Merge branch 'master' into 2849_add_new_mdm_param
This commit is contained in:
Nick Goupinets
commit
1bd1b36668
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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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@ -221,11 +221,15 @@ public class SearchBuilder implements ISearchBuilder {
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SearchContainedModeEnum searchContainedMode = theParams.getSearchContainedMode();
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// Handle _id last, since it can typically be tacked onto a different parameter
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List<String> paramNames = myParams.keySet().stream().filter(t -> !t.equals(IAnyResource.SP_RES_ID)).collect(Collectors.toList());
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// Handle _id and _tag last, since they can typically be tacked onto a different parameter
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List<String> paramNames = myParams.keySet().stream().filter(t -> !t.equals(IAnyResource.SP_RES_ID))
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.filter(t -> !t.equals(Constants.PARAM_TAG)).collect(Collectors.toList());
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if (myParams.containsKey(IAnyResource.SP_RES_ID)) {
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paramNames.add(IAnyResource.SP_RES_ID);
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}
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if (myParams.containsKey(Constants.PARAM_TAG)) {
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paramNames.add(Constants.PARAM_TAG);
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}
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// Handle each parameter
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for (String nextParamName : paramNames) {
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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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@ -96,7 +96,7 @@ public class TestUtil {
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.collect(Collectors.toSet());
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}
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ImmutableSet<ClassInfo> classes = ClassPath.from(TestUtil.class.getClassLoader()).getTopLevelClasses(packageName);
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ImmutableSet<ClassInfo> classes = ClassPath.from(TestUtil.class.getClassLoader()).getTopLevelClassesRecursive(packageName);
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Set<String> names = new HashSet<String>();
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if (classes.size() <= 1) {
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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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@ -21,18 +21,29 @@ import ca.uhn.fhir.rest.param.ReferenceParam;
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import ca.uhn.fhir.rest.param.StringParam;
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import ca.uhn.fhir.rest.param.TokenOrListParam;
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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 org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.exception.ExceptionUtils;
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import org.hl7.fhir.instance.model.api.IAnyResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.BodyStructure;
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import org.hl7.fhir.r4.model.CodeableConcept;
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import org.hl7.fhir.r4.model.Coding;
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import org.hl7.fhir.r4.model.DateTimeType;
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import org.hl7.fhir.r4.model.Device;
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import org.hl7.fhir.r4.model.Enumerations;
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import org.hl7.fhir.r4.model.Extension;
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import org.hl7.fhir.r4.model.IdType;
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import org.hl7.fhir.r4.model.Observation;
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import org.hl7.fhir.r4.model.Organization;
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import org.hl7.fhir.r4.model.Patient;
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import org.hl7.fhir.r4.model.Procedure;
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import org.hl7.fhir.r4.model.Provenance;
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import org.hl7.fhir.r4.model.Reference;
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import org.hl7.fhir.r4.model.SearchParameter;
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import org.hl7.fhir.r4.model.StringType;
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import org.hl7.fhir.r4.model.UriType;
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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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@ -906,6 +917,117 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
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}
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@Test
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public void testSearchOnUnderscoreParams_AvoidHFJResourceJoins() {
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// This Issue: https://github.com/hapifhir/hapi-fhir/issues/2942
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// See this PR for a similar type of Fix: https://github.com/hapifhir/hapi-fhir/pull/2909
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SearchParameter searchParameter = new SearchParameter();
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searchParameter.addBase("BodySite").addBase("Procedure");
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searchParameter.setCode("focalAccess");
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searchParameter.setType(Enumerations.SearchParamType.REFERENCE);
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searchParameter.setExpression("Procedure.extension('Procedure#focalAccess')");
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searchParameter.setXpathUsage(SearchParameter.XPathUsageType.NORMAL);
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searchParameter.setStatus(Enumerations.PublicationStatus.ACTIVE);
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IIdType spId = mySearchParameterDao.create(searchParameter).getId().toUnqualifiedVersionless();
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mySearchParamRegistry.forceRefresh();
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BodyStructure bs = new BodyStructure();
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bs.setDescription("BodyStructure in R4 replaced BodySite from DSTU4");
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IIdType bsId = myBodyStructureDao.create(bs, mySrd).getId().toUnqualifiedVersionless();
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Patient patient = new Patient();
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patient.setId("P1");
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patient.setActive(true);
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patient.addName().setFamily("FamilyName");
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Extension extParent = patient
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.addExtension()
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.setUrl("http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity");
