
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tokens.add(new TokenParam(((TokenParam) nextOr).getSystem(), ((TokenParam) nextOr).getValue()));
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paramInverted = true;
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} else {
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tokens.add(nextOr);
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}
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tokens.add(nextOr);
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}
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} else {
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tokens.add(nextOr);
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}
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}
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if (tokens.isEmpty()) {
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@ -1027,14 +1033,37 @@ public class QueryStack {
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}
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String paramName = getParamNameWithPrefix(theSpnamePrefix, theSearchParam.getName());
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Condition predicate;
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BaseJoiningPredicateBuilder join;
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if (paramInverted) {
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SearchQueryBuilder sqlBuilder = mySqlBuilder.newChildSqlBuilder();
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TokenPredicateBuilder tokenSelector = sqlBuilder.addTokenPredicateBuilder(null);
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sqlBuilder.addPredicate(tokenSelector.createPredicateToken(tokens, theResourceName, theSpnamePrefix, theSearchParam, theRequestPartitionId));
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SelectQuery sql = sqlBuilder.getSelect();
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Expression subSelect = new Subquery(sql);
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join = mySqlBuilder.getOrCreateFirstPredicateBuilder();
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if (theSourceJoinColumn == null) {
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predicate = new InCondition(join.getResourceIdColumn(), subSelect).setNegate(true);
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} else {
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//-- for the resource link, need join with target_resource_id
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predicate = new InCondition(theSourceJoinColumn, subSelect).setNegate(true);
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}
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} else {
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TokenPredicateBuilder tokenJoin = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.TOKEN, theSourceJoinColumn, paramName, () -> mySqlBuilder.addTokenPredicateBuilder(theSourceJoinColumn)).getResult();
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TokenPredicateBuilder join = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.TOKEN, theSourceJoinColumn, paramName, () -> mySqlBuilder.addTokenPredicateBuilder(theSourceJoinColumn)).getResult();
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if (theList.get(0).getMissing() != null) {
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return tokenJoin.createPredicateParamMissingForNonReference(theResourceName, paramName, theList.get(0).getMissing(), theRequestPartitionId);
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}
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if (theList.get(0).getMissing() != null) {
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return join.createPredicateParamMissingForNonReference(theResourceName, paramName, theList.get(0).getMissing(), theRequestPartitionId);
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}
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Condition predicate = join.createPredicateToken(tokens, theResourceName, theSpnamePrefix, theSearchParam, theOperation, theRequestPartitionId);
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predicate = tokenJoin.createPredicateToken(tokens, theResourceName, theSpnamePrefix, theSearchParam, theOperation, theRequestPartitionId);
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join = tokenJoin;
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}
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return join.combineWithRequestPartitionIdPredicate(theRequestPartitionId, predicate);
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}
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@ -62,6 +62,7 @@ import ca.uhn.fhir.rest.param.ReferenceParam;
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import ca.uhn.fhir.rest.param.SpecialParam;
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import ca.uhn.fhir.rest.param.StringParam;
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import ca.uhn.fhir.rest.param.TokenParam;
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import ca.uhn.fhir.rest.param.TokenParamModifier;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
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@ -338,6 +339,7 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
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boolean foundChainMatch = false;
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List<String> candidateTargetTypes = new ArrayList<>();
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List<Condition> orPredicates = new ArrayList<>();
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boolean paramInverted = false;
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QueryStack childQueryFactory = myQueryStack.newChildQueryFactoryWithFullBuilderReuse();
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for (String nextType : resourceTypes) {
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String chain = theReferenceParam.getChain();
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@ -383,6 +385,13 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
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if (chainValue == null) {
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continue;
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}
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// For the token param, if it's a :not modifier, need switch OR to AND
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if (!paramInverted && chainValue instanceof TokenParam) {
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if (((TokenParam) chainValue).getModifier() == TokenParamModifier.NOT) {
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paramInverted = true;
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}
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}
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foundChainMatch = true;
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orValues.add(chainValue);
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}
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@ -410,10 +419,17 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
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warnAboutPerformanceOnUnqualifiedResources(theParamName, theRequest, candidateTargetTypes);
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}
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Condition multiTypeOrPredicate = toOrPredicate(orPredicates);
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// If :not modifier for a token, switch OR with AND in the multi-type case
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Condition multiTypePredicate;
