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4244 - Deprecate usages of ResourcePersitentId in jpa (#4245) 

* init rev

* id to jpa and mongo id

* 3444 - replaced methods and constructors of ResourcePersistentId with child constructors and methods

* 3444 - replaced methods and constructors of ResourcePersistentId with child constructors and methods

* fixed conflicts, pulled from master

* fixed code for passing tests successfully

* changed PersistentId to Jpa in MdmSearchInterceptor

* added the todo comments with questions

* added one more question

* renamed TODO questions

* first pass at converting to generic ResourcePersistentId

* fix test

* fix test

* fix test

* make ResourcePersistentId abstract

* Generic type MdmLink

* Final TODOs

* Final TODOs

* cleanup

* fix test

* fix id to string

* fix cyclic package dep

* add <?> to Base so we can extract interface

* Revert "add <?> to Base so we can extract interface"

This reverts commit a806f3d2bc.

* switch to interface

* javadoc

* replace base with interface

* fix test

* add generic template to mdmdao

* remove unneccessary JpaPid casts

* remove unneccessary JpaPid casts

* remove unneccessary JpaPid casts

* remove unneccessary MongoPid casts

* fix test

* fix regression

* fix compile issues arising from merging master

* fix beans

* bump version to 6.3.3-SNAPSHOT

* change logs

* review feedback

* review feedback

* fixme

Co-authored-by: Ken Stevens <ken@smilecdr.com>
This commit is contained in:
kateryna-mironova 2022-12-09 09:30:51 -05:00 committed by GitHub
parent d639a2a86d
commit 017cc4e29c
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277 changed files with 1894 additions and 2087 deletions
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2
hapi-deployable-pom/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-android/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-base/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

4
hapi-fhir-bom/pom.xml
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@ -3,14 +3,14 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-checkstyle/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath>
</parent>

2
hapi-fhir-cli/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-client-okhttp/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-client/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-converter/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-dist/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-docs/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_1_0/3379-mdm-operation-fixes.yaml
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@ -1,5 +1,5 @@
---
type: fix
issue: 3379
title: "Fixed an issue where FindCandidateByLinkSvc still uses long to store persistent ids rather than ResourcePersistentId,
title: "Fixed an issue where FindCandidateByLinkSvc still uses long to store persistent ids rather than IResourcePersistentId,
also fixed an issue where MdmLinkCreateSvc was not setting the resource type of MdmLinks properly"

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4245-replace-resourcepersitentid-with-interface.yaml Normal file
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@ -0,0 +1,5 @@
---
type: change
issue: 4244
title: "Replace usages of ResourcePersistentId with an interface IResourcePersistentId and parameterize specific
implementations of it in classes that rely on a specific implementation."

2
hapi-fhir-jacoco/pom.xml
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@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jaxrsserver-base/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpa/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