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extParent
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.addExtension()
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.setUrl("ombCategory")
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.setValue(new CodeableConcept().addCoding(new Coding().setSystem("urn:oid:2.16.840.1.113883.5.50")
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.setCode("2186-5")
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.setDisplay("Not Hispanic or Latino")));
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extParent
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.addExtension()
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.setUrl("text")
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.setValue(new StringType("Not Hispanic or Latino"));
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myPatientDao.update(patient);
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CodeableConcept categoryCodeableConcept1 = new CodeableConcept().addCoding(new Coding().setSystem("acc_proccat_fkc")
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.setCode("CANN")
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.setDisplay("Cannulation"));
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Procedure procedure = new Procedure();
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procedure.setSubject(new Reference("Patient/P1"));
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procedure.setStatus(Procedure.ProcedureStatus.COMPLETED);
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procedure.setCategory(categoryCodeableConcept1);
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Extension extProcedure = procedure
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.addExtension()
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.setUrl("Procedure#focalAccess")
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.setValue(new UriType("BodyStructure/" + bsId.getIdPartAsLong()));
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procedure.getMeta()
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.addTag("acc_procext_fkc", "1STCANN2NDL", "First Successful Cannulation with 2 Needles");
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IIdType procedureId = myProcedureDao.create(procedure).getId().toUnqualifiedVersionless();
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logAllResources();
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logAllResourceTags();
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logAllResourceVersions();
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// Search example 1:
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// http://FHIR_SERVER/fhir_request/Procedure
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// ?status%3Anot=entered-in-error&subject=B
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// &category=CANN&focalAccess=BodySite%2F3530342921&_tag=TagValue
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// NOTE: This gets sorted once so the order is different once it gets executed!
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{
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// IMPORTANT: Keep the query param order exactly as shown below!
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SearchParameterMap map = SearchParameterMap.newSynchronous();
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// _tag, category, status, subject, focalAccess
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map.add("_tag", new TokenParam("TagValue"));
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map.add("category", new TokenParam("CANN"));
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map.add("status", new TokenParam("entered-in-error").setModifier(TokenParamModifier.NOT));
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map.add("subject", new ReferenceParam("Patient/P1"));
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map.add("focalAccess", new ReferenceParam("BodyStructure/" + bsId.getIdPart()));
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myCaptureQueriesListener.clear();
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IBundleProvider outcome = myProcedureDao.search(map, new SystemRequestDetails());
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ourLog.info("Search returned {} resources.", outcome.getResources(0, 999).size());
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myCaptureQueriesListener.logSelectQueriesForCurrentThread();
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String selectQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
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// Check for a particular WHERE CLAUSE in the generated SQL to make sure we are verifying the correct query
|
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assertEquals(2, StringUtils.countMatches(selectQuery.toLowerCase(), " join hfj_res_link "), selectQuery);
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// Ensure that we do NOT see a couple of particular WHERE clauses
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assertEquals(0, StringUtils.countMatches(selectQuery.toLowerCase(), ".res_type = 'procedure'"), selectQuery);
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assertEquals(0, StringUtils.countMatches(selectQuery.toLowerCase(), ".res_deleted_at is null"), selectQuery);
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}
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// Search example 2:
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// http://FHIR_SERVER/fhir_request/Procedure
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// ?status%3Anot=entered-in-error&category=CANN&focalAccess=3692871435
|
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// &_tag=1STCANN1NDL%2C1STCANN2NDL&outcome=SUCCESS&_count=1&_requestTrace=True
|
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// NOTE: This gets sorted once so the order is different once it gets executed!
|
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{
|
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// IMPORTANT: Keep the query param order exactly as shown below!
|
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// NOTE: The "outcome" SearchParameter is not being used below, but it doesn't affect the test.
|
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SearchParameterMap map = SearchParameterMap.newSynchronous();
|
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// _tag, category, status, focalAccess
|
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map.add("_tag", new TokenParam("TagValue"));
|
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map.add("category", new TokenParam("CANN"));
|
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map.add("status", new TokenParam("entered-in-error").setModifier(TokenParamModifier.NOT));
|
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map.add("focalAccess", new ReferenceParam("BodyStructure/" + bsId.getIdPart()));
|
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myCaptureQueriesListener.clear();
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IBundleProvider outcome = myProcedureDao.search(map, new SystemRequestDetails());
|
||||
ourLog.info("Search returned {} resources.", outcome.getResources(0, 999).size());
|
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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() {
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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)));
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -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;
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue