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Merge pull request #2487 from hapifhir/mdm-expansion-interceptor 

MDM Expansion Interceptor (poc)
This commit is contained in:
Tadgh 2021-04-09 11:23:04 -04:00 committed by GitHub
parent fa921a3cc9 82fc7b7457
commit 99e10de5fb
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GPG Key ID: 4AEE18F83AFDEB23
28 changed files with 638 additions and 24 deletions
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6
hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/Pointcut.java
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@ -1202,6 +1202,9 @@ public enum Pointcut implements IPointcut {
* pulled out of the servlet request. This parameter is identical to the RequestDetails parameter above but will
* only be populated when operating in a RestfulServer implementation. It is provided as a convenience.
* </li>
* <li>
* ca.uhn.fhir.jpa.searchparam.SearchParameterMap - Contains the details of the search being checked. This can be modified.
* </li>
* </ul>
* <p>
* Hooks should return <code>void</code>.
@ -1210,7 +1213,8 @@ public enum Pointcut implements IPointcut {
STORAGE_PRESEARCH_REGISTERED(void.class,
"ca.uhn.fhir.rest.server.util.ICachedSearchDetails",
"ca.uhn.fhir.rest.api.server.RequestDetails",
"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails"
"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails",
"ca.uhn.fhir.jpa.searchparam.SearchParameterMap"
),
/**

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java
View File

@ -205,6 +205,7 @@ public class Constants {
public static final String PARAMQUALIFIER_STRING_CONTAINS = ":contains";
public static final String PARAMQUALIFIER_STRING_EXACT = ":exact";
public static final String PARAMQUALIFIER_TOKEN_TEXT = ":text";
public static final String PARAMQUALIFIER_MDM = ":mdm";
public static final int STATUS_HTTP_200_OK = 200;
public static final int STATUS_HTTP_201_CREATED = 201;
public static final int STATUS_HTTP_204_NO_CONTENT = 204;

23
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/ReferenceParam.java
View File

@ -22,6 +22,7 @@ package ca.uhn.fhir.rest.param;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.util.CoverageIgnore;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
@ -41,6 +42,7 @@ public class ReferenceParam extends BaseParam /*implements IQueryParameterType*/
private String myBaseUrl;
private String myValue;
private String myIdPart;
private Boolean myMdmExpand;
/**
* Constructor
@ -90,8 +92,8 @@ public class ReferenceParam extends BaseParam /*implements IQueryParameterType*/
}
}
@Override
String doGetQueryParameterQualifier() {
private String defaultGetQueryParameterQualifier() {
StringBuilder b = new StringBuilder();
if (isNotBlank(myChain)) {
if (isNotBlank(getResourceType())) {
@ -106,6 +108,10 @@ public class ReferenceParam extends BaseParam /*implements IQueryParameterType*/
}
return null;
}
@Override
String doGetQueryParameterQualifier() {
return this.myMdmExpand != null ? ":mdm" : defaultGetQueryParameterQualifier();
}
@Override
String doGetValueAsQueryToken(FhirContext theContext) {
@ -121,6 +127,11 @@ public class ReferenceParam extends BaseParam /*implements IQueryParameterType*/
@Override
void doSetValueAsQueryToken(FhirContext theContext, String theParamName, String theQualifier, String theValue) {
if (Constants.PARAMQUALIFIER_MDM.equals(theQualifier)) {
myMdmExpand = true;
theQualifier = "";
}
String q = theQualifier;
if (isNotBlank(q)) {
if (q.startsWith(":")) {
@ -166,6 +177,14 @@ public class ReferenceParam extends BaseParam /*implements IQueryParameterType*/
return myBaseUrl;
}
public boolean isMdmExpand() {
return myMdmExpand != null && myMdmExpand;
}
public ReferenceParam setMdmExpand(boolean theMdmExpand) {
myMdmExpand = theMdmExpand;
return this;
}
public String getChain() {
return myChain;

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2520-support-mdm-expansion-in-search.yaml Normal file
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@ -0,0 +1,5 @@
---
type: add
issue: 2520
title: "Add support for `:mdm` search parameter qualifier on reference search parameters. Details about enabling this feature
can be found [in the documentation](/hapi-fhir/docs/server_jpa_mdm/mdm_expansion.html)."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/files.properties
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@ -67,6 +67,7 @@ page.server_jpa_mdm.mdm_rules=MDM Rules
page.server_jpa_mdm.mdm_eid=MDM Enterprise Identifiers
page.server_jpa_mdm.mdm_operations=MDM Operations
page.server_jpa_mdm.mdm_details=MDM Technical Details
page.server_jpa_mdm.mdm_expansion=MDM Search Expansion
section.server_jpa_partitioning.title=JPA Server: Partitioning and Multitenancy
page.server_jpa_partitioning.partitioning=Partitioning and Multitenancy