2
hapi-fhir-jpaserver-base/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

113
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/JpaBulkExportProcessor.java
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@ -37,6 +37,7 @@ import ca.uhn.fhir.jpa.dao.IResultIterator;
import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
import ca.uhn.fhir.jpa.dao.mdm.MdmExpansionCacheSvc;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@ -47,7 +48,6 @@ import ca.uhn.fhir.mdm.model.MdmPidTuple;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.HasOrListParam;
import ca.uhn.fhir.rest.param.HasParam;
import ca.uhn.fhir.rest.param.ReferenceOrListParam;
@ -72,6 +72,7 @@ import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Optional;
@ -81,7 +82,7 @@ import java.util.stream.Collectors;
import static ca.uhn.fhir.rest.api.Constants.PARAM_HAS;
import static ca.uhn.fhir.rest.api.Constants.PARAM_ID;
public class JpaBulkExportProcessor implements IBulkExportProcessor {
public class JpaBulkExportProcessor implements IBulkExportProcessor<JpaPid> {
private static final Logger ourLog = LoggerFactory.getLogger(JpaBulkExportProcessor.class);
public static final int QUERY_CHUNK_SIZE = 100;
@ -100,10 +101,10 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
private DaoRegistry myDaoRegistry;
@Autowired
protected SearchBuilderFactory mySearchBuilderFactory;
protected SearchBuilderFactory<JpaPid> mySearchBuilderFactory;
@Autowired
private IIdHelperService myIdHelperService;
private IIdHelperService<JpaPid> myIdHelperService;
@Autowired
private IMdmLinkDao myMdmLinkDao;
@ -118,12 +119,12 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
@Transactional
@Override
public Iterator<ResourcePersistentId> getResourcePidIterator(ExportPIDIteratorParameters theParams) {
public Iterator<JpaPid> getResourcePidIterator(ExportPIDIteratorParameters theParams) {
String resourceType = theParams.getResourceType();
String jobId = theParams.getJobId();
RuntimeResourceDefinition def = myContext.getResourceDefinition(resourceType);
Set<ResourcePersistentId> pids;
LinkedHashSet<JpaPid> pids;
if (theParams.getExportStyle() == BulkDataExportOptions.ExportStyle.PATIENT) {
pids = getPidsForPatientStyleExport(theParams, resourceType, jobId, def);
} else if (theParams.getExportStyle() == BulkDataExportOptions.ExportStyle.GROUP) {
@ -136,8 +137,8 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
return pids.iterator();
}
private Set<ResourcePersistentId> getPidsForPatientStyleExport(ExportPIDIteratorParameters theParams, String resourceType, String jobId, RuntimeResourceDefinition def) {
Set<ResourcePersistentId> pids = new HashSet<>();
private LinkedHashSet<JpaPid> getPidsForPatientStyleExport(ExportPIDIteratorParameters theParams, String resourceType, String jobId, RuntimeResourceDefinition def) {
LinkedHashSet<JpaPid> pids = new LinkedHashSet<>();
// Patient
if (myDaoConfig.getIndexMissingFields() == DaoConfig.IndexEnabledEnum.DISABLED) {
String errorMessage = "You attempted to start a Patient Bulk Export, but the system has `Index Missing Fields` disabled. It must be enabled for Patient Bulk Export";
@ -152,12 +153,12 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
//Ensure users did not monkey with the patient compartment search parameter.
validateSearchParametersForPatient(map, theParams);
ISearchBuilder searchBuilder = getSearchBuilderForResourceType(theParams.getResourceType());
ISearchBuilder<JpaPid> searchBuilder = getSearchBuilderForResourceType(theParams.getResourceType());
filterBySpecificPatient(theParams, resourceType, patientSearchParam, map);
SearchRuntimeDetails searchRuntime = new SearchRuntimeDetails(null, jobId);
IResultIterator resultIterator = searchBuilder.createQuery(map, searchRuntime, null, RequestPartitionId.allPartitions());
IResultIterator<JpaPid> resultIterator = searchBuilder.createQuery(map, searchRuntime, null, RequestPartitionId.allPartitions());
while (resultIterator.hasNext()) {
pids.add(resultIterator.next());
}
@ -190,15 +191,15 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
return referenceOrListParam;
}
private Set<ResourcePersistentId> getPidsForSystemStyleExport(ExportPIDIteratorParameters theParams, String theJobId, RuntimeResourceDefinition theDef) {
Set<ResourcePersistentId> pids = new HashSet<>();
private LinkedHashSet<JpaPid> getPidsForSystemStyleExport(ExportPIDIteratorParameters theParams, String theJobId, RuntimeResourceDefinition theDef) {
LinkedHashSet<JpaPid> pids = new LinkedHashSet<>();
// System
List<SearchParameterMap> maps = myBulkExportHelperSvc.createSearchParameterMapsForResourceType(theDef, theParams);
ISearchBuilder searchBuilder = getSearchBuilderForResourceType(theParams.getResourceType());
ISearchBuilder<JpaPid> searchBuilder = getSearchBuilderForResourceType(theParams.getResourceType());
for (SearchParameterMap map : maps) {
// requires a transaction
IResultIterator resultIterator = searchBuilder.createQuery(map,
IResultIterator<JpaPid> resultIterator = searchBuilder.createQuery(map,
