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Add non-standard __pid SP for breaking ties cheaply during sorts. (#5428) 

Add a non-standard __pid SP.
This commit is contained in:
michaelabuckley 2023-11-03 16:55:32 -04:00 committed by GitHub
parent 33ca4e9b99
commit 2ef2924b86
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11 changed files with 259 additions and 3 deletions
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2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java
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@ -199,6 +199,8 @@ public class Constants {
public static final String PARAM_PRETTY_VALUE_FALSE = "false";
public static final String PARAM_PRETTY_VALUE_TRUE = "true";
public static final String PARAM_PROFILE = "_profile";
public static final String PARAM__PID = "__pid";
public static final String PARAM_QUERY = "_query";
public static final String PARAM_RESPONSE_URL = "response-url"; // Used in messaging
public static final String PARAM_REVINCLUDE = "_revinclude";

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_10_0/5428-pid-sp.yaml Normal file
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@ -0,0 +1,5 @@
---
type: add
issue: 5428
title: "Add support for non-standard __pid SearchParameter to the the JPA engine.
This new SP provides an efficient tie-breaking sort key."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/search.md
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@ -22,6 +22,10 @@ Searching on Location.Position using `near` currently uses a box search, not a r
The special `_filter` is only partially implemented.
### __pid
The JPA server implements a non-standard special `__pid` which matches/sorts on the raw internal database id.
This sort is useful for imposing tie-breaking sort order in an efficient way.
<a name="uplifted-refchains"/>

40
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java
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@ -285,6 +285,12 @@ public class QueryStack {
mySqlBuilder.addSortString(resourceTablePredicateBuilder.getColumnFhirId(), theAscending, myUseAggregate);
}
/** Sort on RES_ID -- used to break ties for reliable sort */
public void addSortOnResourcePID(boolean theAscending) {
BaseJoiningPredicateBuilder predicateBuilder = mySqlBuilder.getOrCreateFirstPredicateBuilder();
mySqlBuilder.addSortString(predicateBuilder.getResourceIdColumn(), theAscending);
}
public void addSortOnResourceLink(
String theResourceName,
String theReferenceTargetType,
@ -2287,6 +2293,10 @@ public class QueryStack {
null,
theSearchForIdsParams.myRequestPartitionId);
case Constants.PARAM__PID:
return createPredicateResourcePID(
theSearchForIdsParams.mySourceJoinColumn, theSearchForIdsParams.myAndOrParams);
case PARAM_HAS:
return createPredicateHas(
theSearchForIdsParams.mySourceJoinColumn,
@ -2337,6 +2347,36 @@ public class QueryStack {
}
}
/**
* Raw match on RES_ID
*/
private Condition createPredicateResourcePID(
DbColumn theSourceJoinColumn, List<List<IQueryParameterType>> theAndOrParams) {
DbColumn pidColumn = theSourceJoinColumn;
if (pidColumn == null) {
BaseJoiningPredicateBuilder predicateBuilder = mySqlBuilder.getOrCreateFirstPredicateBuilder();
pidColumn = predicateBuilder.getResourceIdColumn();
}
// we don't support any modifiers for now
Set<Long> pids = theAndOrParams.stream()
.map(orList -> orList.stream()
.map(v -> v.getValueAsQueryToken(myFhirContext))
.map(Long::valueOf)
.collect(Collectors.toSet()))
.reduce(Sets::intersection)
.orElse(Set.of());
if (pids.isEmpty()) {
mySqlBuilder.setMatchNothing();
return null;
}
return toEqualToOrInPredicate(pidColumn, mySqlBuilder.generatePlaceholders(pids));
}
private Condition createReverseSearchPredicateLastUpdated(
List<List<IQueryParameterType>> theAndOrParams, DbColumn theSourceColumn) {

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java
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@ -838,6 +838,10 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
theQueryStack.addSortOnResourceId(ascending);
} else if (Constants.PARAM__PID.equals(theSort.getParamName())) {
theQueryStack.addSortOnResourcePID(ascending);
} else if (Constants.PARAM_LASTUPDATED.equals(theSort.getParamName())) {
theQueryStack.addSortOnLastUpdated(ascending);

2
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/ResourceMetaParams.java
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@ -51,6 +51,8 @@ public class ResourceMetaParams {
Map<String, Class<? extends IQueryParameterAnd<?>>> resourceMetaAndParams = new HashMap<>();
resourceMetaParams.put(IAnyResource.SP_RES_ID, StringParam.class);
resourceMetaAndParams.put(IAnyResource.SP_RES_ID, StringAndListParam.class);
resourceMetaParams.put(Constants.PARAM__PID, TokenParam.class);
resourceMetaAndParams.put(Constants.PARAM__PID, TokenAndListParam.class);
resourceMetaParams.put(Constants.PARAM_TAG, TokenParam.class);
resourceMetaAndParams.put(Constants.PARAM_TAG, TokenAndListParam.class);
resourceMetaParams.put(Constants.PARAM_PROFILE, UriParam.class);