33
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_expansion.md Normal file
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@ -0,0 +1,33 @@
# MDM Expansion
Once you have MDM enabled, and you have many linked resources, it can be useful to search across all linked resources. Let's say you have the following MDM links in your database:
```bash
Patient/1 --> Patient/3
Patient/2 --> Patient/3
```
This indicates that both Patient/1 and Patient/2 are MDM-matched to the same golden resource (Patient/3).
What if you want to get all observations from Patient/1, but also include any observations from all of their linked resources. You could do this by first querying the [$mdm-query-links](/docs/server_jpa_mdm/mdm_operations.html) endpoint, and then making a subsequent call like the following
```http request
GET http://example.com:8000/Observation?subject=Patient/1,Patient/2,Patient/3
```
But HAPI-FHIR allows a shorthand for this, by means of a Search Parameter qualifier, as follows:
```http request
GET http://example.com:8000/Observation?subject:mdm=Patient/1
```
This `:mdm` parameter qualifier instructs an interceptor in HAPI fhir to expand the set of resources included in the search by their MDM-matched resources. The two above HTTP requests will return the same result.
<div class="helpWarningCalloutBox">
One important caveat is that chaining is currently not supported when using this prefix.
</div>
## Enabling MDM Expansion
On top of needing to instantiate an MDM module, you must enable this feature in the [DaoConfig](/hapi-fhir/apidocs/hapi-fhir-jpaserver-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html) bean, using the [Allow MDM Expansion](/hapi-fhir/apidocs/hapi-fhir-jpaserver-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setAllowMdmExpansion(boolean)) property.
<div class="helpWarningCalloutBox">
It is important to note that enabling this functionality can lead to incorrect data being returned by a request, if your MDM links are incorrect. Use with caution.
</div>

30
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java
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@ -1716,6 +1716,36 @@ public class DaoConfig {
this.myModelConfig.setAllowContainsSearches(theAllowContainsSearches);
}
/**
* If enabled, the server will support the use of :mdm search parameter qualifier on Reference Search Parameters.
* This Parameter Qualifier is HAPI-specific, and not defined anywhere in the FHIR specification. Using this qualifier
* will result in an MDM expansion being done on the reference, which will expand the search scope. For example, if Patient/1
* is MDM-matched to Patient/2 and you execute the search:
* Observation?subject:mdm=Patient/1 , you will receive observations for both Patient/1 and Patient/2.
* <p>
* Default is <code>false</code>
* </p>
* @since 5.4.0
*/
public boolean isAllowMdmExpansion() {
return myModelConfig.isAllowMdmExpansion();
}
/**
* If enabled, the server will support the use of :mdm search parameter qualifier on Reference Search Parameters.
* This Parameter Qualifier is HAPI-specific, and not defined anywhere in the FHIR specification. Using this qualifier
* will result in an MDM expansion being done on the reference, which will expand the search scope. For example, if Patient/1
* is MDM-matched to Patient/2 and you execute the search:
* Observation?subject:mdm=Patient/1 , you will receive observations for both Patient/1 and Patient/2.
* <p>
* Default is <code>false</code>
* </p>
* @since 5.4.0
*/
public void setAllowMdmExpansion(boolean theAllowMdmExpansion) {
myModelConfig.setAllowMdmExpansion(theAllowMdmExpansion);
}
/**
* This setting may be used to advise the server that any references found in
* resources that have any of the base URLs given here will be replaced with

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
View File

@ -41,6 +41,7 @@ import ca.uhn.fhir.jpa.dao.index.DaoResourceLinkResolver;
import ca.uhn.fhir.jpa.dao.index.DaoSearchParamSynchronizer;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.dao.index.SearchParamWithInlineReferencesExtractor;
import ca.uhn.fhir.jpa.dao.mdm.MdmLinkExpandSvc;
import ca.uhn.fhir.jpa.dao.predicate.PredicateBuilder;
import ca.uhn.fhir.jpa.dao.predicate.PredicateBuilderCoords;
import ca.uhn.fhir.jpa.dao.predicate.PredicateBuilderDate;
@ -60,6 +61,7 @@ import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.graphql.JpaStorageServices;
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
import ca.uhn.fhir.jpa.interceptor.JpaConsentContextServices;
import ca.uhn.fhir.jpa.interceptor.MdmSearchExpandingInterceptor;
import ca.uhn.fhir.jpa.interceptor.OverridePathBasedReferentialIntegrityForDeletesInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseTerminologyTranslationInterceptor;
import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingRuleBuilder;
@ -473,6 +475,17 @@ public abstract class BaseConfig {
return new RequestTenantPartitionInterceptor();
}
@Bean
@Lazy
public MdmSearchExpandingInterceptor mdmSearchExpandingInterceptor() {
return new MdmSearchExpandingInterceptor();
}
@Bean
public MdmLinkExpandSvc myMdmLinkExpandSvc() {
return new MdmLinkExpandSvc();
}
@Bean
@Lazy
public TerminologyUploaderProvider terminologyUploaderProvider() {

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IMdmLinkDao.java
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@ -58,4 +58,13 @@ public interface IMdmLinkDao extends JpaRepository<MdmLink, Long> {
Long getSourcePid();
}
@Query("SELECT ml.myGoldenResourcePid as goldenPid, ml.mySourcePid as sourcePid " +
"FROM MdmLink ml " +
"INNER JOIN MdmLink ml2 " +
"on ml.myGoldenResourcePid=ml2.myGoldenResourcePid " +
"WHERE ml2.mySourcePid=:sourcePid " +
"AND ml2.myMatchResult=:matchResult " +
"AND ml.myMatchResult=:matchResult")
List<MdmPidTuple> expandPidsBySourcePidAndMatchResult(@Param("sourcePid") Long theSourcePid, @Param("matchResult") MdmMatchResultEnum theMdmMatchResultEnum);
}

