honeymoose
/
hapi-fhir
mirror of https://github.com/hapifhir/hapi-fhir.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Initial quick implementation of paging with tests

This commit is contained in:
Tadgh 2021-06-29 17:46:03 -04:00
parent 795fb31a3a
commit a770d577cb
8 changed files with 141 additions and 25 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/sql/SearchQueryBuilder.java
View File

@ -428,7 +428,6 @@ public class SearchQueryBuilder {
startOfQueryParameterIndex = bindOffsetParameter(bindVariables, offset, limitHandler, startOfQueryParameterIndex, bindLimitParametersFirst);
bindCountParameter(bindVariables, maxResultsToFetch, limitHandler, startOfQueryParameterIndex, bindLimitParametersFirst);
}
}
}

8
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/dao/MdmLinkDaoSvc.java
View File

@ -33,6 +33,9 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Example;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Pageable;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
@ -286,8 +289,9 @@ public class MdmLinkDaoSvc {
* @param theExampleLink The MDM link containing the data we would like to search for.
* @return a list of {@link MdmLink} entities which match the example.
*/
public List<MdmLink> findMdmLinkByExample(Example<MdmLink> theExampleLink) {
return myMdmLinkDao.findAll(theExampleLink);
public Page<MdmLink> findMdmLinkByExample(Example<MdmLink> theExampleLink, int theOffset, int theCount) {
PageRequest of = PageRequest.of(theOffset / theCount, theCount);
return myMdmLinkDao.findAll(theExampleLink, of);
}
/**

9
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmControllerSvcImpl.java
View File

@ -66,18 +66,17 @@ public class MdmControllerSvcImpl implements IMdmControllerSvc {
}
@Override
public Stream<MdmLinkJson> queryLinks(@Nullable String theGoldenResourceId, @Nullable String theSourceResourceId, @Nullable String theMatchResult, @Nullable String theLinkSource, MdmTransactionContext theMdmTransactionContext) {
public Stream<MdmLinkJson> queryLinks(@Nullable String theGoldenResourceId, @Nullable String theSourceResourceId, @Nullable String theMatchResult, @Nullable String theLinkSource, MdmTransactionContext theMdmTransactionContext, int theOffset, int theCount) {
IIdType goldenResourceId = MdmControllerUtil.extractGoldenResourceIdDtOrNull(ProviderConstants.MDM_QUERY_LINKS_GOLDEN_RESOURCE_ID, theGoldenResourceId);
IIdType sourceId = MdmControllerUtil.extractSourceIdDtOrNull(ProviderConstants.MDM_QUERY_LINKS_RESOURCE_ID, theSourceResourceId);
MdmMatchResultEnum matchResult = MdmControllerUtil.extractMatchResultOrNull(theMatchResult);
MdmLinkSourceEnum linkSource = MdmControllerUtil.extractLinkSourceOrNull(theLinkSource);
return myMdmLinkQuerySvc.queryLinks(goldenResourceId, sourceId, matchResult, linkSource, theMdmTransactionContext);
return myMdmLinkQuerySvc.queryLinks(goldenResourceId, sourceId, matchResult, linkSource, theMdmTransactionContext, theOffset, theCount);
}
@Override
public Stream<MdmLinkJson> getDuplicateGoldenResources(MdmTransactionContext theMdmTransactionContext) {
return myMdmLinkQuerySvc.getDuplicateGoldenResources(theMdmTransactionContext);
public Stream<MdmLinkJson> getDuplicateGoldenResources(MdmTransactionContext theMdmTransactionContext, int theOffset, int theCount) {
return myMdmLinkQuerySvc.getDuplicateGoldenResources(theMdmTransactionContext, theOffset, theCount);
}
@Override

12
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkQuerySvcImpl.java
View File