new SearchRuntimeDetails(null, theJobId),
null,
RequestPartitionId.allPartitions());
@ -209,8 +210,8 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
return pids;
}
private Set<ResourcePersistentId> getPidsForGroupStyleExport(ExportPIDIteratorParameters theParams, String theResourceType, RuntimeResourceDefinition theDef) {
Set<ResourcePersistentId> pids;
private LinkedHashSet<JpaPid> getPidsForGroupStyleExport(ExportPIDIteratorParameters theParams, String theResourceType, RuntimeResourceDefinition theDef) {
LinkedHashSet<JpaPid> pids;
if (theResourceType.equalsIgnoreCase("Patient")) {
ourLog.info("Expanding Patients of a Group Bulk Export.");
@ -224,9 +225,9 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
return pids;
}
private Set<ResourcePersistentId> getRelatedResourceTypePids(ExportPIDIteratorParameters theParams, RuntimeResourceDefinition theDef) {
Set<ResourcePersistentId> pids = new HashSet<>();
Set<ResourcePersistentId> expandedMemberResourceIds = expandAllPatientPidsFromGroup(theParams);
private LinkedHashSet<JpaPid> getRelatedResourceTypePids(ExportPIDIteratorParameters theParams, RuntimeResourceDefinition theDef) {
LinkedHashSet<JpaPid> pids = new LinkedHashSet<>();
Set<JpaPid> expandedMemberResourceIds = expandAllPatientPidsFromGroup(theParams);
assert expandedMemberResourceIds != null && !expandedMemberResourceIds.isEmpty();
if (ourLog.isDebugEnabled()) {
ourLog.debug("{} has been expanded to members:[{}]", theParams.getGroupId(), expandedMemberResourceIds);
@ -234,17 +235,17 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
//Next, let's search for the target resources, with their correct patient references, chunked.
//The results will be jammed into myReadPids
QueryChunker<ResourcePersistentId> queryChunker = new QueryChunker<>();
QueryChunker<JpaPid> queryChunker = new QueryChunker<>();
queryChunker.chunk(expandedMemberResourceIds, QUERY_CHUNK_SIZE, (idChunk) -> {
queryResourceTypeWithReferencesToPatients(pids, idChunk, theParams, theDef);
});
return pids;
}
private Set<ResourcePersistentId> getSingletonGroupList(ExportPIDIteratorParameters theParams) {
private LinkedHashSet<JpaPid> getSingletonGroupList(ExportPIDIteratorParameters theParams) {
IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(theParams.getGroupId()), SystemRequestDetails.newSystemRequestAllPartitions());
ResourcePersistentId pidOrNull = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), group);
Set<ResourcePersistentId> pids = new HashSet<>();
JpaPid pidOrNull = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), group);
LinkedHashSet<JpaPid> pids = new LinkedHashSet<>();
pids.add(pidOrNull);
return pids;
}
@ -252,7 +253,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
/**
* Get a ISearchBuilder for the given resource type this partition is responsible for.
*/
protected ISearchBuilder getSearchBuilderForResourceType(String theResourceType) {
protected ISearchBuilder<JpaPid> getSearchBuilderForResourceType(String theResourceType) {
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(theResourceType);
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResourceType);
Class<? extends IBaseResource> typeClass = def.getImplementingClass();
@ -307,21 +308,21 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
* In case we are doing a Group Bulk Export and resourceType `Patient` is requested, we can just return the group members,
* possibly expanded by MDM, and don't have to go and fetch other resource DAOs.
*/
private Set<ResourcePersistentId> getExpandedPatientList(ExportPIDIteratorParameters theParameters) {
List<ResourcePersistentId> members = getMembersFromGroupWithFilter(theParameters);
private LinkedHashSet<JpaPid> getExpandedPatientList(ExportPIDIteratorParameters theParameters) {
List<JpaPid> members = getMembersFromGroupWithFilter(theParameters);
List<IIdType> ids = members.stream().map(member -> new IdDt("Patient/" + member)).collect(Collectors.toList());
ourLog.info("While extracting patients from a group, we found {} patients.", ids.size());
ourLog.info("Found patients: {}", ids.stream().map(id -> id.getValue()).collect(Collectors.joining(", ")));
// Are bulk exports partition aware or care about partition at all? This does
List<ResourcePersistentId> pidsOrThrowException = members;
Set<ResourcePersistentId> patientPidsToExport = new HashSet<>(pidsOrThrowException);
List<JpaPid> pidsOrThrowException = members;
LinkedHashSet<JpaPid> patientPidsToExport = new LinkedHashSet<>(pidsOrThrowException);
if (theParameters.isExpandMdm()) {
SystemRequestDetails srd = SystemRequestDetails.newSystemRequestAllPartitions();
IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(theParameters.getGroupId()), srd);
ResourcePersistentId pidOrNull = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), group);
List<MdmPidTuple> goldenPidSourcePidTuple = myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult(pidOrNull, MdmMatchResultEnum.MATCH);
JpaPid pidOrNull = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), group);