23
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java
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@ -380,6 +380,29 @@ public class IdHelperService {
}
}
/**
*
* Given a set of PIDs, return a set of public FHIR Resource IDs.
* This function will resolve a forced ID if it resolves, and if it fails to resolve to a forced it, will just return the pid
* Example:
* Let's say we have Patient/1(pid == 1), Patient/pat1 (pid == 2), Patient/3 (pid == 3), their pids would resolve as follows:
*
* [1,2,3] -> ["1","pat1","3"]
*
* @param thePids The Set of pids you would like to resolve to external FHIR Resource IDs.
* @return A Set of strings representing the FHIR IDs of the pids.
*/
public Set<String> translatePidsToFhirResourceIds(Set<Long> thePids) {
Map<Long, Optional<String>> pidToForcedIdMap = translatePidsToForcedIds(thePids);
//If the result of the translation is an empty optional, it means there is no forced id, and we can use the PID as the resource ID.
Set<String> resolvedResourceIds = pidToForcedIdMap.entrySet().stream()
.map(entry -> entry.getValue().isPresent() ? entry.getValue().get() : entry.getKey().toString())
.collect(Collectors.toSet());
return resolvedResourceIds;
}
public Map<Long, Optional<String>> translatePidsToForcedIds(Set<Long> thePids) {
Map<Long, Optional<String>> retVal = new HashMap<>(myMemoryCacheService.getAllPresent(MemoryCacheService.CacheEnum.FORCED_ID, thePids));

95
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/mdm/MdmLinkExpandSvc.java Normal file
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@ -0,0 +1,95 @@
package ca.uhn.fhir.jpa.dao.mdm;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 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%
*/
import ca.uhn.fhir.jpa.dao.data.IMdmLinkDao;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
@Service
public class MdmLinkExpandSvc {
private static final Logger ourLog = Logs.getMdmTroubleshootingLog();
@Autowired
private IMdmLinkDao myMdmLinkDao;
@Autowired
private IdHelperService myIdHelperService;
/**
* Given a source resource, perform MDM expansion and return all the resource IDs of all resources that are
* MDM-Matched to this resource.
*
* @param theResource The resource to MDM-Expand
* @return A set of strings representing the FHIR IDs of the expanded resources.
*/
public Set<String> expandMdmBySourceResource(IBaseResource theResource) {
ourLog.debug("About to MDM-expand source resource {}", theResource);
return expandMdmBySourceResourceId(theResource.getIdElement());
}
/**
* Given a resource ID of a source resource, perform MDM expansion and return all the resource IDs of all resources that are
* MDM-Matched to this resource.
*
* @param theId The Resource ID of the resource to MDM-Expand
* @return A set of strings representing the FHIR ids of the expanded resources.
*/
public Set<String> expandMdmBySourceResourceId(IIdType theId) {
ourLog.debug("About to expand source resource with resource id {}", theId);
Long pidOrThrowException = myIdHelperService.getPidOrThrowException(theId);
return expandMdmBySourceResourcePid(pidOrThrowException);
}
/**
* Given a PID of a source resource, perform MDM expansion and return all the resource IDs of all resources that are
* MDM-Matched to this resource.
*
* @param theSourceResourcePid The PID of the resource to MDM-Expand
* @return A set of strings representing the FHIR ids of the expanded resources.
*/
public Set<String> expandMdmBySourceResourcePid(Long theSourceResourcePid) {
ourLog.debug("About to expand source resource with PID {}", theSourceResourcePid);
List<IMdmLinkDao.MdmPidTuple> goldenPidSourcePidTuples = myMdmLinkDao.expandPidsBySourcePidAndMatchResult(theSourceResourcePid, MdmMatchResultEnum.MATCH);
Set<Long> flattenedPids = new HashSet<>();
goldenPidSourcePidTuples.forEach(tuple -> {
flattenedPids.add(tuple.getSourcePid());
flattenedPids.add(tuple.getGoldenPid());
});
Set<String> resourceIds = myIdHelperService.translatePidsToFhirResourceIds(flattenedPids);
ourLog.debug("Pid {} has been expanded to [{}]", theSourceResourcePid, String.join(",", resourceIds));
return resourceIds;
}
}

