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Merge branch 'master' into rel_7_4_mb_20240813

This commit is contained in:
Tadgh 2024-08-19 16:38:57 -07:00
parent a3f19a1b15 3e2d84d0f7
commit 359984e06c
14 changed files with 403 additions and 79 deletions
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7
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TaskChunker.java
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@ -20,10 +20,12 @@ package ca.uhn.fhir.util;
* #L%
*/
import com.google.common.collect.Streams;
import jakarta.annotation.Nonnull;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Iterator;
import java.util.List;
import java.util.function.Consumer;
import java.util.stream.Stream;
@ -57,4 +59,9 @@ public class TaskChunker<T> {
public <T> Stream<List<T>> chunk(Stream<T> theStream, int theChunkSize) {
return StreamUtil.partition(theStream, theChunkSize);
}
@Nonnull
public void chunk(Iterator<T> theIterator, int theChunkSize, Consumer<List<T>> theListConsumer) {
chunk(Streams.stream(theIterator), theChunkSize).forEach(theListConsumer);
}
}

35
hapi-fhir-base/src/test/java/ca/uhn/fhir/util/TaskChunkerTest.java
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@ -3,14 +3,21 @@ package ca.uhn.fhir.util;
import jakarta.annotation.Nonnull;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.mockito.ArgumentCaptor;
import org.mockito.Captor;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import java.util.function.Consumer;
import java.util.stream.IntStream;
import java.util.stream.Stream;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.Mockito.times;
@ -43,8 +50,32 @@ public class TaskChunkerTest {
@Nonnull
private static List<Integer> newIntRangeList(int startInclusive, int endExclusive) {
List<Integer> input = IntStream.range(startInclusive, endExclusive).boxed().toList();
return input;
return IntStream.range(startInclusive, endExclusive).boxed().toList();
}
@ParameterizedTest
@MethodSource("testIteratorChunkArguments")
void testIteratorChunk(List<Integer> theListToChunk, List<List<Integer>> theExpectedChunks) {
// given
Iterator<Integer> iter = theListToChunk.iterator();
ArrayList<List<Integer>> result = new ArrayList<>();
// when
new TaskChunker<Integer>().chunk(iter, 3, result::add);
// then
assertEquals(theExpectedChunks, result);
}
public static Stream<Arguments> testIteratorChunkArguments() {
return Stream.of(
Arguments.of(Collections.emptyList(), Collections.emptyList()),
Arguments.of(List.of(1), List.of(List.of(1))),
Arguments.of(List.of(1,2), List.of(List.of(1,2))),
Arguments.of(List.of(1,2,3), List.of(List.of(1,2,3))),
Arguments.of(List.of(1,2,3,4), List.of(List.of(1,2,3), List.of(4))),
Arguments.of(List.of(1,2,3,4,5,6,7,8,9), List.of(List.of(1,2,3), List.of(4,5,6), List.of(7,8,9)))
);
}
}

8
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6216-fulltext-searching-not-returning-expected-results.yml Normal file
View File

@ -0,0 +1,8 @@
---
type: fix
issue: 6216
jira: SMILE-8806
title: "Previously, searches combining the `_text` query parameter (using Lucene/Elasticsearch) with query parameters
using the database (e.g. `identifier` or `date`) could miss matches when more than 500 results match the `_text` query
parameter. This has been fixed, but may be slow if many results match the `_text` query and must be checked against the
database parameters."

