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

Slightly more portable solution for paging

This commit is contained in:
Tadgh 2021-06-30 11:54:59 -04:00
parent a770d577cb
commit 61260dd1b1
15 changed files with 253 additions and 66 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

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

@ -27,6 +27,7 @@ import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmMatchOutcome;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.api.paging.MdmPageRequest;
import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -34,8 +35,6 @@ 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;
@ -289,9 +288,8 @@ 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 Page<MdmLink> findMdmLinkByExample(Example<MdmLink> theExampleLink, int theOffset, int theCount) {
PageRequest of = PageRequest.of(theOffset / theCount, theCount);
return myMdmLinkDao.findAll(theExampleLink, of);
public Page<MdmLink> findMdmLinkByExample(Example<MdmLink> theExampleLink, MdmPageRequest thePageRequest) {
return myMdmLinkDao.findAll(theExampleLink, thePageRequest.toPageRequest());
}
/**

11
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmControllerSvcImpl.java
View File

@ -27,6 +27,7 @@ import ca.uhn.fhir.mdm.api.IMdmLinkUpdaterSvc;
import ca.uhn.fhir.mdm.api.MdmLinkJson;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.api.paging.MdmPageRequest;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.mdm.provider.MdmControllerHelper;
import ca.uhn.fhir.mdm.provider.MdmControllerUtil;
@ -34,10 +35,10 @@ import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Page;
import org.springframework.stereotype.Service;
import javax.annotation.Nullable;
import java.util.stream.Stream;
/**
* This class acts as a layer between MdmProviders and MDM services to support a REST API that's not a FHIR Operation API.
@ -66,17 +67,17 @@ public class MdmControllerSvcImpl implements IMdmControllerSvc {
}
@Override
public Stream<MdmLinkJson> queryLinks(@Nullable String theGoldenResourceId, @Nullable String theSourceResourceId, @Nullable String theMatchResult, @Nullable String theLinkSource, MdmTransactionContext theMdmTransactionContext, int theOffset, int theCount) {
public Page<MdmLinkJson> queryLinks(@Nullable String theGoldenResourceId, @Nullable String theSourceResourceId, @Nullable String theMatchResult, @Nullable String theLinkSource, MdmTransactionContext theMdmTransactionContext, MdmPageRequest thePageRequest) {
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, theOffset, theCount);
return myMdmLinkQuerySvc.queryLinks(goldenResourceId, sourceId, matchResult, linkSource, theMdmTransactionContext, thePageRequest);
}
@Override
public Stream<MdmLinkJson> getDuplicateGoldenResources(MdmTransactionContext theMdmTransactionContext, int theOffset, int theCount) {
return myMdmLinkQuerySvc.getDuplicateGoldenResources(theMdmTransactionContext, theOffset, theCount);
public Page<MdmLinkJson> getDuplicateGoldenResources(MdmTransactionContext theMdmTransactionContext, MdmPageRequest thePageRequest) {
return myMdmLinkQuerySvc.getDuplicateGoldenResources(theMdmTransactionContext, thePageRequest);
}
@Override

16
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkQuerySvcImpl.java
View File