92
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/MdmSearchExpandingInterceptor.java Normal file
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@ -0,0 +1,92 @@
package ca.uhn.fhir.jpa.interceptor;
/*-
* #%L
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2021 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%
*/
import ca.uhn.fhir.interceptor.api.Hook;
import ca.uhn.fhir.interceptor.api.Interceptor;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.dao.mdm.MdmLinkExpandSvc;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.ReferenceParam;
import joptsimple.internal.Strings;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
import static org.slf4j.LoggerFactory.getLogger;
/**
* This interceptor replaces the auto-generated CapabilityStatement that is generated
* by the HAPI FHIR Server with a static hard-coded resource.
*/
@Interceptor
public class MdmSearchExpandingInterceptor {
private static final Logger ourLog = Logs.getMdmTroubleshootingLog();
@Autowired
private MdmLinkExpandSvc myMdmLinkExpandSvc;
@Autowired
private DaoConfig myDaoConfig;
@Hook(Pointcut.STORAGE_PRESEARCH_REGISTERED)
public void hook(SearchParameterMap theSearchParameterMap) {
if (myDaoConfig.isAllowMdmExpansion()) {
for (List<List<IQueryParameterType>> andList : theSearchParameterMap.values()) {
for (List<IQueryParameterType> orList : andList) {
expandAnyReferenceParameters(orList);
}
}
}
}
/**
* If a Parameter is a reference parameter, and it has been set to expand MDM, perform the expansion.
*/
private void expandAnyReferenceParameters(List<IQueryParameterType> orList) {
List<IQueryParameterType> toRemove = new ArrayList<>();
List<IQueryParameterType> toAdd = new ArrayList<>();
for (IQueryParameterType iQueryParameterType : orList) {
if (iQueryParameterType instanceof ReferenceParam) {
ReferenceParam refParam = (ReferenceParam) iQueryParameterType;
if (refParam.isMdmExpand()) {
ourLog.debug("Found a reference parameter to expand: {}", refParam.toString());
Set<String> expandedResourceIds = myMdmLinkExpandSvc.expandMdmBySourceResourceId(new IdDt(refParam.getValue()));
if (!expandedResourceIds.isEmpty()) {
ourLog.debug("Parameter has been expanded to: {}", String.join(", ", expandedResourceIds));
toRemove.add(refParam);
expandedResourceIds.stream().map(resourceId -> new ReferenceParam(refParam.getResourceType() + "/" + resourceId)).forEach(toAdd::add);
}
}
}
}
orList.removeAll(toRemove);
orList.addAll(toAdd);
}
}

39
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
View File

@ -305,8 +305,18 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
public IBundleProvider registerSearch(final IFhirResourceDao<?> theCallingDao, final SearchParameterMap theParams, String theResourceType, CacheControlDirective theCacheControlDirective, RequestDetails theRequestDetails, RequestPartitionId theRequestPartitionId) {
final String searchUuid = UUID.randomUUID().toString();
final String queryString = theParams.toNormalizedQueryString(myContext);
ourLog.debug("Registering new search {}", searchUuid);
Search search = new Search();
populateSearchEntity(theParams, theResourceType, searchUuid, queryString, search, theRequestPartitionId);
// Interceptor call: STORAGE_PRESEARCH_REGISTERED
HookParams params = new HookParams()
.add(ICachedSearchDetails.class, search)
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
.add(SearchParameterMap.class, theParams);
JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.STORAGE_PRESEARCH_REGISTERED, params);
Class<? extends IBaseResource> resourceTypeClass = myContext.getResourceDefinition(theResourceType).getImplementingClass();
final ISearchBuilder sb = mySearchBuilderFactory.newSearchBuilder(theCallingDao, theResourceType, resourceTypeClass);
sb.setFetchSize(mySyncSize);
@ -327,7 +337,6 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
cacheStatus = SearchCacheStatusEnum.NOT_TRIED;
}
final String queryString = theParams.toNormalizedQueryString(myContext);
if (cacheStatus != SearchCacheStatusEnum.NOT_TRIED) {
if (theParams.getEverythingMode() == null) {
if (myDaoConfig.getReuseCachedSearchResultsForMillis() != null) {
@ -340,7 +349,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
}
}
PersistedJpaSearchFirstPageBundleProvider retVal = submitSearch(theCallingDao, theParams, theResourceType, theRequestDetails, searchUuid, sb, queryString, theRequestPartitionId);
PersistedJpaSearchFirstPageBundleProvider retVal = submitSearch(theCallingDao, theParams, theResourceType, theRequestDetails, searchUuid, sb, queryString, theRequestPartitionId, search);
retVal.setCacheStatus(cacheStatus);
return retVal;
@ -379,23 +388,25 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
}
@NotNull
private PersistedJpaSearchFirstPageBundleProvider submitSearch(IDao theCallingDao, SearchParameterMap theParams, String theResourceType, RequestDetails theRequestDetails, String theSearchUuid, ISearchBuilder theSb, String theQueryString, RequestPartitionId theRequestPartitionId) {
private PersistedJpaSearchFirstPageBundleProvider submitSearch(IDao theCallingDao, SearchParameterMap theParams, String theResourceType, RequestDetails theRequestDetails, String theSearchUuid, ISearchBuilder theSb, String theQueryString, RequestPartitionId theRequestPartitionId, Search theSearch) {
StopWatch w = new StopWatch();
Search search = new Search();
populateSearchEntity(theParams, theResourceType, theSearchUuid, theQueryString, search, theRequestPartitionId);
// Search search = new Search();
//TODO GGG MOVE THIS POPULATE AND ALSO THE HOOK CALL HIGHER UP IN THE STACK.
// populateSearchEntity(theParams, theResourceType, theSearchUuid, theQueryString, search, theRequestPartitionId);
// Interceptor call: STORAGE_PRESEARCH_REGISTERED
HookParams params = new HookParams()
.add(ICachedSearchDetails.class, search)
.add(RequestDetails.class, theRequestDetails)
.addIfMatchesType(ServletRequestDetails.class, theRequestDetails);
JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.STORAGE_PRESEARCH_REGISTERED, params);
// Interceptor call: STORAGE_PRESEARCH_REGISTERED
// HookParams params = new HookParams()
// .add(ICachedSearchDetails.class, search)
// .add(RequestDetails.class, theRequestDetails)
// .addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
// .add(SearchParameterMap.class, theParams);
// JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.STORAGE_PRESEARCH_REGISTERED, params);
SearchTask task = new SearchTask(search, theCallingDao, theParams, theResourceType, theRequestDetails, theRequestPartitionId);
myIdToSearchTask.put(search.getUuid(), task);
SearchTask task = new SearchTask(theSearch, theCallingDao, theParams, theResourceType, theRequestDetails, theRequestPartitionId);
myIdToSearchTask.put(theSearch.getUuid(), task);
myExecutor.submit(task);
PersistedJpaSearchFirstPageBundleProvider retVal = myPersistedJpaBundleProviderFactory.newInstanceFirstPage(theRequestDetails, search, task, theSb);
PersistedJpaSearchFirstPageBundleProvider retVal = myPersistedJpaBundleProviderFactory.newInstanceFirstPage(theRequestDetails, theSearch, task, theSb);
ourLog.debug("Search initial phase completed in {}ms", w.getMillis());
return retVal;