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FulltextSearchSvcImpl.java
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@ -32,6 +32,7 @@ import ca.uhn.fhir.jpa.dao.search.ExtendedHSearchResourceProjection;
import ca.uhn.fhir.jpa.dao.search.ExtendedHSearchSearchBuilder;
import ca.uhn.fhir.jpa.dao.search.IHSearchSortHelper;
import ca.uhn.fhir.jpa.dao.search.LastNOperation;
import ca.uhn.fhir.jpa.dao.search.SearchScrollQueryExecutorAdaptor;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.search.ExtendedHSearchBuilderConsumeAdvancedQueryClausesParams;
@ -40,6 +41,7 @@ import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.search.autocomplete.ValueSetAutocompleteOptions;
import ca.uhn.fhir.jpa.search.autocomplete.ValueSetAutocompleteSearch;
import ca.uhn.fhir.jpa.search.builder.ISearchQueryExecutor;
import ca.uhn.fhir.jpa.search.builder.SearchBuilder;
import ca.uhn.fhir.jpa.search.builder.SearchQueryExecutors;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamExtractor;
@ -183,6 +185,19 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
return doSearch(theResourceName, theParams, null, theMaxResultsToFetch, theRequestDetails);
}
@Transactional
@Override
public ISearchQueryExecutor searchScrolled(
String theResourceType, SearchParameterMap theParams, RequestDetails theRequestDetails) {
validateHibernateSearchIsEnabled();
SearchQueryOptionsStep<?, Long, SearchLoadingOptionsStep, ?, ?> searchQueryOptionsStep =
getSearchQueryOptionsStep(theResourceType, theParams, null);
logQuery(searchQueryOptionsStep, theRequestDetails);
return new SearchScrollQueryExecutorAdaptor(searchQueryOptionsStep.scroll(SearchBuilder.getMaximumPageSize()));
}
// keep this in sync with supportsSomeOf();
@SuppressWarnings("rawtypes")
private ISearchQueryExecutor doSearch(

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFulltextSearchSvc.java
View File

@ -62,6 +62,17 @@ public interface IFulltextSearchSvc {
Integer theMaxResultsToFetch,
RequestDetails theRequestDetails);
/**
* Query the index for a complete iterator of ALL results. (scrollable search result).
*
* @param theResourceName e.g. Patient
* @param theParams The search query
* @param theRequestDetails The request details
* @return Iterator of result PIDs
*/
ISearchQueryExecutor searchScrolled(
String theResourceName, SearchParameterMap theParams, RequestDetails theRequestDetails);
/**
* Autocomplete search for NIH $expand contextDirection=existing
* @param theOptions operation options