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if (paramInverted) {
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multiTypePredicate = toAndPredicate(orPredicates);
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} else {
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multiTypePredicate = toOrPredicate(orPredicates);
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}
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List<String> pathsToMatch = createResourceLinkPaths(theResourceName, theParamName);
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Condition pathPredicate = createPredicateSourcePaths(pathsToMatch);
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return toAndPredicate(pathPredicate, multiTypeOrPredicate);
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return toAndPredicate(pathPredicate, multiTypePredicate);
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}
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@Nonnull
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@ -63,6 +63,7 @@ import org.hl7.fhir.dstu3.model.AllergyIntolerance;
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import org.hl7.fhir.dstu3.model.Appointment;
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import org.hl7.fhir.dstu3.model.AuditEvent;
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import org.hl7.fhir.dstu3.model.Binary;
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import org.hl7.fhir.dstu3.model.BodySite;
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import org.hl7.fhir.dstu3.model.Bundle;
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import org.hl7.fhir.dstu3.model.CarePlan;
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import org.hl7.fhir.dstu3.model.CodeSystem;
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@ -95,6 +96,7 @@ import org.hl7.fhir.dstu3.model.Organization;
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import org.hl7.fhir.dstu3.model.Patient;
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import org.hl7.fhir.dstu3.model.Practitioner;
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import org.hl7.fhir.dstu3.model.PractitionerRole;
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import org.hl7.fhir.dstu3.model.Procedure;
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import org.hl7.fhir.dstu3.model.ProcedureRequest;
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import org.hl7.fhir.dstu3.model.Questionnaire;
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import org.hl7.fhir.dstu3.model.QuestionnaireResponse;
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@ -317,6 +319,12 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
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@Qualifier("myTaskDaoDstu3")
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protected IFhirResourceDao<Task> myTaskDao;
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@Autowired
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@Qualifier("myBodySiteDaoDstu3")
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protected IFhirResourceDao<BodySite> myBodySiteDao;
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@Autowired
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@Qualifier("myProcedureDaoDstu3")
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protected IFhirResourceDao<Procedure> myProcedureDao;
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@Autowired
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protected ITermConceptDao myTermConceptDao;
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@Autowired
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protected ITermCodeSystemDao myTermCodeSystemDao;
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@ -0,0 +1,77 @@
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package ca.uhn.fhir.jpa.provider.dstu3;
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import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
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import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
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import ca.uhn.fhir.jpa.searchparam.ResourceSearch;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.rest.api.server.IBundleProvider;
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import org.hl7.fhir.dstu3.model.BodySite;
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import org.hl7.fhir.dstu3.model.CodeableConcept;
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import org.hl7.fhir.dstu3.model.Coding;
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import org.hl7.fhir.dstu3.model.Encounter;
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import org.hl7.fhir.dstu3.model.Observation;
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import org.hl7.fhir.dstu3.model.Patient;
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import org.hl7.fhir.dstu3.model.Procedure;
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import org.hl7.fhir.dstu3.model.Reference;
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import org.hl7.fhir.dstu3.model.SearchParameter;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.junit.jupiter.api.Test;
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import org.springframework.beans.factory.annotation.Autowired;
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import java.util.Collections;
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import static org.hamcrest.MatcherAssert.assertThat;
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import static org.hamcrest.Matchers.equalTo;
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import static org.hamcrest.Matchers.is;
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public class ResourceProviderSearchModifierDstu3Test extends BaseResourceProviderDstu3Test{
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@Autowired
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MatchUrlService myMatchUrlService;
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@Test
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public void testReplicateBugWithNotDuringChain() {
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Encounter enc = new Encounter();
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enc.setType(Collections.singletonList(new CodeableConcept().addCoding(new Coding("system", "value", "display"))));
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IIdType encId = myEncounterDao.create(enc).getId();
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Observation obs = new Observation();
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obs.setContext(new Reference(encId));
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myObservationDao.create(obs).getId();
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{
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//Works when not chained:
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String encounterSearchString = "Encounter?type:not=system|value";
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ResourceSearch resourceSearch = myMatchUrlService.getResourceSearch(encounterSearchString);
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SearchParameterMap searchParameterMap = resourceSearch.getSearchParameterMap();
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IBundleProvider search = myEncounterDao.search(searchParameterMap);
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assertThat(search.size(), is(equalTo(0)));
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}
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{
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//Works without the NOT qualifier.