@ -24,6 +24,7 @@ import ca.uhn.fhir.mdm.api.MdmLinkJson;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.api.IMdmLinkQuerySvc;
import ca.uhn.fhir.mdm.api.paging.MdmPageRequest;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc;
@ -35,8 +36,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Example;
import org.springframework.data.domain.Page;
import java.util.stream.Stream;
public class MdmLinkQuerySvcImpl implements IMdmLinkQuerySvc {
private static final Logger ourLog = LoggerFactory.getLogger(MdmLinkQuerySvcImpl.class);
@ -47,16 +46,19 @@ public class MdmLinkQuerySvcImpl implements IMdmLinkQuerySvc {
MdmLinkDaoSvc myMdmLinkDaoSvc;
@Override
public Stream<MdmLinkJson> queryLinks(IIdType theGoldenResourceId, IIdType theSourceResourceId, MdmMatchResultEnum theMatchResult, MdmLinkSourceEnum theLinkSource, MdmTransactionContext theMdmContext, int theOffset, int theCount) {
public Page<MdmLinkJson> queryLinks(IIdType theGoldenResourceId, IIdType theSourceResourceId, MdmMatchResultEnum theMatchResult, MdmLinkSourceEnum theLinkSource, MdmTransactionContext theMdmContext, MdmPageRequest thePageRequest) {
Example<MdmLink> exampleLink = exampleLinkFromParameters(theGoldenResourceId, theSourceResourceId, theMatchResult, theLinkSource);
Page<MdmLink> mdmLinkByExample = myMdmLinkDaoSvc.findMdmLinkByExample(exampleLink, theOffset, theCount);
return mdmLinkByExample.stream().map(this::toJson);
Page<MdmLink> mdmLinkByExample = myMdmLinkDaoSvc.findMdmLinkByExample(exampleLink, thePageRequest);
Page<MdmLinkJson> map = mdmLinkByExample.map(this::toJson);
return map;
}
@Override
public Stream<MdmLinkJson> getDuplicateGoldenResources(MdmTransactionContext theMdmContext, int theOffset, int theCount) {
public Page<MdmLinkJson> getDuplicateGoldenResources(MdmTransactionContext theMdmContext, MdmPageRequest thePageRequest) {
Example<MdmLink> exampleLink = exampleLinkFromParameters(null, null, MdmMatchResultEnum.POSSIBLE_DUPLICATE, null);
return myMdmLinkDaoSvc.findMdmLinkByExample(exampleLink, theOffset, theCount).stream().map(this::toJson);
Page<MdmLink> mdmLinkPage = myMdmLinkDaoSvc.findMdmLinkByExample(exampleLink, thePageRequest);
Page<MdmLinkJson> map = mdmLinkPage.map(this::toJson);
return map;
}
private MdmLinkJson toJson(MdmLink theLink) {

5
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/provider/BaseProviderR4Test.java
View File

@ -7,6 +7,7 @@ import ca.uhn.fhir.mdm.api.IMdmMatchFinderSvc;
import ca.uhn.fhir.mdm.api.IMdmSubmitSvc;
import ca.uhn.fhir.mdm.provider.MdmProviderDstu3Plus;
import ca.uhn.fhir.mdm.rules.config.MdmSettings;
import ca.uhn.fhir.rest.server.IRestfulServerDefaults;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.AfterEach;
@ -29,6 +30,8 @@ public abstract class BaseProviderR4Test extends BaseMdmR4Test {
private IMdmSubmitSvc myMdmSubmitSvc;
@Autowired
private MdmSettings myMdmSettings;
@Autowired
private IRestfulServerDefaults myRestfulServerDefaults;
private String defaultScript;
@ -42,7 +45,7 @@ public abstract class BaseProviderR4Test extends BaseMdmR4Test {
@BeforeEach
public void before() {
myMdmProvider = new MdmProviderDstu3Plus(myFhirContext, myMdmControllerSvc, myMdmMatchFinderSvc, myMdmExpungeSvc, myMdmSubmitSvc);
myMdmProvider = new MdmProviderDstu3Plus(myFhirContext, myMdmControllerSvc, myMdmMatchFinderSvc, myMdmExpungeSvc, myMdmSubmitSvc, myRestfulServerDefaults);
defaultScript = myMdmSettings.getScriptText();
}
@AfterEach

2
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/provider/MdmProviderQueryLinkR4Test.java
View File

@ -90,7 +90,7 @@ public class MdmProviderQueryLinkR4Test extends BaseLinkR4Test {
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)));
assertThat(parameter.size(), is(lessThanOrEqualTo(3)));
//We have stopped finding patients.
if (StringUtils.isEmpty(sourceResourceIds)) {

5
hapi-fhir-server-mdm/pom.xml
View File

@ -27,6 +27,11 @@
<artifactId>hapi-fhir-server</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-commons</artifactId>
<version>${spring_data_version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu3</artifactId>

7
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/api/IMdmControllerSvc.java
View File

@ -20,17 +20,18 @@ package ca.uhn.fhir.mdm.api;
* #L%
*/
import ca.uhn.fhir.mdm.api.paging.MdmPageRequest;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.springframework.data.domain.Page;
import javax.annotation.Nullable;
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, int theOffset, int theCount);
Page<MdmLinkJson> queryLinks(@Nullable String theGoldenResourceId, @Nullable String theSourceResourceId, @Nullable String theMatchResult, @Nullable String theLinkSource, MdmTransactionContext theMdmTransactionContext, MdmPageRequest thePageRequest);
Stream<MdmLinkJson> getDuplicateGoldenResources(MdmTransactionContext theMdmTransactionContext, int theOffset, int theCount);
Page<MdmLinkJson> getDuplicateGoldenResources(MdmTransactionContext theMdmTransactionContext, MdmPageRequest thePageRequest);
void notDuplicateGoldenResource(String theGoldenResourceId, String theTargetGoldenResourceId, MdmTransactionContext theMdmTransactionContext);