73
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java
View File

@ -101,7 +101,6 @@ import ca.uhn.fhir.util.StringUtil;
import ca.uhn.fhir.util.UrlUtil;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.Lists;
import com.google.common.collect.Streams;
import com.healthmarketscience.sqlbuilder.Condition;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
@ -141,7 +140,9 @@ import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.model.util.JpaConstants.UNDESIRED_RESOURCE_LINKAGES_FOR_EVERYTHING_ON_PATIENT_INSTANCE;
import static ca.uhn.fhir.jpa.search.builder.QueryStack.LOCATION_POSITION;
import static ca.uhn.fhir.jpa.search.builder.QueryStack.SearchForIdsParams.with;
import static ca.uhn.fhir.jpa.util.InClauseNormalizer.*;
import static java.util.Objects.requireNonNull;
import static org.apache.commons.collections4.CollectionUtils.isNotEmpty;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -205,9 +206,6 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
@Autowired(required = false)
private IElasticsearchSvc myIElasticsearchSvc;
@Autowired
private FhirContext myCtx;
@Autowired
private IJpaStorageResourceParser myJpaStorageResourceParser;
@ -332,8 +330,7 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
init(theParams, theSearchUuid, theRequestPartitionId);
if (checkUseHibernateSearch()) {
long count = myFulltextSearchSvc.count(myResourceName, theParams.clone());
return count;
return myFulltextSearchSvc.count(myResourceName, theParams.clone());
}
List<ISearchQueryExecutor> queries = createQuery(theParams.clone(), null, null, null, true, theRequest, null);
@ -404,8 +401,16 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
fulltextMatchIds = queryHibernateSearchForEverythingPids(theRequest);
resultCount = fulltextMatchIds.size();
} else {
fulltextExecutor = myFulltextSearchSvc.searchNotScrolled(
myResourceName, myParams, myMaxResultsToFetch, theRequest);
// todo performance MB - some queries must intersect with JPA (e.g. they have a chain, or we haven't
// enabled SP indexing).
// and some queries don't need JPA. We only need the scroll when we need to intersect with JPA.
// It would be faster to have a non-scrolled search in this case, since creating the scroll requires
// extra work in Elastic.
// if (eligibleToSkipJPAQuery) fulltextExecutor = myFulltextSearchSvc.searchNotScrolled( ...
// we might need to intersect with JPA. So we might need to traverse ALL results from lucene, not just
// a page.
fulltextExecutor = myFulltextSearchSvc.searchScrolled(myResourceName, myParams, theRequest);
}
if (fulltextExecutor == null) {
@ -457,7 +462,8 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
// We break the pids into chunks that fit in the 1k limit for jdbc bind params.
new QueryChunker<Long>()
.chunk(
Streams.stream(fulltextExecutor).collect(Collectors.toList()),
fulltextExecutor,
SearchBuilder.getMaximumPageSize(),
t -> doCreateChunkedQueries(
theParams, t, theOffset, sort, theCountOnlyFlag, theRequest, queries));
}
@ -560,8 +566,9 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
boolean theCount,
RequestDetails theRequest,
ArrayList<ISearchQueryExecutor> theQueries) {
if (thePids.size() < getMaximumPageSize()) {
normalizeIdListForLastNInClause(thePids);
thePids = normalizeIdListForInClause(thePids);
}
createChunkedQuery(theParams, sort, theOffset, thePids.size(), theCount, theRequest, thePids, theQueries);
}
@ -885,41 +892,7 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
&& theParams.values().stream()
.flatMap(Collection::stream)
.flatMap(Collection::stream)