@ -33,6 +33,7 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Example;
import org.springframework.data.domain.Page;
import java.util.stream.Stream;
@ -46,17 +47,16 @@ public class MdmLinkQuerySvcImpl implements IMdmLinkQuerySvc {
MdmLinkDaoSvc myMdmLinkDaoSvc;
@Override
public Stream<MdmLinkJson> queryLinks(IIdType theGoldenResourceId, IIdType theSourceResourceId, MdmMatchResultEnum theMatchResult, MdmLinkSourceEnum theLinkSource, MdmTransactionContext theMdmContext) {
public Stream<MdmLinkJson> queryLinks(IIdType theGoldenResourceId, IIdType theSourceResourceId, MdmMatchResultEnum theMatchResult, MdmLinkSourceEnum theLinkSource, MdmTransactionContext theMdmContext, int theOffset, int theCount) {
Example<MdmLink> exampleLink = exampleLinkFromParameters(theGoldenResourceId, theSourceResourceId, theMatchResult, theLinkSource);
return myMdmLinkDaoSvc.findMdmLinkByExample(exampleLink).stream()
.filter(mdmLink -> mdmLink.getMatchResult() != MdmMatchResultEnum.POSSIBLE_DUPLICATE)
.map(this::toJson);
Page<MdmLink> mdmLinkByExample = myMdmLinkDaoSvc.findMdmLinkByExample(exampleLink, theOffset, theCount);
return mdmLinkByExample.stream().map(this::toJson);
}
@Override
public Stream<MdmLinkJson> getDuplicateGoldenResources(MdmTransactionContext theMdmContext) {
public Stream<MdmLinkJson> getDuplicateGoldenResources(MdmTransactionContext theMdmContext, int theOffset, int theCount) {
Example<MdmLink> exampleLink = exampleLinkFromParameters(null, null, MdmMatchResultEnum.POSSIBLE_DUPLICATE, null);
return myMdmLinkDaoSvc.findMdmLinkByExample(exampleLink).stream().map(this::toJson);
return myMdmLinkDaoSvc.findMdmLinkByExample(exampleLink, theOffset, theCount).stream().map(this::toJson);
}
private MdmLinkJson toJson(MdmLink theLink) {

91
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/provider/MdmProviderQueryLinkR4Test.java
View File

@ -1,10 +1,15 @@
package ca.uhn.fhir.jpa.mdm.provider;
import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.jpa.util.CircularQueueCaptureQueriesListener;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.StopWatch;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.dstu3.model.UnsignedIntType;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.BooleanType;
@ -16,12 +21,16 @@ import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.List;
import java.util.stream.Collectors;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.lessThanOrEqualTo;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
@ -31,6 +40,8 @@ public class MdmProviderQueryLinkR4Test extends BaseLinkR4Test {
private StringType myLinkSource;
private StringType myGoldenResource1Id;
private StringType myGoldenResource2Id;
@Autowired
protected CircularQueueCaptureQueriesListener myCaptureQueriesListener;
@Override
@BeforeEach
@ -55,7 +66,7 @@ public class MdmProviderQueryLinkR4Test extends BaseLinkR4Test {
@Test
public void testQueryLinkOneMatch() {
Parameters result = (Parameters) myMdmProvider.queryLinks(mySourcePatientId, myPatientId, null, null, myRequestDetails);
Parameters result = (Parameters) myMdmProvider.queryLinks(mySourcePatientId, myPatientId, null, null, new UnsignedIntType(0), new UnsignedIntType(10), myRequestDetails);
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(result));
List<Parameters.ParametersParameterComponent> list = result.getParameter();
assertThat(list, hasSize(1));
@ -63,6 +74,82 @@ public class MdmProviderQueryLinkR4Test extends BaseLinkR4Test {
assertMdmLink(7, part, mySourcePatientId.getValue(), myPatientId.getValue(), MdmMatchResultEnum.POSSIBLE_MATCH, "false", "true", null);
}
@Test
public void testQueryLinkPages() {
for (int i = 0; i < 10; i++) {
createPatientAndUpdateLinks(buildJanePatient());
}
int offset = 0;
int count = 2;
StopWatch sw = new StopWatch();
while (true) {
Parameters result = (Parameters) myMdmProvider.queryLinks(null, null, null, myLinkSource, new UnsignedIntType(offset), new UnsignedIntType(count), myRequestDetails);
List<Parameters.ParametersParameterComponent> parameter = result.getParameter();
String sourceResourceIds = parameter.stream().flatMap(p -> p.getPart().stream()).filter(part -> part.getName().equals("sourceResourceId")).map(part -> part.getValue().toString()).collect(Collectors.joining(","));
ourLog.warn("Search at offset {} took {}ms",offset, sw.getMillisAndRestart());
ourLog.warn("Found source resource IDs: {}", sourceResourceIds);
offset += count;
assertThat(parameter.size(), is(lessThanOrEqualTo(2)));
//We have stopped finding patients.
if (StringUtils.isEmpty(sourceResourceIds)) {
break;
}
}
}
@Test
public void testQueryWithIllegalPagingValuesFails() {
//Given
int count = 0;
int offset = 0;
try {
//When
myMdmProvider.queryLinks(
null, null,
null, myLinkSource,
new UnsignedIntType(offset),
new UnsignedIntType(count),
myRequestDetails);
} catch (InvalidRequestException e) {
//Then
assertThat(e.getMessage(), is(equalTo("_count must be greater than 0.")));
}
//Given
count = 1;
offset= -1;
try {
//When
myMdmProvider.queryLinks(
null, null,
null, myLinkSource,
new UnsignedIntType(offset),
new UnsignedIntType(count),
myRequestDetails);
} catch (InvalidRequestException e) {
//Then
assertThat(e.getMessage(), is(equalTo("_offset must be greater than or equal to 0. ")));
}
//Given
count = 0;
offset= -1;
try {
//When
myMdmProvider.queryLinks(
null, null,
null, myLinkSource,
new UnsignedIntType(offset),
new UnsignedIntType(count),
myRequestDetails);
} catch (InvalidRequestException e) {
//Then
assertThat(e.getMessage(), is(equalTo("_offset must be greater than or equal to 0. _count must be greater than 0.")));
}
}
@Test
public void testQueryLinkThreeMatches() {
// Add a third patient
@ -71,7 +158,7 @@ public class MdmProviderQueryLinkR4Test extends BaseLinkR4Test {
IAnyResource goldenResource = getGoldenResourceFromTargetResource(patient);
IIdType goldenResourceId = goldenResource.getIdElement().toVersionless();
Parameters result = (Parameters) myMdmProvider.queryLinks(null, null, null, myLinkSource, myRequestDetails);
Parameters result = (Parameters) myMdmProvider.queryLinks(null, null, null, myLinkSource, new UnsignedIntType(0), new UnsignedIntType(10), myRequestDetails);
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(result));
List<Parameters.ParametersParameterComponent> list = result.getParameter();
assertThat(list, hasSize(3));