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String resultSearchString = "Observation?context.type=system|value";
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ResourceSearch resourceSearch = myMatchUrlService.getResourceSearch(resultSearchString);
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SearchParameterMap searchParameterMap = resourceSearch.getSearchParameterMap();
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IBundleProvider search = myObservationDao.search(searchParameterMap);
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assertThat(search.size(), is(equalTo(1)));
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}
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{
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//Works in a chain
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String noResultSearchString = "Observation?context.type:not=system|value";
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ResourceSearch resourceSearch = myMatchUrlService.getResourceSearch(noResultSearchString);
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SearchParameterMap searchParameterMap = resourceSearch.getSearchParameterMap();
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IBundleProvider search = myObservationDao.search(searchParameterMap);
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assertThat(search.size(), is(equalTo(0)));
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}
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{
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//Works in a chain with only value
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String noResultSearchString = "Observation?context.type:not=value";
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ResourceSearch resourceSearch = myMatchUrlService.getResourceSearch(noResultSearchString);
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SearchParameterMap searchParameterMap = resourceSearch.getSearchParameterMap();
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IBundleProvider search = myObservationDao.search(searchParameterMap);
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assertThat(search.size(), is(equalTo(0)));
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}
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}
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}
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@ -0,0 +1,249 @@
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package ca.uhn.fhir.jpa.provider.r4;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import java.io.IOException;
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import java.nio.charset.StandardCharsets;
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import java.util.ArrayList;
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import java.util.List;
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import org.apache.commons.io.IOUtils;
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import org.apache.http.client.methods.CloseableHttpResponse;
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import org.apache.http.client.methods.HttpGet;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.Bundle;
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import org.hl7.fhir.r4.model.CodeableConcept;
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import org.hl7.fhir.r4.model.DateTimeType;
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import org.hl7.fhir.r4.model.Observation;
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import org.hl7.fhir.r4.model.Observation.ObservationStatus;
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import org.hl7.fhir.r4.model.Patient;
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import org.hl7.fhir.r4.model.Quantity;
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import org.junit.jupiter.api.AfterEach;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Test;
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import ca.uhn.fhir.jpa.api.config.DaoConfig;
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import ca.uhn.fhir.parser.StrictErrorHandler;
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import ca.uhn.fhir.rest.client.interceptor.CapturingInterceptor;
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public class ResourceProviderSearchModifierR4Test extends BaseResourceProviderR4Test {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderSearchModifierR4Test.class);
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private CapturingInterceptor myCapturingInterceptor = new CapturingInterceptor();
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@Override
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@AfterEach
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public void after() throws Exception {
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super.after();
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myDaoConfig.setAllowMultipleDelete(new DaoConfig().isAllowMultipleDelete());
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myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
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myDaoConfig.setReuseCachedSearchResultsForMillis(new DaoConfig().getReuseCachedSearchResultsForMillis());
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myDaoConfig.setCountSearchResultsUpTo(new DaoConfig().getCountSearchResultsUpTo());
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myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
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myDaoConfig.setAllowContainsSearches(new DaoConfig().isAllowContainsSearches());
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myDaoConfig.setIndexMissingFields(new DaoConfig().getIndexMissingFields());
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myClient.unregisterInterceptor(myCapturingInterceptor);
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}
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@BeforeEach
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@Override
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public void before() throws Exception {
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super.before();
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myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
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myDaoConfig.setAllowMultipleDelete(true);
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myClient.registerInterceptor(myCapturingInterceptor);
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myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
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}
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@BeforeEach