150
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QuerySandbox.java Normal file
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@ -0,0 +1,150 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.api.Hook;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.dao.TestDaoSearch;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.jpa.util.SqlQuery;
import ca.uhn.fhir.jpa.util.SqlQueryList;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.storage.test.DaoTestDataBuilder;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.junit.jupiter.api.extension.RegisterExtension;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.annotation.DirtiesContext;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.TestContext;
import org.springframework.test.context.TestExecutionListeners;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import org.springframework.test.context.support.DependencyInjectionTestExecutionListener;
import org.springframework.test.context.support.DirtiesContextTestExecutionListener;
import org.springframework.transaction.PlatformTransactionManager;
import java.util.ArrayList;
import java.util.List;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.not;
/**
* Sandbox for implementing queries.
* This will NOT run during the build - use this class as a convenient
* place to explore, debug, profile, and optimize.
*/
@ExtendWith(SpringExtension.class)
@ContextConfiguration(classes = {
TestR4Config.class,
TestHSearchAddInConfig.NoFT.class,
DaoTestDataBuilder.Config.class,
TestDaoSearch.Config.class
})
@DirtiesContext(classMode = DirtiesContext.ClassMode.AFTER_CLASS)
@TestExecutionListeners(listeners = {
DependencyInjectionTestExecutionListener.class
, FhirResourceDaoR4QuerySandbox.TestDirtiesContextTestExecutionListener.class
})
public class FhirResourceDaoR4QuerySandbox extends BaseJpaTest {
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoR4QuerySandbox.class);
@Autowired
PlatformTransactionManager myTxManager;
@Autowired
FhirContext myFhirCtx;
@RegisterExtension
@Autowired
DaoTestDataBuilder myDataBuilder;
@Autowired
TestDaoSearch myTestDaoSearch;
@Override
protected PlatformTransactionManager getTxManager() {
return myTxManager;
}
@Override
protected FhirContext getFhirContext() {
return myFhirCtx;
}
List<String> myCapturedQueries = new ArrayList<>();
@BeforeEach
void registerLoggingInterceptor() {
registerInterceptor(new Object(){
@Hook(Pointcut.JPA_PERFTRACE_RAW_SQL)
public void captureSql(RequestDetails theRequestDetails, SqlQueryList theQueries) {
for (SqlQuery next : theQueries) {
String output = next.getSql(true, true, true);
ourLog.info("Query: {}", output);
myCapturedQueries.add(output);
}
}
});
}
@Test
public void testSearches_logQueries() {
myDataBuilder.createPatient();
myTestDaoSearch.searchForIds("Patient?name=smith");
assertThat(myCapturedQueries, not(empty()));
}
@Test
void testQueryByPid() {
// sentinel for over-match
myDataBuilder.createPatient();
String id = myDataBuilder.createPatient(
myDataBuilder.withBirthdate("1971-01-01"),
myDataBuilder.withActiveTrue(),
myDataBuilder.withFamily("Smith")).getIdPart();
myTestDaoSearch.assertSearchFindsOnly("search by server assigned id", "Patient?__pid=" + id, id);
}
@Test
void testQueryByPid_withOtherSPAvoidsResourceTable() {
// sentinel for over-match
myDataBuilder.createPatient();
String id = myDataBuilder.createPatient(
myDataBuilder.withBirthdate("1971-01-01"),
myDataBuilder.withActiveTrue(),
myDataBuilder.withFamily("Smith")).getIdPart();
myTestDaoSearch.assertSearchFindsOnly("search by server assigned id", "Patient?name=smith&__pid=" + id, id);
}
@Test
void testSortByPid() {
String id1 = myDataBuilder.createPatient(myDataBuilder.withFamily("Smithy")).getIdPart();
String id2 = myDataBuilder.createPatient(myDataBuilder.withFamily("Smithwick")).getIdPart();
String id3 = myDataBuilder.createPatient(myDataBuilder.withFamily("Smith")).getIdPart();
myTestDaoSearch.assertSearchFindsInOrder("sort by server assigned id", "Patient?family=smith&_sort=__pid", id1,id2,id3);
myTestDaoSearch.assertSearchFindsInOrder("reverse sort by server assigned id", "Patient?family=smith&_sort=-__pid", id3,id2,id1);
}
public static final class TestDirtiesContextTestExecutionListener extends DirtiesContextTestExecutionListener {
@Override
protected void beforeOrAfterTestClass(TestContext testContext, DirtiesContext.ClassMode requiredClassMode) throws Exception {
if (!testContext.getTestClass().getName().contains("$")) {
super.beforeOrAfterTestClass(testContext, requiredClassMode);
}
}
}
}

35
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4StandardQueriesNoFTTest.java
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@ -4,10 +4,10 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.TestDaoSearch;
import ca.uhn.fhir.jpa.search.BaseSourceSearchParameterTestCases;
import ca.uhn.fhir.jpa.search.CompositeSearchParameterTestCases;
import ca.uhn.fhir.jpa.search.IIdSearchTestTemplate;
import ca.uhn.fhir.jpa.search.QuantitySearchParameterTestCases;
import ca.uhn.fhir.jpa.search.BaseSourceSearchParameterTestCases;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
@ -38,9 +38,14 @@ import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.hasItem;
import static org.hamcrest.Matchers.hasItems;
import static org.hamcrest.Matchers.not;
/**
* Verify that our query behaviour matches the spec.
* Note: we do not extend BaseJpaR4Test here.
* That does a full purge in @AfterEach which is a bit slow.
* Instead, this test tracks all created resources in DaoTestDataBuilder, and deletes them in teardown.
*/
@ExtendWith(SpringExtension.class)
@ContextConfiguration(classes = {
TestR4Config.class,
@ -499,6 +504,32 @@ public class FhirResourceDaoR4StandardQueriesNoFTTest extends BaseJpaTest {
}
@Test
void testQueryByPid() {
// sentinel for over-match
myDataBuilder.createPatient();
String id = myDataBuilder.createPatient(
myDataBuilder.withBirthdate("1971-01-01"),
myDataBuilder.withActiveTrue(),
myDataBuilder.withFamily("Smith")).getIdPart();
myTestDaoSearch.assertSearchFindsOnly("search by server assigned id", "Patient?__pid=" + id, id);
myTestDaoSearch.assertSearchFindsOnly("search by server assigned id", "Patient?family=smith&__pid=" + id, id);
}
@Test
void testSortByPid() {
String id1 = myDataBuilder.createPatient(myDataBuilder.withFamily("Smithy")).getIdPart();
String id2 = myDataBuilder.createPatient(myDataBuilder.withFamily("Smithwick")).getIdPart();
String id3 = myDataBuilder.createPatient(myDataBuilder.withFamily("Smith")).getIdPart();
myTestDaoSearch.assertSearchFindsInOrder("sort by server assigned id", "Patient?family=smith&_sort=__pid", id1,id2,id3);
myTestDaoSearch.assertSearchFindsInOrder("reverse sort by server assigned id", "Patient?family=smith&_sort=-__pid", id3,id2,id1);
}
@Nested
public class IdSearch implements IIdSearchTestTemplate {
@Override

12
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/dao/TestDaoSearch.java
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@ -48,6 +48,7 @@ import javax.annotation.Nonnull;
import static org.apache.commons.lang3.ArrayUtils.EMPTY_STRING_ARRAY;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.everyItem;
import static org.hamcrest.Matchers.hasItems;
import static org.hamcrest.Matchers.in;
@ -133,6 +134,17 @@ public class TestDaoSearch {
assertSearchFindsInOrder(theReason, theQueryUrl, theIds.toArray(EMPTY_STRING_ARRAY));
}
public void assertSearchFindsOnly(String theReason, String theQueryUrl, String... theIds) {
assertSearchIdsMatch(theReason, theQueryUrl, containsInAnyOrder(theIds));
}
public void assertSearchIdsMatch(
String theReason, String theQueryUrl, Matcher<? super Iterable<String>> theMatchers) {
List<String> ids = searchForIds(theQueryUrl);
MatcherAssert.assertThat(theReason, ids, theMatchers);
}
public void assertSearchResultIds(String theQueryUrl, String theReason, Matcher<Iterable<String>> matcher) {
List<String> ids = searchForIds(theQueryUrl);

5
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/BaseJpaTest.java
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@ -431,6 +431,11 @@ public abstract class BaseJpaTest extends BaseTest {
return deliveryLatch;
}
protected void registerInterceptor(Object theInterceptor) {
myRegisteredInterceptors.add(theInterceptor);
myInterceptorRegistry.registerInterceptor(theInterceptor);
}
protected void purgeHibernateSearch(EntityManager theEntityManager) {
runInTransaction(() -> {
if (myFulltestSearchSvc != null && !myFulltestSearchSvc.isDisabled()) {

3
hapi-fhir-storage-test-utilities/src/main/java/ca/uhn/fhir/storage/test/DaoTestDataBuilder.java
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@ -39,7 +39,8 @@ import org.springframework.context.annotation.Configuration;
/**
* Implements ITestDataBuilder via a live DaoRegistry.
*
* Note: this implements {@link AfterEachCallback} and will delete any resources created when registered
* via {@link org.junit.jupiter.api.extension.RegisterExtension}.
* Add the inner {@link Config} to your spring context to inject this.
* For convenience, you can still implement ITestDataBuilder on your test class, and delegate the missing methods to this bean.
*/