.anyMatch(t -> t instanceof ReferenceParam);
}
private List<Long> normalizeIdListForLastNInClause(List<Long> lastnResourceIds) {
/*
The following is a workaround to a known issue involving Hibernate. If queries are used with "in" clauses with large and varying
numbers of parameters, this can overwhelm Hibernate's QueryPlanCache and deplete heap space. See the following link for more info:
https://stackoverflow.com/questions/31557076/spring-hibernate-query-plan-cache-memory-usage.
Normalizing the number of parameters in the "in" clause stabilizes the size of the QueryPlanCache, so long as the number of
arguments never exceeds the maximum specified below.
*/
int listSize = lastnResourceIds.size();
if (listSize > 1 && listSize < 10) {
padIdListWithPlaceholders(lastnResourceIds, 10);
} else if (listSize > 10 && listSize < 50) {
padIdListWithPlaceholders(lastnResourceIds, 50);
} else if (listSize > 50 && listSize < 100) {
padIdListWithPlaceholders(lastnResourceIds, 100);
} else if (listSize > 100 && listSize < 200) {
padIdListWithPlaceholders(lastnResourceIds, 200);
} else if (listSize > 200 && listSize < 500) {
padIdListWithPlaceholders(lastnResourceIds, 500);
} else if (listSize > 500 && listSize < 800) {
padIdListWithPlaceholders(lastnResourceIds, 800);
}
return lastnResourceIds;
}
private void padIdListWithPlaceholders(List<Long> theIdList, int preferredListSize) {
while (theIdList.size() < preferredListSize) {
theIdList.add(-1L);
}
.anyMatch(ReferenceParam.class::isInstance);
}
private void createSort(QueryStack theQueryStack, SortSpec theSort, SearchParameterMap theParams) {
@ -1154,7 +1127,7 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
List<Long> versionlessPids = JpaPid.toLongList(thePids);
if (versionlessPids.size() < getMaximumPageSize()) {
versionlessPids = normalizeIdListForLastNInClause(versionlessPids);
versionlessPids = normalizeIdListForInClause(versionlessPids);
}
// -- get the resource from the searchView
@ -1243,7 +1216,7 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
Map<Long, Collection<ResourceTag>> tagMap = new HashMap<>();
// -- no tags
if (thePidList.size() == 0) return tagMap;
if (thePidList.isEmpty()) return tagMap;
// -- get all tags for the idList
Collection<ResourceTag> tagList = myResourceTagDao.findByResourceIds(thePidList);
@ -1383,7 +1356,6 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
EntityManager entityManager = theParameters.getEntityManager();
Integer maxCount = theParameters.getMaxCount();
FhirContext fhirContext = theParameters.getFhirContext();
DateRangeParam lastUpdated = theParameters.getLastUpdated();
RequestDetails request = theParameters.getRequestDetails();
String searchIdOrDescription = theParameters.getSearchIdOrDescription();
List<String> desiredResourceTypes = theParameters.getDesiredResourceTypes();
@ -1922,11 +1894,10 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
}
assert !targetResourceTypes.isEmpty();
Set<Long> identityHashesForTypes = targetResourceTypes.stream()
return targetResourceTypes.stream()
.map(type -> BaseResourceIndexedSearchParam.calculateHashIdentity(
myPartitionSettings, myRequestPartitionId, type, "url"))
.collect(Collectors.toSet());
return identityHashesForTypes;
}
private <T> List<Collection<T>> partition(Collection<T> theNextRoundMatches, int theMaxLoad) {
@ -2506,7 +2477,7 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
private void retrieveNextIteratorQuery() {
close();
if (myQueryList != null && myQueryList.size() > 0) {
if (isNotEmpty(myQueryList)) {
myResultsIterator = myQueryList.remove(0);
myHasNextIteratorQuery = true;
} else {

65
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/InClauseNormalizer.java Normal file
View File

@ -0,0 +1,65 @@
package ca.uhn.fhir.jpa.util;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
/*
This class encapsulate the implementation providing a workaround to a known issue involving Hibernate. If queries are used with "in" clauses with large and varying
numbers of parameters, this can overwhelm Hibernate's QueryPlanCache and deplete heap space. See the following link for more info:
https://stackoverflow.com/questions/31557076/spring-hibernate-query-plan-cache-memory-usage.
Normalizing the number of parameters in the "in" clause stabilizes the size of the QueryPlanCache, so long as the number of
arguments never exceeds the maximum specified below.
*/
public class InClauseNormalizer {
public static List<Long> normalizeIdListForInClause(List<Long> theResourceIds) {
List<Long> retVal = theResourceIds;
int listSize = theResourceIds.size();
if (listSize > 1 && listSize < 10) {
retVal = padIdListWithPlaceholders(theResourceIds, 10);
} else if (listSize > 10 && listSize < 50) {
retVal = padIdListWithPlaceholders(theResourceIds, 50);
} else if (listSize > 50 && listSize < 100) {
retVal = padIdListWithPlaceholders(theResourceIds, 100);
} else if (listSize > 100 && listSize < 200) {
retVal = padIdListWithPlaceholders(theResourceIds, 200);
} else if (listSize > 200 && listSize < 500) {
retVal = padIdListWithPlaceholders(theResourceIds, 500);
} else if (listSize > 500 && listSize < 800) {
retVal = padIdListWithPlaceholders(theResourceIds, 800);
}
return retVal;
}
private static List<Long> padIdListWithPlaceholders(List<Long> theIdList, int preferredListSize) {
List<Long> retVal = theIdList;
if (isUnmodifiableList(theIdList)) {
retVal = new ArrayList<>(preferredListSize);
retVal.addAll(theIdList);
}
while (retVal.size() < preferredListSize) {
retVal.add(-1L);
}
return retVal;
}
private static boolean isUnmodifiableList(List<Long> theList) {
try {
theList.addAll(Collections.emptyList());
} catch (Exception e) {
return true;
}
return false;
}
private InClauseNormalizer() {}
}

72
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/util/InClauseNormalizerTest.java Normal file
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@ -0,0 +1,72 @@
package ca.uhn.fhir.util;
import ca.uhn.fhir.jpa.util.InClauseNormalizer;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Stream;
import static java.util.Collections.nCopies;
import static java.util.Collections.unmodifiableList;
import static org.assertj.core.api.Assertions.assertThat;
public class InClauseNormalizerTest {
private static final Long ourResourceId = 1L;
private static final Long ourPaddingValue = -1L;
@ParameterizedTest
@MethodSource("arguments")
public void testNormalizeUnmodifiableList_willCreateNewListAndPadToSize(int theInitialListSize, int theExpectedNormalizedListSize) {
List<Long> initialList = new ArrayList<>(nCopies(theInitialListSize, ourResourceId));
initialList = unmodifiableList(initialList);
List<Long> normalizedList = InClauseNormalizer.normalizeIdListForInClause(initialList);
assertNormalizedList(initialList, normalizedList, theInitialListSize, theExpectedNormalizedListSize);
}
@ParameterizedTest
@MethodSource("arguments")
public void testNormalizeListToSizeAndPad(int theInitialListSize, int theExpectedNormalizedListSize) {
List<Long> initialList = new ArrayList<>(nCopies(theInitialListSize, ourResourceId));
List<Long> normalizedList = InClauseNormalizer.normalizeIdListForInClause(initialList);
assertNormalizedList(initialList, normalizedList, theInitialListSize, theExpectedNormalizedListSize);
}
private void assertNormalizedList(List<Long> theInitialList, List<Long> theNormalizedList, int theInitialListSize, int theExpectedNormalizedListSize) {
List<Long> expectedPaddedSubList = new ArrayList<>(nCopies(theExpectedNormalizedListSize - theInitialListSize, ourPaddingValue));
assertThat(theNormalizedList).startsWith(listToArray(theInitialList));
assertThat(theNormalizedList).hasSize(theExpectedNormalizedListSize);
assertThat(theNormalizedList).endsWith(listToArray(expectedPaddedSubList));
}
static Long[] listToArray(List<Long> theList) {
return theList.toArray(new Long[0]);
}
private static Stream<Arguments> arguments(){
return Stream.of(
Arguments.of(0, 0),
Arguments.of(1, 1),
Arguments.of(2, 10),
Arguments.of(10, 10),
Arguments.of(12, 50),
Arguments.of(50, 50),
Arguments.of(51, 100),
Arguments.of(100, 100),
Arguments.of(150, 200),
Arguments.of(300, 500),
Arguments.of(500, 500),
Arguments.of(700, 800),
Arguments.of(800, 800),
Arguments.of(801, 801)
);
}
}

3
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNIT.java
View File

@ -56,8 +56,6 @@ public class FhirResourceDaoR4SearchLastNIT extends BaseR4SearchLastN {
@Mock
private IHSearchEventListener mySearchEventListener;
@Test
public void testLastNChunking() {
@ -108,7 +106,6 @@ public class FhirResourceDaoR4SearchLastNIT extends BaseR4SearchLastN {
secondQueryPattern.append("\\).*");
assertThat(queries.get(1).toUpperCase().replaceAll(" , ", ",")).matches(secondQueryPattern.toString());
assertThat(queries.get(3).toUpperCase().replaceAll(" , ", ",")).matches(secondQueryPattern.toString());
}
@Test

2
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/batch2/Batch2CoordinatorIT.java
View File

@ -763,7 +763,7 @@ public class Batch2CoordinatorIT extends BaseJpaR4Test {
myFirstStepLatch.awaitExpected();
// validate
myBatch2JobHelper.awaitJobHasStatusWithForcedMaintenanceRuns(instanceId, StatusEnum.IN_PROGRESS);
myBatch2JobHelper.awaitJobHasStatusWithForcedMaintenanceRuns(instanceId, StatusEnum.ERRORED);
// execute
ourLog.info("Cancel job {}", instanceId);

112
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSearchDaoR4Test.java
View File

@ -1,8 +1,8 @@
package ca.uhn.fhir.jpa.dao.r4;
import static org.junit.jupiter.api.Assertions.assertEquals;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.search.builder.SearchBuilder;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.rest.api.Constants;
@ -12,6 +12,9 @@ import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.StringOrListParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenAndListParam;
import ca.uhn.fhir.rest.param.TokenOrListParam;
import ca.uhn.fhir.rest.param.TokenParam;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.Test;
@ -19,9 +22,11 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.dao.InvalidDataAccessApiUsageException;
import org.springframework.transaction.support.TransactionSynchronizationManager;
import java.util.ArrayList;
import java.util.List;
import static org.assertj.core.api.Assertions.assertThat;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class FhirSearchDaoR4Test extends BaseJpaR4Test {
@ -51,11 +56,11 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
patient.addName().addGiven(content).setFamily("hirasawa");
id1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getIdPartAsLong();
}
Long id2;
{
Patient patient = new Patient();
patient.addName().addGiven("mio").setFamily("akiyama");
id2 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getIdPartAsLong();
myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getIdPartAsLong();
}
SearchParameterMap params = new SearchParameterMap();
@ -257,4 +262,105 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
}
}
@Test
public void testSearchNarrativeWithLuceneSearch() {
final int numberOfPatientsToCreate = SearchBuilder.getMaximumPageSize() + 10;
List<String> expectedActivePatientIds = new ArrayList<>(numberOfPatientsToCreate);
for (int i = 0; i < numberOfPatientsToCreate; i++)
{
Patient patient = new Patient();
patient.getText().setDivAsString("<div>AAAS<p>FOO</p> CCC </div>");
expectedActivePatientIds.add(myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getIdPart());
}
{
Patient patient = new Patient();
patient.getText().setDivAsString("<div>AAAB<p>FOO</p> CCC </div>");
myPatientDao.create(patient, mySrd);
}
{
Patient patient = new Patient();
patient.getText().setDivAsString("<div>ZZYZXY</div>");
myPatientDao.create(patient, mySrd);
}
SearchParameterMap map = new SearchParameterMap().setLoadSynchronous(true);
map.add(Constants.PARAM_TEXT, new StringParam("AAAS"));
IBundleProvider searchResultBundle = myPatientDao.search(map, mySrd);
List<String> resourceIdsFromSearchResult = searchResultBundle.getAllResourceIds();
assertThat(resourceIdsFromSearchResult).containsExactlyInAnyOrderElementsOf(expectedActivePatientIds);
}
@Test
public void testLuceneNarrativeSearchQueryIntersectingJpaQuery() {
final int numberOfPatientsToCreate = SearchBuilder.getMaximumPageSize() + 10;
List<String> expectedActivePatientIds = new ArrayList<>(numberOfPatientsToCreate);
// create active and non-active patients with the same narrative
for (int i = 0; i < numberOfPatientsToCreate; i++)
{
Patient activePatient = new Patient();
activePatient.getText().setDivAsString("<div>AAAS<p>FOO</p> CCC </div>");
activePatient.setActive(true);
String patientId = myPatientDao.create(activePatient, mySrd).getId().toUnqualifiedVersionless().getIdPart();
expectedActivePatientIds.add(patientId);
Patient nonActivePatient = new Patient();
nonActivePatient.getText().setDivAsString("<div>AAAS<p>FOO</p> CCC </div>");
nonActivePatient.setActive(false);
myPatientDao.create(nonActivePatient, mySrd);
}
SearchParameterMap map = new SearchParameterMap().setLoadSynchronous(true);
TokenAndListParam tokenAndListParam = new TokenAndListParam();
tokenAndListParam.addAnd(new TokenOrListParam().addOr(new TokenParam().setValue("true")));
map.add("active", tokenAndListParam);
map.add(Constants.PARAM_TEXT, new StringParam("AAAS"));
IBundleProvider searchResultBundle = myPatientDao.search(map, mySrd);
List<String> resourceIdsFromSearchResult = searchResultBundle.getAllResourceIds();
assertThat(resourceIdsFromSearchResult).containsExactlyInAnyOrderElementsOf(expectedActivePatientIds);
}
@Test
public void testLuceneContentSearchQueryIntersectingJpaQuery() {
final int numberOfPatientsToCreate = SearchBuilder.getMaximumPageSize() + 10;
final String patientFamilyName = "Flanders";
List<String> expectedActivePatientIds = new ArrayList<>(numberOfPatientsToCreate);
// create active and non-active patients with the same narrative
for (int i = 0; i < numberOfPatientsToCreate; i++)
{
Patient activePatient = new Patient();
activePatient.addName().setFamily(patientFamilyName);
activePatient.setActive(true);
String patientId = myPatientDao.create(activePatient, mySrd).getId().toUnqualifiedVersionless().getIdPart();
expectedActivePatientIds.add(patientId);
Patient nonActivePatient = new Patient();
nonActivePatient.addName().setFamily(patientFamilyName);
nonActivePatient.setActive(false);
myPatientDao.create(nonActivePatient, mySrd);
}
SearchParameterMap map = new SearchParameterMap().setLoadSynchronous(true);
TokenAndListParam tokenAndListParam = new TokenAndListParam();
tokenAndListParam.addAnd(new TokenOrListParam().addOr(new TokenParam().setValue("true")));
map.add("active", tokenAndListParam);
map.add(Constants.PARAM_CONTENT, new StringParam(patientFamilyName));
IBundleProvider searchResultBundle = myPatientDao.search(map, mySrd);
List<String> resourceIdsFromSearchResult = searchResultBundle.getAllResourceIds();
assertThat(resourceIdsFromSearchResult).containsExactlyInAnyOrderElementsOf(expectedActivePatientIds);
}
}