60
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/helper/SearchParamHelper.java Normal file
View File

@ -0,0 +1,60 @@
package ca.uhn.fhir.jpa.search.helper;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@Service
public class SearchParamHelper {
@Autowired
private FhirContext myFhirContext;
public Collection<RuntimeSearchParam> getPatientSearchParamsForResourceType(String theResourceType) {
RuntimeResourceDefinition runtimeResourceDefinition = myFhirContext.getResourceDefinition(theResourceType);
Map<String, RuntimeSearchParam> searchParams = new HashMap<>();
RuntimeSearchParam patientSearchParam = runtimeResourceDefinition.getSearchParam("patient");
if (patientSearchParam != null) {
searchParams.put(patientSearchParam.getName(), patientSearchParam);
}
RuntimeSearchParam subjectSearchParam = runtimeResourceDefinition.getSearchParam("subject");
if (subjectSearchParam != null) {
searchParams.put(subjectSearchParam.getName(), subjectSearchParam);
}
List<RuntimeSearchParam> compartmentSearchParams = getPatientCompartmentRuntimeSearchParams(runtimeResourceDefinition);
compartmentSearchParams.forEach(param -> searchParams.put(param.getName(), param));
return searchParams.values();
}
/**
* Search the resource definition for a compartment named 'patient' and return its related Search Parameter.
*/
public List<RuntimeSearchParam> getPatientCompartmentRuntimeSearchParams(RuntimeResourceDefinition runtimeResourceDefinition) {
List<RuntimeSearchParam> patientSearchParam = new ArrayList<>();
List<RuntimeSearchParam> searchParams = runtimeResourceDefinition.getSearchParamsForCompartmentName("Patient");
return searchParams;
// if (searchParams == null || searchParams.size() == 0) {
// String errorMessage = String.format("Resource type [%s] is not eligible for this type of export, as it contains no Patient compartment, and no `patient` or `subject` search parameter", myResourceType);
// throw new IllegalArgumentException(errorMessage);
// } else if (searchParams.size() == 1) {
// patientSearchParam = searchParams.get(0);
// } else {
// String errorMessage = String.format("Resource type [%s] is not eligible for Group Bulk export, as we are unable to disambiguate which patient search parameter we should be searching by.", myResourceType);
// throw new IllegalArgumentException(errorMessage);
// }
// return patientSearchParam;
}
}

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
View File

@ -2054,6 +2054,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
@CoverageIgnore
@Override
public IValidationSupport.CodeValidationResult validateCode(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl) {
//TODO GGG TRY TO JUST AUTO_PASS HERE AND SEE WHAT HAPPENS.
invokeRunnableForUnitTest();
if (isNotBlank(theValueSetUrl)) {

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/JpaValidationSupportChain.java
View File

@ -74,6 +74,7 @@ public class JpaValidationSupportChain extends ValidationSupportChain {
public void postConstruct() {
addValidationSupport(myDefaultProfileValidationSupport);
addValidationSupport(myJpaValidationSupport);
//TODO MAKE SURE THAT THIS IS BEING CAL
addValidationSupport(myTerminologyService);
addValidationSupport(new SnapshotGeneratingValidationSupport(myFhirContext));
addValidationSupport(new InMemoryTerminologyServerValidationSupport(myFhirContext));

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
View File

@ -134,6 +134,7 @@ import org.hl7.fhir.r4.model.DocumentReference;
import org.hl7.fhir.r4.model.Encounter;
import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
import org.hl7.fhir.r4.model.EpisodeOfCare;
import org.hl7.fhir.r4.model.ExplanationOfBenefit;
import org.hl7.fhir.r4.model.Group;
import org.hl7.fhir.r4.model.Immunization;
import org.hl7.fhir.r4.model.ImmunizationRecommendation;
@ -387,6 +388,9 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
@Qualifier("myPatientDaoR4")
protected IFhirResourceDaoPatient<Patient> myPatientDao;
@Autowired
@Qualifier("myExplanationOfBenefitDaoR4")
protected IFhirResourceDao<ExplanationOfBenefit> myExplanationOfBenefitDao;
@Autowired
protected IResourceTableDao myResourceTableDao;
@Autowired
protected IResourceHistoryTableDao myResourceHistoryTableDao;