8
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/api/IMdmLinkQuerySvc.java
View File

@ -20,15 +20,15 @@ package ca.uhn.fhir.mdm.api;
* #L%
*/
import ca.uhn.fhir.mdm.api.paging.MdmPageRequest;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import org.hl7.fhir.instance.model.api.IIdType;
import java.util.stream.Stream;
import org.springframework.data.domain.Page;
/**
* 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, int theOffset, int theCount);
Stream<MdmLinkJson> getDuplicateGoldenResources(MdmTransactionContext theMdmContext, int theOffset, int theCount);
Page<MdmLinkJson> queryLinks(IIdType theGoldenResourceId, IIdType theSourceResourceId, MdmMatchResultEnum theMatchResult, MdmLinkSourceEnum theLinkSource, MdmTransactionContext theMdmContext, MdmPageRequest thePageRequest);
Page<MdmLinkJson> getDuplicateGoldenResources(MdmTransactionContext theMdmContext, MdmPageRequest thePageRequest);
}

38
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/api/paging/MdmPageLinkBuilder.java Normal file
View File

@ -0,0 +1,38 @@
package ca.uhn.fhir.mdm.api.paging;
import ca.uhn.fhir.mdm.api.MdmLinkJson;
import ca.uhn.fhir.rest.server.RestfulServerUtils;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.ParametersUtil;
import org.springframework.data.domain.Page;
import java.util.Arrays;
import static ca.uhn.fhir.rest.api.Constants.PARAM_COUNT;
import static ca.uhn.fhir.rest.api.Constants.PARAM_OFFSET;
public final class MdmPageLinkBuilder {
public static MdmPageLinkTuple buildMdmPageLinks(ServletRequestDetails theServletRequestDetails, Page<MdmLinkJson> theCurrentPage, MdmPageRequest thePageRequest) {
MdmPageLinkTuple tuple = new MdmPageLinkTuple();
String urlWithoutPaging = RestfulServerUtils.createLinkSelfWithoutGivenParameters(theServletRequestDetails.getFhirServerBase(), theServletRequestDetails, Arrays.asList(PARAM_OFFSET, PARAM_COUNT));
tuple.setSelfLink(buildLinkWithOffsetAndCount(urlWithoutPaging, thePageRequest.getCount(), thePageRequest.getOffset()));
if (theCurrentPage.hasNext()) {
tuple.setNextLink(buildLinkWithOffsetAndCount(urlWithoutPaging,thePageRequest.getCount(), thePageRequest.getNextOffset()));
}
if (theCurrentPage.hasPrevious()) {
tuple.setPreviousLink(buildLinkWithOffsetAndCount(urlWithoutPaging,thePageRequest.getCount(), thePageRequest.getPreviousOffset()));
}
return tuple;
}
protected static String buildLinkWithOffsetAndCount(String theStartingUrl, int theCount, int theOffset) {
StringBuilder builder = new StringBuilder();
builder.append(theStartingUrl);
if (!theStartingUrl.contains("?")) {
builder.append("?");
}
builder.append(PARAM_OFFSET).append("=").append(theOffset);
builder.append(PARAM_COUNT).append("=").append(theCount);
return builder.toString();
}
}

36
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/api/paging/MdmPageLinkTuple.java Normal file
View File

@ -0,0 +1,36 @@
package ca.uhn.fhir.mdm.api.paging;
import java.util.Optional;
public class MdmPageLinkTuple {
private String myPreviousLink = null;
private String mySelfLink = null;
private String myNextLink = null;
MdmPageLinkTuple() {
}
public Optional<String> getPreviousLink() {
return Optional.ofNullable(myPreviousLink);
}
public void setPreviousLink(String thePreviousLink) {
this.myPreviousLink = thePreviousLink;
}
public String getSelfLink() {
return mySelfLink;
}
public void setSelfLink(String theSelfLink) {
this.mySelfLink = theSelfLink;
}
public Optional<String> getNextLink() {
return Optional.ofNullable(myNextLink);
}
public void setNextLink(String theNextLink) {
this.myNextLink = theNextLink;
}
}

69
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/api/paging/MdmPageRequest.java Normal file
View File

@ -0,0 +1,69 @@
package ca.uhn.fhir.mdm.api.paging;
import ca.uhn.fhir.rest.server.IRestfulServerDefaults;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.dstu3.model.UnsignedIntType;
import org.slf4j.Logger;
import org.springframework.data.domain.PageRequest;
import static ca.uhn.fhir.rest.api.Constants.PARAM_COUNT;
import static ca.uhn.fhir.rest.api.Constants.PARAM_OFFSET;
import static org.slf4j.LoggerFactory.getLogger;
public class MdmPageRequest {
private static final Logger ourLog = getLogger(MdmPageRequest.class);
private int myPage;
private int myOffset;
private int myCount;
private IRestfulServerDefaults myRestfulServerDefaults;
public MdmPageRequest(UnsignedIntType theOffset, UnsignedIntType theCount, IRestfulServerDefaults theDefaults) {
myOffset = theOffset == null ? 0 : theOffset.getValue();
myCount = theCount == null ? theDefaults.getDefaultPageSize() : theCount.getValue();
validatePagingParameters(myOffset, myCount);
this.myPage = myOffset / myCount;
}
public PageRequest toPageRequest() {
return PageRequest.of(this.myPage, this.myCount);
}
private void validatePagingParameters(int theOffset, int theCount) {
String errorMessage = "";
if (theOffset < 0) {
errorMessage += PARAM_OFFSET + " must be greater than or equal to 0. ";
}
if (theCount <= 0 ) {
errorMessage += PARAM_COUNT + " must be greater than 0.";
}
if (myRestfulServerDefaults.getMaximumPageSize() != null && theCount > myRestfulServerDefaults.getMaximumPageSize() ) {
ourLog.debug("Shrinking page size down to {}, as this is the maximum allowed.", myRestfulServerDefaults.getMaximumPageSize());
}
if (StringUtils.isNotEmpty(errorMessage)) {
throw new InvalidRequestException(errorMessage);
}
}
public int getOffset() {
return myOffset;
}
public int getPage() {
return myPage;
}
public int getCount() {
return myCount;
}
public int getNextOffset() {
return myOffset + myCount;
}
public int getPreviousOffset() {
return myOffset - myCount;
}
}

26
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/provider/BaseMdmProvider.java
View File

@ -23,17 +23,26 @@ package ca.uhn.fhir.mdm.provider;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.mdm.api.MdmLinkJson;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.api.paging.MdmPageLinkBuilder;
import ca.uhn.fhir.mdm.api.paging.MdmPageLinkTuple;
import ca.uhn.fhir.mdm.api.paging.MdmPageRequest;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.RestfulServerUtils;
import ca.uhn.fhir.rest.server.TransactionLogMessages;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.ParametersUtil;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.springframework.data.domain.Page;
import java.util.stream.Stream;
import java.util.Arrays;
import static ca.uhn.fhir.rest.api.Constants.PARAM_COUNT;
import static ca.uhn.fhir.rest.api.Constants.PARAM_OFFSET;
public abstract class BaseMdmProvider {
@ -92,9 +101,9 @@ public abstract class BaseMdmProvider {
return theString.getValue();
}
protected IBaseParameters parametersFromMdmLinks(Stream<MdmLinkJson> theMdmLinkStream, boolean includeResultAndSource) {
protected IBaseParameters parametersFromMdmLinks(Page<MdmLinkJson> theMdmLinkStream, boolean includeResultAndSource, ServletRequestDetails theServletRequestDetails, MdmPageRequest thePageRequest) {
IBaseParameters retval = ParametersUtil.newInstance(myFhirContext);
addPagingParameters(retval, theMdmLinkStream, theServletRequestDetails, thePageRequest);
theMdmLinkStream.forEach(mdmLink -> {
IBase resultPart = ParametersUtil.addParameterToParameters(myFhirContext, retval, "link");
ParametersUtil.addPartString(myFhirContext, resultPart, "goldenResourceId", mdmLink.getGoldenResourceId());
@ -111,4 +120,15 @@ public abstract class BaseMdmProvider {
return retval;
}
protected void addPagingParameters(IBaseParameters theParameters, Page<MdmLinkJson> theCurrentPage, ServletRequestDetails theServletRequestDetails, MdmPageRequest thePageRequest) {
MdmPageLinkTuple mdmPageLinkTuple = MdmPageLinkBuilder.buildMdmPageLinks(theServletRequestDetails, theCurrentPage, thePageRequest);
ParametersUtil.addParameterToParametersUri(myFhirContext, theParameters, "self", mdmPageLinkTuple.getSelfLink());
if (mdmPageLinkTuple.getNextLink().isPresent()) {
ParametersUtil.addParameterToParametersUri(myFhirContext, theParameters, "next", mdmPageLinkTuple.getNextLink().get());
}
if (mdmPageLinkTuple.getPreviousLink().isPresent()) {
ParametersUtil.addParameterToParametersUri(myFhirContext, theParameters, "prev", mdmPageLinkTuple.getPreviousLink().get());
}
}
}

58
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/provider/MdmProviderDstu3Plus.java
View File

@ -28,6 +28,7 @@ import ca.uhn.fhir.mdm.api.IMdmSubmitSvc;
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.api.paging.MdmPageRequest;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.rest.annotation.IdParam;
@ -35,6 +36,7 @@ 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.IRestfulServerDefaults;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
@ -52,6 +54,8 @@ import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.slf4j.Logger;
import org.springframework.data.domain.Page;
import javax.annotation.Nonnull;
import java.math.BigDecimal;
@ -59,17 +63,19 @@ import java.util.Comparator;
import java.util.Date;
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;
import static org.slf4j.LoggerFactory.getLogger;
public class MdmProviderDstu3Plus extends BaseMdmProvider {
private static final Logger ourLog = getLogger(MdmProviderDstu3Plus.class);
private final IMdmControllerSvc myMdmControllerSvc;
private final IMdmMatchFinderSvc myMdmMatchFinderSvc;
private final IMdmExpungeSvc myMdmExpungeSvc;
private final IMdmSubmitSvc myMdmSubmitSvc;
private final IRestfulServerDefaults myRestfulServerDefaults;
/**
* Constructor
@ -77,12 +83,13 @@ public class MdmProviderDstu3Plus extends BaseMdmProvider {
* Note that this is not a spring bean. Any necessary injections should
* happen in the constructor
*/
public MdmProviderDstu3Plus(FhirContext theFhirContext, IMdmControllerSvc theMdmControllerSvc, IMdmMatchFinderSvc theMdmMatchFinderSvc, IMdmExpungeSvc theMdmExpungeSvc, IMdmSubmitSvc theMdmSubmitSvc) {
public MdmProviderDstu3Plus(FhirContext theFhirContext, IMdmControllerSvc theMdmControllerSvc, IMdmMatchFinderSvc theMdmMatchFinderSvc, IMdmExpungeSvc theMdmExpungeSvc, IMdmSubmitSvc theMdmSubmitSvc, IRestfulServerDefaults theRestfulServerDefaults) {
super(theFhirContext);
myMdmControllerSvc = theMdmControllerSvc;
myMdmMatchFinderSvc = theMdmMatchFinderSvc;
myMdmExpungeSvc = theMdmExpungeSvc;
myMdmSubmitSvc = theMdmSubmitSvc;
myRestfulServerDefaults = theRestfulServerDefaults;
}
@Operation(name = ProviderConstants.EMPI_MATCH, typeName = "Patient")
@ -199,40 +206,38 @@ public class MdmProviderDstu3Plus extends BaseMdmProvider {
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)
@OperationParam(name = PARAM_OFFSET, min = 0, max = 1)
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)
@OperationParam(name = Constants.PARAM_COUNT, min = 0, max = 1)
UnsignedIntType theCount,
ServletRequestDetails theRequestDetails) {
validatePagingParameters(theOffset, theCount);
Stream<MdmLinkJson> mdmLinkJson = myMdmControllerSvc.queryLinks(extractStringOrNull(theGoldenResourceId),
MdmPageRequest mdmPageRequest = new MdmPageRequest(theOffset, theCount, myRestfulServerDefaults);
Page<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)), theOffset.getValue(), theCount.getValue()
);
return parametersFromMdmLinks(mdmLinkJson, true);
getResourceType(ProviderConstants.MDM_QUERY_LINKS_GOLDEN_RESOURCE_ID, theGoldenResourceId)), mdmPageRequest);
return parametersFromMdmLinks(mdmLinkJson, true, theRequestDetails, mdmPageRequest);
}
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),0,10);
return parametersFromMdmLinks(possibleDuplicates, false);
public IBaseParameters getDuplicateGoldenResources(
@Description(formalDefinition="Results from this method are returned across multiple pages. This parameter controls the offset when fetching a page.")
@OperationParam(name = PARAM_OFFSET, min = 0, max = 1)
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, min = 0, max = 1)
UnsignedIntType theCount,
ServletRequestDetails theRequestDetails) {
MdmPageRequest mdmPageRequest = new MdmPageRequest(theOffset, theCount, myRestfulServerDefaults);
Page<MdmLinkJson> possibleDuplicates = myMdmControllerSvc.getDuplicateGoldenResources(createMdmContext(theRequestDetails, MdmTransactionContext.OperationType.DUPLICATE_GOLDEN_RESOURCES, (String) null), mdmPageRequest);
return parametersFromMdmLinks(possibleDuplicates, false, theRequestDetails, mdmPageRequest);
}
@Operation(name = ProviderConstants.MDM_NOT_DUPLICATE)
@ -260,7 +265,6 @@ public class MdmProviderDstu3Plus extends BaseMdmProvider {
ServletRequestDetails theRequestDetails) {
String criteria = convertStringTypeToString(theCriteria);
String resourceType = convertStringTypeToString(theResourceType);
long submittedCount;
if (resourceType != null) {
submittedCount = myMdmSubmitSvc.submitSourceResourceTypeToMdm(resourceType, criteria);