4
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/api/IMdmControllerSvc.java
View File

@ -28,9 +28,9 @@ import java.util.stream.Stream;
public interface IMdmControllerSvc {
Stream<MdmLinkJson> queryLinks(@Nullable String theGoldenResourceId, @Nullable String theSourceResourceId, @Nullable String theMatchResult, @Nullable String theLinkSource, MdmTransactionContext theMdmTransactionContext);
Stream<MdmLinkJson> queryLinks(@Nullable String theGoldenResourceId, @Nullable String theSourceResourceId, @Nullable String theMatchResult, @Nullable String theLinkSource, MdmTransactionContext theMdmTransactionContext, int theOffset, int theCount);
Stream<MdmLinkJson> getDuplicateGoldenResources(MdmTransactionContext theMdmTransactionContext);
Stream<MdmLinkJson> getDuplicateGoldenResources(MdmTransactionContext theMdmTransactionContext, int theOffset, int theCount);
void notDuplicateGoldenResource(String theGoldenResourceId, String theTargetGoldenResourceId, MdmTransactionContext theMdmTransactionContext);

4
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/api/IMdmLinkQuerySvc.java
View File

@ -29,6 +29,6 @@ import java.util.stream.Stream;
* This service supports the MDM operation providers for those services that return multiple MDM links.
*/
public interface IMdmLinkQuerySvc {
Stream<MdmLinkJson> queryLinks(IIdType theGoldenResourceId, IIdType theSourceResourceId, MdmMatchResultEnum theMatchResult, MdmLinkSourceEnum theLinkSource, MdmTransactionContext theMdmContext);
Stream<MdmLinkJson> getDuplicateGoldenResources(MdmTransactionContext theMdmContext);
Stream<MdmLinkJson> queryLinks(IIdType theGoldenResourceId, IIdType theSourceResourceId, MdmMatchResultEnum theMatchResult, MdmLinkSourceEnum theLinkSource, MdmTransactionContext theMdmContext, int theOffset, int theCount);
Stream<MdmLinkJson> getDuplicateGoldenResources(MdmTransactionContext theMdmContext, int theOffset, int theCount);
}

37
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/provider/MdmProviderDstu3Plus.java
View File