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchCustomSearchParamTest.java
View File

@ -38,6 +38,7 @@ import org.hl7.fhir.r4.model.DiagnosticReport;
import org.hl7.fhir.r4.model.Encounter;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
import org.hl7.fhir.r4.model.ExplanationOfBenefit;
import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.Group;
import org.hl7.fhir.r4.model.IntegerType;
@ -193,10 +194,8 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
search = myPatientDao.search(SearchParameterMap.newSynchronous("future-appointment-count", new NumberParam("lt0")));
assertEquals(0, search.size());
}
/**
* Draft search parameters should be ok even if they aren't completely valid
*/

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderCustomSearchParamR4Test.java
View File

@ -13,9 +13,11 @@ import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.gclient.DateClientParam;
import ca.uhn.fhir.rest.gclient.ReferenceClientParam;
import ca.uhn.fhir.rest.gclient.StringClientParam;
import ca.uhn.fhir.rest.gclient.TokenClientParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.BundleUtil;
import org.apache.commons.io.IOUtils;
@ -332,9 +334,9 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
List<String> foundResources = toUnqualifiedVersionlessIdValues(bundle);
assertThat(foundResources, contains(p1id.getValue()));
}
@SuppressWarnings("unused")
@Test
public void testSearchQualifiedWithCustomReferenceParam() {

6
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/config/MdmConsumerConfig.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.mdm.config;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.interceptor.MdmSearchExpandingInterceptor;
import ca.uhn.fhir.jpa.mdm.svc.MdmSurvivorshipSvcImpl;
import ca.uhn.fhir.mdm.api.IMdmControllerSvc;
import ca.uhn.fhir.mdm.api.IMdmExpungeSvc;
@ -79,6 +80,11 @@ public class MdmConsumerConfig {
return new MdmStorageInterceptor();
}
@Bean
MdmSearchExpandingInterceptor myMdmSearchExpandingInterceptorInterceptor() {
return new MdmSearchExpandingInterceptor();
}
@Bean
IMdmSurvivorshipService mdmSurvivorshipService() { return new MdmSurvivorshipSvcImpl(); }

5
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmStorageInterceptor.java
View File

@ -36,6 +36,8 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.ForbiddenOperationException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.Patient;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
@ -57,13 +59,10 @@ public class MdmStorageInterceptor implements IMdmStorageInterceptor {
private EIDHelper myEIDHelper;
@Autowired
private IMdmSettings myMdmSettings;
@Autowired
private GoldenResourceHelper myGoldenResourceHelper;
@Hook(Pointcut.STORAGE_PRESTORAGE_RESOURCE_CREATED)
public void blockManualResourceManipulationOnCreate(IBaseResource theBaseResource, RequestDetails theRequestDetails, ServletRequestDetails theServletRequestDetails) {
//If running in single EID mode, forbid multiple eids.
if (myMdmSettings.isPreventMultipleEids()) {
forbidIfHasMultipleEids(theBaseResource);

4
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmSubmitterInterceptorLoader.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.mdm.interceptor;
* #L%
*/
import ca.uhn.fhir.jpa.interceptor.MdmSearchExpandingInterceptor;
import ca.uhn.fhir.mdm.api.IMdmSettings;
import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.interceptor.api.IInterceptorService;
@ -41,6 +42,8 @@ public class MdmSubmitterInterceptorLoader {
@Autowired
private IMdmStorageInterceptor myIMdmStorageInterceptor;
@Autowired
private MdmSearchExpandingInterceptor myMdmSearchExpandingInterceptorInterceptor;
@Autowired
private IInterceptorService myInterceptorService;
@Autowired
private SubscriptionSubmitInterceptorLoader mySubscriptionSubmitInterceptorLoader;
@ -53,6 +56,7 @@ public class MdmSubmitterInterceptorLoader {
myDaoConfig.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.MESSAGE);
myInterceptorService.registerInterceptor(myIMdmStorageInterceptor);
myInterceptorService.registerInterceptor(myMdmSearchExpandingInterceptorInterceptor);
ourLog.info("MDM interceptor registered");
// We need to call SubscriptionSubmitInterceptorLoader.start() again in case there were no subscription types the first time it was called.
mySubscriptionSubmitInterceptorLoader.start();

4
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/BaseMdmR4Test.java
View File

@ -44,6 +44,7 @@ import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.ContactPoint;
import org.hl7.fhir.r4.model.DateType;
import org.hl7.fhir.r4.model.Medication;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Practitioner;
@ -96,6 +97,8 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test {
@Autowired
protected IFhirResourceDao<Practitioner> myPractitionerDao;
@Autowired
protected IFhirResourceDao<Observation> myObservationDao;
@Autowired
protected MdmResourceMatcherSvc myMdmResourceMatcherSvc;
@Autowired
protected IMdmLinkDao myMdmLinkDao;
@ -182,7 +185,6 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test {
Patient patient = (Patient) outcome.getResource();
patient.setId(outcome.getId());
return patient;
}
@Nonnull

55
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/dao/MdmLinkDaoSvcTest.java
View File