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public void beforeDisableResultReuse() {
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myDaoConfig.setReuseCachedSearchResultsForMillis(null);
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}
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@Test
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public void testSearch_SingleCode_not_modifier() throws Exception {
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List<IIdType> obsList = createObs(10, false);
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String uri = ourServerBase + "/Observation?code:not=2345-3";
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List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
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assertEquals(9, ids.size());
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assertEquals(obsList.get(0).toString(), ids.get(0));
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assertEquals(obsList.get(1).toString(), ids.get(1));
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assertEquals(obsList.get(2).toString(), ids.get(2));
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assertEquals(obsList.get(4).toString(), ids.get(3));
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assertEquals(obsList.get(5).toString(), ids.get(4));
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assertEquals(obsList.get(6).toString(), ids.get(5));
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assertEquals(obsList.get(7).toString(), ids.get(6));
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assertEquals(obsList.get(8).toString(), ids.get(7));
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assertEquals(obsList.get(9).toString(), ids.get(8));
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}
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@Test
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public void testSearch_SingleCode_multiple_not_modifier() throws Exception {
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List<IIdType> obsList = createObs(10, false);
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String uri = ourServerBase + "/Observation?code:not=2345-3&code:not=2345-7&code:not=2345-9";
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List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
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assertEquals(7, ids.size());
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assertEquals(obsList.get(0).toString(), ids.get(0));
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assertEquals(obsList.get(1).toString(), ids.get(1));
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assertEquals(obsList.get(2).toString(), ids.get(2));
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assertEquals(obsList.get(4).toString(), ids.get(3));
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assertEquals(obsList.get(5).toString(), ids.get(4));
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assertEquals(obsList.get(6).toString(), ids.get(5));
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assertEquals(obsList.get(8).toString(), ids.get(6));
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}
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@Test
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public void testSearch_SingleCode_mix_modifier() throws Exception {
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List<IIdType> obsList = createObs(10, false);
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// Observation?code:not=2345-3&code:not=2345-7&code:not=2345-9
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// slower than Observation?code:not=2345-3&code=2345-7&code:not=2345-9
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String uri = ourServerBase + "/Observation?code:not=2345-3&code=2345-7&code:not=2345-9";
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List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
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assertEquals(1, ids.size());
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assertEquals(obsList.get(7).toString(), ids.get(0));
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}
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@Test
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public void testSearch_SingleCode_or_not_modifier() throws Exception {
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List<IIdType> obsList = createObs(10, false);
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String uri = ourServerBase + "/Observation?code:not=2345-3,2345-7,2345-9";
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List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
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assertEquals(7, ids.size());
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assertEquals(obsList.get(0).toString(), ids.get(0));
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assertEquals(obsList.get(1).toString(), ids.get(1));
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assertEquals(obsList.get(2).toString(), ids.get(2));
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assertEquals(obsList.get(4).toString(), ids.get(3));
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assertEquals(obsList.get(5).toString(), ids.get(4));
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assertEquals(obsList.get(6).toString(), ids.get(5));
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assertEquals(obsList.get(8).toString(), ids.get(6));
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}
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@Test
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public void testSearch_MultiCode_not_modifier() throws Exception {
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List<IIdType> obsList = createObs(10, true);
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String uri = ourServerBase + "/Observation?code:not=2345-3";
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List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
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assertEquals(8, ids.size());
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assertEquals(obsList.get(0).toString(), ids.get(0));
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assertEquals(obsList.get(1).toString(), ids.get(1));
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assertEquals(obsList.get(4).toString(), ids.get(2));
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assertEquals(obsList.get(5).toString(), ids.get(3));
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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;
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue