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Merge pull request #656 from aehrc/feature/scalable_searchbuilder

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Improve SearchBuilder query generation for code:modifier searches
This commit is contained in:
James Agnew 2017-06-07 21:35:50 -04:00 committed by GitHub
commit 4caa5dfa8d
2 changed files with 120 additions and 28 deletions
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42
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java
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@ -24,7 +24,6 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.substring;
import java.math.BigDecimal;
import java.math.MathContext;
@ -44,6 +43,7 @@ import javax.persistence.EntityManager;
import javax.persistence.TypedQuery;
import javax.persistence.criteria.AbstractQuery;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaBuilder.In;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Expression;
import javax.persistence.criteria.From;
@ -62,13 +62,27 @@ import org.apache.commons.lang3.tuple.Pair;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeDeclaredChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
import ca.uhn.fhir.context.RuntimeChildResourceDefinition;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
import ca.uhn.fhir.jpa.entity.BaseHasResource;
@ -1219,9 +1233,24 @@ public class SearchBuilder implements ISearchBuilder {
} else {
List<Predicate> orPredicates = new ArrayList<Predicate>();
Map<String, List<VersionIndependentConcept>> map = new HashMap<String, List<VersionIndependentConcept>>();
for (VersionIndependentConcept nextCode : codes) {
Predicate systemPredicate = theBuilder.equal(theFrom.get("mySystem"), nextCode.getSystem());
Predicate codePredicate = theBuilder.equal(theFrom.get("myValue"), nextCode.getCode());
List<VersionIndependentConcept> systemCodes = map.get(nextCode.getSystem());
if (null == systemCodes) {
systemCodes = new ArrayList<VersionIndependentConcept>();
map.put(nextCode.getSystem(), systemCodes);
}
systemCodes.add(nextCode);
}
// Use "in" in case of large numbers of codes due to param modifiers
final Path<String> systemExpression = theFrom.get("mySystem");
final Path<String> valueExpression = theFrom.get("myValue");
for (Map.Entry<String, List<VersionIndependentConcept>> entry: map.entrySet()) {
Predicate systemPredicate = theBuilder.equal(systemExpression, entry.getKey());
In<String> codePredicate = theBuilder.in(valueExpression);
for (VersionIndependentConcept nextCode: entry.getValue()) {
codePredicate.value(nextCode.getCode());
}
orPredicates.add(theBuilder.and(systemPredicate, codePredicate));
}
@ -1814,6 +1843,7 @@ public class SearchBuilder implements ISearchBuilder {
}
}
@Override
public void setType(Class<? extends IBaseResource> theResourceType, String theResourceName) {
myResourceType = theResourceType;
myResourceName = theResourceName;

62
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
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@ -118,6 +118,38 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
return codeSystem;
}
private CodeSystem createExternalCsLarge() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
TermConcept parentA = new TermConcept(cs, "codeA").setDisplay("CodeA");
cs.getConcepts().add(parentA);
for (int i = 0; i < 450; i++) {
TermConcept childI = new TermConcept(cs, "subCodeA"+i).setDisplay("Sub-code A"+i);
parentA.addChild(childI, RelationshipTypeEnum.ISA);
}
TermConcept parentB = new TermConcept(cs, "codeB").setDisplay("CodeB");
cs.getConcepts().add(parentB);
for (int i = 0; i < 450; i++) {
TermConcept childI = new TermConcept(cs, "subCodeB"+i).setDisplay("Sub-code B"+i);
parentB.addChild(childI, RelationshipTypeEnum.ISA);
}
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, cs);
return codeSystem;
}
private void createExternalCsAndLocalVs() {
CodeSystem codeSystem = createExternalCs();
@ -934,6 +966,36 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
}
@Test
public void testSearchCodeBelowExternalCodesystemLarge() {
createExternalCsLarge();
Observation obs0 = new Observation();
obs0.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("codeA");
IIdType id0 = myObservationDao.create(obs0, mySrd).getId().toUnqualifiedVersionless();
Observation obs1 = new Observation();
obs1.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("subCodeA1");
IIdType id1 = myObservationDao.create(obs1, mySrd).getId().toUnqualifiedVersionless();
Observation obs2 = new Observation();
obs2.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("subCodeA2");
IIdType id2 = myObservationDao.create(obs2, mySrd).getId().toUnqualifiedVersionless();
Observation obs3 = new Observation();
obs3.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("subCodeB3");
IIdType id3 = myObservationDao.create(obs3, mySrd).getId().toUnqualifiedVersionless();
SearchParameterMap params = new SearchParameterMap();
params.add(Observation.SP_CODE, new TokenParam(URL_MY_CODE_SYSTEM, "codeA").setModifier(TokenParamModifier.BELOW));
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), containsInAnyOrder(id0.getValue(), id1.getValue(), id2.getValue()));
params = new SearchParameterMap();
params.add(Observation.SP_CODE, new TokenParam(URL_MY_CODE_SYSTEM, "subCodeB1").setModifier(TokenParamModifier.BELOW));
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), empty());
}
@Test
public void testSearchCodeInBuiltInValueSet() {
AllergyIntolerance ai1 = new AllergyIntolerance();