19
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/embedded/OracleCondition.java
View File

@ -1,3 +1,22 @@
/*-
* #%L
* HAPI FHIR JPA Server Test Utilities
* %%
* Copyright (C) 2014 - 2024 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
package ca.uhn.fhir.jpa.embedded;
import org.apache.commons.lang3.StringUtils;

19
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/embedded/annotation/OracleTest.java
View File

@ -1,3 +1,22 @@
/*-
* #%L
* HAPI FHIR JPA Server Test Utilities
* %%
* Copyright (C) 2014 - 2024 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
package ca.uhn.fhir.jpa.embedded.annotation;
import ca.uhn.fhir.jpa.embedded.OracleCondition;

41
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/Batch2JobHelper.java
View File

@ -25,6 +25,7 @@ import ca.uhn.fhir.batch2.api.IJobPersistence;
import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.StatusEnum;
import ca.uhn.fhir.jpa.batch.models.Batch2JobStartResponse;
import com.google.common.annotations.VisibleForTesting;
import org.awaitility.Awaitility;
import org.awaitility.core.ConditionTimeoutException;
import org.slf4j.Logger;
@ -50,6 +51,8 @@ public class Batch2JobHelper {
private static final Logger ourLog = LoggerFactory.getLogger(Batch2JobHelper.class);
private static final int BATCH_SIZE = 100;
public static final int DEFAULT_WAIT_DEADLINE = 30;
public static final Duration DEFAULT_WAIT_DURATION = Duration.of(DEFAULT_WAIT_DEADLINE, ChronoUnit.SECONDS);
private final IJobMaintenanceService myJobMaintenanceService;
private final IJobCoordinator myJobCoordinator;
@ -82,11 +85,11 @@ public class Batch2JobHelper {
}
public JobInstance awaitJobHasStatus(String theInstanceId, StatusEnum... theExpectedStatus) {
return awaitJobHasStatus(theInstanceId, 30, theExpectedStatus);
return awaitJobHasStatus(theInstanceId, DEFAULT_WAIT_DEADLINE, theExpectedStatus);
}
public JobInstance awaitJobHasStatusWithoutMaintenancePass(String theInstanceId, StatusEnum... theExpectedStatus) {
return awaitJobawaitJobHasStatusWithoutMaintenancePass(theInstanceId, 10, theExpectedStatus);
return awaitJobawaitJobHasStatusWithoutMaintenancePass(theInstanceId, DEFAULT_WAIT_DEADLINE, theExpectedStatus);
}
public JobInstance awaitJobHasStatus(String theInstanceId, int theSecondsToWait, StatusEnum... theExpectedStatus) {
@ -144,7 +147,7 @@ public class Batch2JobHelper {
return myJobCoordinator.getInstance(theBatchJobId);
}
private boolean checkStatusWithMaintenancePass(String theInstanceId, StatusEnum... theExpectedStatuses) throws InterruptedException {
private boolean checkStatusWithMaintenancePass(String theInstanceId, StatusEnum... theExpectedStatuses) {
if (hasStatus(theInstanceId, theExpectedStatuses)) {
return true;
}
@ -170,37 +173,41 @@ public class Batch2JobHelper {
return awaitJobHasStatus(theInstanceId, StatusEnum.ERRORED, StatusEnum.FAILED);
}
public void awaitJobHasStatusWithForcedMaintenanceRuns(String theInstanceId, StatusEnum theStatusEnum) {
public void awaitJobHasStatusWithForcedMaintenanceRuns(String theInstanceId, StatusEnum... theStatusEnums) {
AtomicInteger counter = new AtomicInteger();
Duration waitDuration = DEFAULT_WAIT_DURATION;
try {
await()
.atMost(Duration.of(10, ChronoUnit.SECONDS))
.atMost(waitDuration)
.until(() -> {
counter.getAndIncrement();
forceRunMaintenancePass();
return hasStatus(theInstanceId, theStatusEnum);
return hasStatus(theInstanceId, theStatusEnums);
});
} catch (ConditionTimeoutException ex) {
StatusEnum status = getStatus(theInstanceId);
String msg = String.format(
"Job %s has state %s after 10s timeout and %d checks",
fail(String.format(
"Job %s has state %s after %s timeout and %d checks",
theInstanceId,
status.name(),
waitDuration,
counter.get()
);
), ex);
}
}
public void awaitJobInProgress(String theInstanceId) {
Duration waitDuration = DEFAULT_WAIT_DURATION;
try {
await()
.atMost(Duration.of(10, ChronoUnit.SECONDS))
.atMost(waitDuration)
.until(() -> checkStatusWithMaintenancePass(theInstanceId, StatusEnum.IN_PROGRESS));
} catch (ConditionTimeoutException ex) {
StatusEnum statusEnum = getStatus(theInstanceId);
String msg = String.format("Job %s still has status %s after 10 seconds.",
String msg = String.format("Job %s still has status %s after %s seconds.",
theInstanceId,
statusEnum.name());
statusEnum.name(),
waitDuration);
fail(msg);
}
}
@ -291,12 +298,7 @@ public class Batch2JobHelper {
}
if (!map.isEmpty()) {
ourLog.error(
"Found Running Jobs "
+ map.keySet().stream()
.map(k -> k + " : " + map.get(k))
.collect(Collectors.joining("\n"))
);
ourLog.error("Found Running Jobs {}",map.keySet().stream().map(k -> k + " : " + map.get(k)).collect(Collectors.joining("\n")));
return true;
}
@ -305,7 +307,7 @@ public class Batch2JobHelper {
public void awaitNoJobsRunning(boolean theExpectAtLeastOneJobToExist) {
HashMap<String, String> map = new HashMap<>();
Awaitility.await().atMost(10, TimeUnit.SECONDS)
Awaitility.await().atMost(DEFAULT_WAIT_DURATION)
.until(() -> {
myJobMaintenanceService.runMaintenancePass();
@ -335,6 +337,7 @@ public class Batch2JobHelper {
myJobMaintenanceService.runMaintenancePass();
}
@VisibleForTesting
public void enableMaintenanceRunner(boolean theEnabled) {
myJobMaintenanceService.enableMaintenancePass(theEnabled);
}