Merge pull request #656 from aehrc/feature/scalable_searchbuilder
Improve SearchBuilder query generation for code:modifier searches
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commit
4caa5dfa8d
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@ -24,7 +24,6 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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import static org.apache.commons.lang3.StringUtils.substring;
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import java.math.BigDecimal;
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import java.math.BigDecimal;
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import java.math.MathContext;
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import java.math.MathContext;
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@ -44,6 +43,7 @@ import javax.persistence.EntityManager;
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import javax.persistence.TypedQuery;
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import javax.persistence.TypedQuery;
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import javax.persistence.criteria.AbstractQuery;
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import javax.persistence.criteria.AbstractQuery;
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import javax.persistence.criteria.CriteriaBuilder;
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import javax.persistence.criteria.CriteriaBuilder;
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import javax.persistence.criteria.CriteriaBuilder.In;
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import javax.persistence.criteria.CriteriaQuery;
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import javax.persistence.criteria.CriteriaQuery;
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import javax.persistence.criteria.Expression;
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import javax.persistence.criteria.Expression;
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import javax.persistence.criteria.From;
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import javax.persistence.criteria.From;
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@ -62,13 +62,27 @@ import org.apache.commons.lang3.tuple.Pair;
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import org.hl7.fhir.instance.model.api.IAnyResource;
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import org.hl7.fhir.instance.model.api.IAnyResource;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.springframework.transaction.annotation.Propagation;
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import org.springframework.transaction.annotation.Transactional;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Sets;
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import com.google.common.collect.Sets;
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import ca.uhn.fhir.context.*;
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import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
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import ca.uhn.fhir.context.BaseRuntimeDeclaredChildDefinition;
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import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
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import ca.uhn.fhir.context.ConfigurationException;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.FhirVersionEnum;
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import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
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import ca.uhn.fhir.context.RuntimeChildResourceDefinition;
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import ca.uhn.fhir.context.RuntimeResourceDefinition;
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import ca.uhn.fhir.context.RuntimeSearchParam;
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import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
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import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
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import ca.uhn.fhir.jpa.dao.IDao;
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import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
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import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
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import ca.uhn.fhir.jpa.dao.ISearchBuilder;
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import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
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import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
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import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
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import ca.uhn.fhir.jpa.entity.BaseHasResource;
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import ca.uhn.fhir.jpa.entity.BaseHasResource;
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@ -1219,9 +1233,24 @@ public class SearchBuilder implements ISearchBuilder {
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} else {
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} else {
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List<Predicate> orPredicates = new ArrayList<Predicate>();
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List<Predicate> orPredicates = new ArrayList<Predicate>();
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Map<String, List<VersionIndependentConcept>> map = new HashMap<String, List<VersionIndependentConcept>>();
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for (VersionIndependentConcept nextCode : codes) {
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for (VersionIndependentConcept nextCode : codes) {
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Predicate systemPredicate = theBuilder.equal(theFrom.get("mySystem"), nextCode.getSystem());
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List<VersionIndependentConcept> systemCodes = map.get(nextCode.getSystem());
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Predicate codePredicate = theBuilder.equal(theFrom.get("myValue"), nextCode.getCode());
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if (null == systemCodes) {
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systemCodes = new ArrayList<VersionIndependentConcept>();
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map.put(nextCode.getSystem(), systemCodes);
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}
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systemCodes.add(nextCode);
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}
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// Use "in" in case of large numbers of codes due to param modifiers
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final Path<String> systemExpression = theFrom.get("mySystem");
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final Path<String> valueExpression = theFrom.get("myValue");
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for (Map.Entry<String, List<VersionIndependentConcept>> entry: map.entrySet()) {
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Predicate systemPredicate = theBuilder.equal(systemExpression, entry.getKey());
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In<String> codePredicate = theBuilder.in(valueExpression);
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for (VersionIndependentConcept nextCode: entry.getValue()) {
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codePredicate.value(nextCode.getCode());
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}
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orPredicates.add(theBuilder.and(systemPredicate, codePredicate));
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orPredicates.add(theBuilder.and(systemPredicate, codePredicate));
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}
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}
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@ -1814,6 +1843,7 @@ public class SearchBuilder implements ISearchBuilder {
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}
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}
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}
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}
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@Override
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public void setType(Class<? extends IBaseResource> theResourceType, String theResourceName) {
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public void setType(Class<? extends IBaseResource> theResourceType, String theResourceName) {
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myResourceType = theResourceType;
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myResourceType = theResourceType;
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myResourceName = theResourceName;
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myResourceName = theResourceName;
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@ -118,6 +118,38 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
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return codeSystem;
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return codeSystem;
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}
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}
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private CodeSystem createExternalCsLarge() {
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CodeSystem codeSystem = new CodeSystem();
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codeSystem.setUrl(URL_MY_CODE_SYSTEM);
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codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
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IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
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ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
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TermCodeSystemVersion cs = new TermCodeSystemVersion();
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cs.setResource(table);
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cs.setResourceVersionId(table.getVersion());
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TermConcept parentA = new TermConcept(cs, "codeA").setDisplay("CodeA");
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cs.getConcepts().add(parentA);
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for (int i = 0; i < 450; i++) {
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TermConcept childI = new TermConcept(cs, "subCodeA"+i).setDisplay("Sub-code A"+i);
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parentA.addChild(childI, RelationshipTypeEnum.ISA);
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}
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TermConcept parentB = new TermConcept(cs, "codeB").setDisplay("CodeB");
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cs.getConcepts().add(parentB);
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for (int i = 0; i < 450; i++) {
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TermConcept childI = new TermConcept(cs, "subCodeB"+i).setDisplay("Sub-code B"+i);
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parentB.addChild(childI, RelationshipTypeEnum.ISA);
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}
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myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, cs);
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return codeSystem;
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}
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private void createExternalCsAndLocalVs() {
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private void createExternalCsAndLocalVs() {
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CodeSystem codeSystem = createExternalCs();
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CodeSystem codeSystem = createExternalCs();
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@ -934,6 +966,36 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
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}
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}
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@Test
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public void testSearchCodeBelowExternalCodesystemLarge() {
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createExternalCsLarge();
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Observation obs0 = new Observation();
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obs0.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("codeA");
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IIdType id0 = myObservationDao.create(obs0, mySrd).getId().toUnqualifiedVersionless();
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Observation obs1 = new Observation();
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obs1.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("subCodeA1");
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IIdType id1 = myObservationDao.create(obs1, mySrd).getId().toUnqualifiedVersionless();
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Observation obs2 = new Observation();
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obs2.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("subCodeA2");
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IIdType id2 = myObservationDao.create(obs2, mySrd).getId().toUnqualifiedVersionless();
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Observation obs3 = new Observation();
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obs3.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("subCodeB3");
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IIdType id3 = myObservationDao.create(obs3, mySrd).getId().toUnqualifiedVersionless();
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SearchParameterMap params = new SearchParameterMap();
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params.add(Observation.SP_CODE, new TokenParam(URL_MY_CODE_SYSTEM, "codeA").setModifier(TokenParamModifier.BELOW));
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assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), containsInAnyOrder(id0.getValue(), id1.getValue(), id2.getValue()));
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params = new SearchParameterMap();
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params.add(Observation.SP_CODE, new TokenParam(URL_MY_CODE_SYSTEM, "subCodeB1").setModifier(TokenParamModifier.BELOW));
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assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), empty());
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}
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@Test
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@Test
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public void testSearchCodeInBuiltInValueSet() {
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public void testSearchCodeInBuiltInValueSet() {
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AllergyIntolerance ai1 = new AllergyIntolerance();
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AllergyIntolerance ai1 = new AllergyIntolerance();
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