5
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/provider/MdmProviderLoader.java
View File

@ -26,6 +26,7 @@ import ca.uhn.fhir.mdm.api.IMdmControllerSvc;
import ca.uhn.fhir.mdm.api.IMdmExpungeSvc;
import ca.uhn.fhir.mdm.api.IMdmMatchFinderSvc;
import ca.uhn.fhir.mdm.api.IMdmSubmitSvc;
import ca.uhn.fhir.rest.server.IRestfulServerDefaults;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
@ -46,6 +47,8 @@ public class MdmProviderLoader {
private IMdmExpungeSvc myMdmExpungeSvc;
@Autowired
private IMdmSubmitSvc myMdmSubmitSvc;
@Autowired
private IRestfulServerDefaults myRestfulServerDefaults;
private BaseMdmProvider myMdmProvider;
@ -54,7 +57,7 @@ public class MdmProviderLoader {
case DSTU3:
case R4:
myResourceProviderFactory.addSupplier(() -> {
myMdmProvider = new MdmProviderDstu3Plus(myFhirContext, myMdmControllerSvc, myMdmMatchFinderSvc, myMdmExpungeSvc, myMdmSubmitSvc);
myMdmProvider = new MdmProviderDstu3Plus(myFhirContext, myMdmControllerSvc, myMdmMatchFinderSvc, myMdmExpungeSvc, myMdmSubmitSvc, myRestfulServerDefaults);
return myMdmProvider;
});
break;

7
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/RestfulServerUtils.java
View File

@ -249,6 +249,10 @@ public class RestfulServerUtils {
public static String createLinkSelf(String theServerBase, RequestDetails theRequest) {
return createLinkSelfWithoutGivenParameters(theServerBase, theRequest, null);
}
public static String createLinkSelfWithoutGivenParameters(String theServerBase, RequestDetails theRequest, List<String> excludedParameterNames) {
StringBuilder b = new StringBuilder();
b.append(theServerBase);
@ -265,6 +269,7 @@ public class RestfulServerUtils {
boolean first = true;
Map<String, String[]> parameters = theRequest.getParameters();
for (String nextParamName : new TreeSet<>(parameters.keySet())) {
if (excludedParameterNames != null && !excludedParameterNames.contains(nextParamName)) {
for (String nextParamValue : parameters.get(nextParamName)) {
if (first) {
b.append('?');
@ -278,8 +283,10 @@ public class RestfulServerUtils {
}
}
}
}
return b.toString();
}
public static String createOffsetPagingLink(BundleLinks theBundleLinks, String requestPath, String tenantId, Integer theOffset, Integer theCount, Map<String, String[]> theRequestParameters) {