@ -29,9 +29,11 @@ import ca.uhn.fhir.mdm.api.MatchedTarget;
import ca.uhn.fhir.mdm.api.MdmConstants;
import ca.uhn.fhir.mdm.api.MdmLinkJson;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
@ -39,6 +41,7 @@ import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.BundleBuilder;
import ca.uhn.fhir.util.ParametersUtil;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.dstu3.model.UnsignedIntType;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
@ -58,6 +61,9 @@ import java.util.List;
import java.util.UUID;
import java.util.stream.Stream;
import static ca.uhn.fhir.rest.api.Constants.PARAM_COUNT;
import static ca.uhn.fhir.rest.api.Constants.PARAM_OFFSET;
public class MdmProviderDstu3Plus extends BaseMdmProvider {
private final IMdmControllerSvc myMdmControllerSvc;
@ -189,22 +195,43 @@ public class MdmProviderDstu3Plus extends BaseMdmProvider {
public IBaseParameters queryLinks(@OperationParam(name = ProviderConstants.MDM_QUERY_LINKS_GOLDEN_RESOURCE_ID, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theGoldenResourceId,
@OperationParam(name = ProviderConstants.MDM_QUERY_LINKS_RESOURCE_ID, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theResourceId,
@OperationParam(name = ProviderConstants.MDM_QUERY_LINKS_MATCH_RESULT, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theMatchResult,
@OperationParam(name = ProviderConstants.MDM_QUERY_LINKS_LINK_SOURCE, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theLinkSource,
@OperationParam(name = ProviderConstants.MDM_QUERY_LINKS_LINK_SOURCE, min = 0, max = 1, typeName = "string")
IPrimitiveType<String> theLinkSource,
@Description(formalDefinition="Results from this method are returned across multiple pages. This parameter controls the offset when fetching a page.")
@OperationParam(name = PARAM_OFFSET)
UnsignedIntType theOffset,
@Description(formalDefinition = "Results from this method are returned across multiple pages. This parameter controls the size of those pages.")
@OperationParam(name = Constants.PARAM_COUNT)
UnsignedIntType theCount,
ServletRequestDetails theRequestDetails) {
validatePagingParameters(theOffset, theCount);
Stream<MdmLinkJson> mdmLinkJson = myMdmControllerSvc.queryLinks(extractStringOrNull(theGoldenResourceId),
extractStringOrNull(theResourceId), extractStringOrNull(theMatchResult), extractStringOrNull(theLinkSource),
createMdmContext(theRequestDetails, MdmTransactionContext.OperationType.QUERY_LINKS,
getResourceType(ProviderConstants.MDM_QUERY_LINKS_GOLDEN_RESOURCE_ID, theGoldenResourceId))
getResourceType(ProviderConstants.MDM_QUERY_LINKS_GOLDEN_RESOURCE_ID, theGoldenResourceId)), theOffset.getValue(), theCount.getValue()
);
return parametersFromMdmLinks(mdmLinkJson, true);
}
private void validatePagingParameters(UnsignedIntType theOffset, UnsignedIntType theCount) {
String errorMessage = "";
if (theOffset!= null && theOffset.getValue() < 0) {
errorMessage += PARAM_OFFSET + " must be greater than or equal to 0. ";
}
if (theCount != null && theCount.getValue() <= 0 ) {
errorMessage += PARAM_COUNT + " must be greater than 0.";
}
if (StringUtils.isNotEmpty(errorMessage)) {
throw new InvalidRequestException(errorMessage);
}
}
@Operation(name = ProviderConstants.MDM_DUPLICATE_GOLDEN_RESOURCES, idempotent = true)
public IBaseParameters getDuplicateGoldenResources(ServletRequestDetails theRequestDetails) {
Stream<MdmLinkJson> possibleDuplicates = myMdmControllerSvc.getDuplicateGoldenResources(
createMdmContext(theRequestDetails, MdmTransactionContext.OperationType.DUPLICATE_GOLDEN_RESOURCES, (String) null)
);
Stream<MdmLinkJson> possibleDuplicates = myMdmControllerSvc.getDuplicateGoldenResources(createMdmContext(theRequestDetails, MdmTransactionContext.OperationType.DUPLICATE_GOLDEN_RESOURCES, (String) null),0,10);
return parametersFromMdmLinks(possibleDuplicates, false);
}