@ -1,16 +1,28 @@
package ca.uhn.fhir.jpa.mdm.dao;
import ca.uhn.fhir.jpa.dao.data.IMdmLinkDao;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.IMdmSettings;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.rules.json.MdmRulesJson;
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.jpa.util.TestUtil;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.ArrayList;
import java.util.Date;
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.in;
import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.isIn;
import static org.hamcrest.Matchers.notNullValue;
import static org.hamcrest.Matchers.nullValue;
import static org.junit.jupiter.api.Assertions.assertEquals;
@ -48,4 +60,47 @@ public class MdmLinkDaoSvcTest extends BaseMdmR4Test {
assertEquals(rules.getVersion(), newLink.getVersion());
}
@Test
public void testExpandPidsWorks() {
Patient golden = createGoldenPatient();
//Create 10 linked patients.
List<MdmLink> mdmLinks = new ArrayList<>();
for (int i = 0; i < 10; i++) {
mdmLinks.add(createPatientAndLinkTo(golden.getIdElement().getIdPartAsLong(), MdmMatchResultEnum.MATCH));
}
//Now lets connect a few as just POSSIBLE_MATCHes and ensure they aren't returned.
for (int i = 0 ; i < 5; i++) {
createPatientAndLinkTo(golden.getIdElement().getIdPartAsLong(), MdmMatchResultEnum.POSSIBLE_MATCH);
}
List<Long> expectedExpandedPids = mdmLinks.stream().map(MdmLink::getSourcePid).collect(Collectors.toList());
//SUT
List<IMdmLinkDao.MdmPidTuple> lists = myMdmLinkDao.expandPidsBySourcePidAndMatchResult(mdmLinks.get(0).getSourcePid(), MdmMatchResultEnum.MATCH);
assertThat(lists, hasSize(10));
lists.stream()
.forEach(tuple -> {
assertThat(tuple.getGoldenPid(), is(equalTo(golden.getIdElement().getIdPartAsLong())));
assertThat(tuple.getSourcePid(), is(in(expectedExpandedPids)));
});
}
private MdmLink createPatientAndLinkTo(Long thePatientPid, MdmMatchResultEnum theMdmMatchResultEnum) {
Patient patient = createPatient();
MdmLink mdmLink = myMdmLinkDaoSvc.newMdmLink();
mdmLink.setLinkSource(MdmLinkSourceEnum.MANUAL);
mdmLink.setMatchResult(theMdmMatchResultEnum);
mdmLink.setCreated(new Date());
mdmLink.setUpdated(new Date());
mdmLink.setGoldenResourcePid(thePatientPid);
mdmLink.setSourcePid(myIdHelperService.getPidOrNull(patient));
MdmLink saved= myMdmLinkDao.save(mdmLink);
return saved;
}
}

4
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmExpungeTest.java
View File

@ -16,6 +16,8 @@ import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.List;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.core.StringContains.containsString;
import static org.junit.jupiter.api.Assertions.assertEquals;
@ -49,6 +51,8 @@ public class MdmExpungeTest extends BaseMdmR4Test {
saveLink(mdmLink);
}
@Test
public void testUninterceptedDeleteRemovesMdmReference() {
assertEquals(1, myMdmLinkDao.count());

102
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmSearchExpandingInterceptorIT.java Normal file
View File

@ -0,0 +1,102 @@
package ca.uhn.fhir.jpa.mdm.interceptor;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
import ca.uhn.fhir.jpa.mdm.helper.MdmHelperConfig;
import ca.uhn.fhir.jpa.mdm.helper.MdmHelperR4;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.mdm.api.MdmConstants;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.ReferenceOrListParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Reference;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.RegisterExtension;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.annotation.DirtiesContext;
import org.springframework.test.context.ContextConfiguration;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.is;
import static org.slf4j.LoggerFactory.getLogger;
@DirtiesContext(classMode = DirtiesContext.ClassMode.AFTER_CLASS)
@ContextConfiguration(classes = {MdmHelperConfig.class})
public class MdmSearchExpandingInterceptorIT extends BaseMdmR4Test {
private static final Logger ourLog = getLogger(MdmSearchExpandingInterceptorIT.class);
@RegisterExtension
@Autowired
public MdmHelperR4 myMdmHelper;
@Autowired
private DaoConfig myDaoConfig;
@Test
public void testReferenceExpansionWorks() throws InterruptedException {
myDaoConfig.setAllowMdmExpansion(false);
MdmHelperR4.OutcomeAndLogMessageWrapper withLatch = myMdmHelper.createWithLatch(addExternalEID(buildJanePatient(), "123"));
MdmHelperR4.OutcomeAndLogMessageWrapper withLatch1 = myMdmHelper.createWithLatch(addExternalEID(buildJanePatient(), "123"));
MdmHelperR4.OutcomeAndLogMessageWrapper withLatch2 = myMdmHelper.createWithLatch(addExternalEID(buildJanePatient(), "123"));
MdmHelperR4.OutcomeAndLogMessageWrapper withLatch3 = myMdmHelper.createWithLatch(addExternalEID(buildJanePatient(), "123"));
assertLinkCount(4);
String id = withLatch.getDaoMethodOutcome().getId().getIdPart();
String id1 = withLatch1.getDaoMethodOutcome().getId().getIdPart();
String id2 = withLatch2.getDaoMethodOutcome().getId().getIdPart();
String id3 = withLatch3.getDaoMethodOutcome().getId().getIdPart();
//Create an Observation for each Patient
createObservationWithSubject(id);
createObservationWithSubject(id1);
createObservationWithSubject(id2);
createObservationWithSubject(id3);
SearchParameterMap searchParameterMap = new SearchParameterMap();
searchParameterMap.setLoadSynchronous(true);
ReferenceOrListParam referenceOrListParam = new ReferenceOrListParam();
referenceOrListParam.addOr(new ReferenceParam("Patient/" + id).setMdmExpand(true));
searchParameterMap.add(Observation.SP_SUBJECT, referenceOrListParam);
//With MDM Expansion disabled, this should return 1 result.
IBundleProvider search = myObservationDao.search(searchParameterMap);
assertThat(search.size(), is(equalTo(1)));
//Once MDM Expansion is allowed, this should now return 4 resourecs.
myDaoConfig.setAllowMdmExpansion(true);
search = myObservationDao.search(searchParameterMap);
assertThat(search.size(), is(equalTo(4)));
}
@Test
public void testReferenceExpansionQuietlyFailsOnMissingMdmMatches() {
myDaoConfig.setAllowMdmExpansion(true);
Patient patient = buildJanePatient();
patient.getMeta().addTag(MdmConstants.SYSTEM_MDM_MANAGED, MdmConstants.CODE_NO_MDM_MANAGED, "Don't MDM on me!");
DaoMethodOutcome daoMethodOutcome = myMdmHelper.doCreateResource(patient, true);
String id = daoMethodOutcome.getId().getIdPart();
createObservationWithSubject(id);
//Even though the user has NO mdm links, that should not cause a request failure.
SearchParameterMap map = new SearchParameterMap();
map.add(Observation.SP_SUBJECT, new ReferenceParam("Patient/" + id).setMdmExpand(true));
IBundleProvider search = myObservationDao.search(map);
assertThat(search.size(), is(equalTo(1)));
}
private Observation createObservationWithSubject(String thePatientId) {
Observation observation = new Observation();
observation.setSubject(new Reference("Patient/" + thePatientId));
observation.setCode(new CodeableConcept().setText("Made for Patient/" + thePatientId));
DaoMethodOutcome daoMethodOutcome = myObservationDao.create(observation);
return (Observation) daoMethodOutcome.getResource();
}
}

8
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmStorageInterceptorIT.java
View File

@ -6,10 +6,12 @@ import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
import ca.uhn.fhir.jpa.mdm.helper.MdmHelperConfig;
import ca.uhn.fhir.jpa.mdm.helper.MdmHelperR4;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.mdm.model.CanonicalEID;
import ca.uhn.fhir.mdm.rules.config.MdmSettings;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.server.TransactionLogMessages;
import ca.uhn.fhir.rest.server.exceptions.ForbiddenOperationException;
import org.hl7.fhir.instance.model.api.IAnyResource;
@ -65,6 +67,12 @@ public class MdmStorageInterceptorIT extends BaseMdmR4Test {
assertLinkCount(1);
}
@Test
public void testSearchExpandingInterceptorWorks() {
SearchParameterMap subject = new SearchParameterMap("subject", new ReferenceParam("Patient/123").setMdmExpand(true)).setLoadSynchronous(true);
myObservationDao.search(subject);
}
@Test
public void testDeleteGoldenResourceDeletesLinks() throws InterruptedException {
myMdmHelper.createWithLatch(buildPaulPatient());

31
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ModelConfig.java
View File

@ -99,6 +99,7 @@ public class ModelConfig {
private Map<String, Set<String>> myTypeToAutoVersionReferenceAtPaths = Collections.emptyMap();
private boolean myRespectVersionsForSearchIncludes;
private boolean myIndexOnContainedResources = false;
private boolean myAllowMdmExpansion = false;
/**
* Constructor
@ -159,6 +160,36 @@ public class ModelConfig {
return myAllowContainsSearches;
}
/**
* If enabled, the server will support the use of :mdm search parameter qualifier on Reference Search Parameters.
* This Parameter Qualifier is HAPI-specific, and not defined anywhere in the FHIR specification. Using this qualifier
* will result in an MDM expansion being done on the reference, which will expand the search scope. For example, if Patient/1
* is MDM-matched to Patient/2 and you execute the search:
* Observation?subject:mdm=Patient/1 , you will receive observations for both Patient/1 and Patient/2.
* <p>
* Default is <code>false</code>
* </p>
* @since 5.4.0
*/
public boolean isAllowMdmExpansion() {
return myAllowMdmExpansion;
}
/**
* If enabled, the server will support the use of :mdm search parameter qualifier on Reference Search Parameters.
* This Parameter Qualifier is HAPI-specific, and not defined anywhere in the FHIR specification. Using this qualifier
* will result in an MDM expansion being done on the reference, which will expand the search scope. For example, if Patient/1
* is MDM-matched to Patient/2 and you execute the search:
* Observation?subject:mdm=Patient/1 , you will receive observations for both Patient/1 and Patient/2.
* <p>
* Default is <code>false</code>
* </p>
* @since 5.4.0
*/
public void setAllowMdmExpansion(boolean theAllowMdmExpansion) {
myAllowMdmExpansion = theAllowMdmExpansion;
}
/**
* If enabled, the server will support the use of :contains searches,
* which are helpful but can have adverse effects on performance.