List<MdmPidTuple<JpaPid>> goldenPidSourcePidTuple = myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult(pidOrNull, MdmMatchResultEnum.MATCH);
goldenPidSourcePidTuple.forEach(tuple -> {
patientPidsToExport.add(tuple.getGoldenPid());
patientPidsToExport.add(tuple.getSourcePid());
@ -336,19 +337,19 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
*
* @return A list of strings representing the Patient IDs of the members (e.g. ["P1", "P2", "P3"]
*/
private List<ResourcePersistentId> getMembersFromGroupWithFilter(ExportPIDIteratorParameters theParameters) {
private List<JpaPid> getMembersFromGroupWithFilter(ExportPIDIteratorParameters theParameters) {
RuntimeResourceDefinition def = myContext.getResourceDefinition("Patient");
List<String> pids = new ArrayList<>();
List<ResourcePersistentId> resPids = new ArrayList<>();
List<JpaPid> resPids = new ArrayList<>();
List<SearchParameterMap> maps = myBulkExportHelperSvc.createSearchParameterMapsForResourceType(def, theParameters);
maps.forEach(map -> addMembershipToGroupClause(map, theParameters.getGroupId()));
for (SearchParameterMap map : maps) {
ISearchBuilder searchBuilder = getSearchBuilderForResourceType("Patient");
ISearchBuilder<JpaPid> searchBuilder = getSearchBuilderForResourceType("Patient");
ourLog.debug("Searching for members of group {} with job id {} with map {}", theParameters.getGroupId(), theParameters.getJobId(), map);
IResultIterator resultIterator = searchBuilder.createQuery(map,
IResultIterator<JpaPid> resultIterator = searchBuilder.createQuery(map,
new SearchRuntimeDetails(null, theParameters.getJobId()),
null,
RequestPartitionId.allPartitions());
@ -376,7 +377,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
/**
* @param thePidTuples
*/
private void populateMdmResourceCache(List<MdmPidTuple> thePidTuples) {
private void populateMdmResourceCache(List<MdmPidTuple<JpaPid>> thePidTuples) {
if (myMdmExpansionCacheSvc.hasBeenPopulated()) {
return;
}
@ -385,7 +386,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
// patient/gold-1 -> [patient/1, patient/2]
// patient/gold-2 -> [patient/3, patient/4]
//}
Map<ResourcePersistentId, Set<ResourcePersistentId>> goldenResourceToSourcePidMap = new HashMap<>();
Map<JpaPid, Set<JpaPid>> goldenResourceToSourcePidMap = new HashMap<>();
extract(thePidTuples, goldenResourceToSourcePidMap);
//Next, lets convert it to an inverted index for fast lookup
@ -410,21 +411,21 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
myMdmExpansionCacheSvc.setCacheContents(sourceResourceIdToGoldenResourceIdMap);
}
private void extract(List<MdmPidTuple> theGoldenPidTargetPidTuples, Map<ResourcePersistentId, Set<ResourcePersistentId>> theGoldenResourceToSourcePidMap) {
for (MdmPidTuple goldenPidTargetPidTuple : theGoldenPidTargetPidTuples) {
ResourcePersistentId goldenPid = goldenPidTargetPidTuple.getGoldenPid();
ResourcePersistentId sourcePid = goldenPidTargetPidTuple.getSourcePid();
private void extract(List<MdmPidTuple<JpaPid>> theGoldenPidTargetPidTuples, Map<JpaPid, Set<JpaPid>> theGoldenResourceToSourcePidMap) {
for (MdmPidTuple<JpaPid> goldenPidTargetPidTuple : theGoldenPidTargetPidTuples) {
JpaPid goldenPid = goldenPidTargetPidTuple.getGoldenPid();
JpaPid sourcePid = goldenPidTargetPidTuple.getSourcePid();
theGoldenResourceToSourcePidMap.computeIfAbsent(goldenPid, key -> new HashSet<>()).add(sourcePid);
}
}
private void queryResourceTypeWithReferencesToPatients(Set<ResourcePersistentId> myReadPids,
List<ResourcePersistentId> resourcePersistentIdChunk,
private void queryResourceTypeWithReferencesToPatients(Set<JpaPid> theReadPids,
List<JpaPid> JpaPidChunk,
ExportPIDIteratorParameters theParams,
RuntimeResourceDefinition theDef) {
//Convert Resource Persistent IDs to actual client IDs.
Set<ResourcePersistentId> pidSet = new HashSet<>(resourcePersistentIdChunk);
Set<JpaPid> pidSet = new HashSet<>(JpaPidChunk);
Set<String> resourceIds = myIdHelperService.translatePidsToFhirResourceIds(pidSet);
//Build SP map
@ -436,7 +437,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
validateSearchParametersForGroup(expandedSpMap, theParams.getResourceType());
// Fetch and cache a search builder for this resource type
ISearchBuilder searchBuilder = getSearchBuilderForResourceType(theParams.getResourceType());
ISearchBuilder<JpaPid> searchBuilder = getSearchBuilderForResourceType(theParams.getResourceType());
// Now, further filter the query with patient references defined by the chunk of IDs we have.
if (PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES.contains(theParams.getResourceType())) {
@ -446,20 +447,20 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
}
//Execute query and all found pids to our local iterator.
IResultIterator resultIterator = searchBuilder.createQuery(expandedSpMap,
IResultIterator<JpaPid> resultIterator = searchBuilder.createQuery(expandedSpMap,
new SearchRuntimeDetails(null, theParams.getJobId()),
null,
RequestPartitionId.allPartitions());
while (resultIterator.hasNext()) {
myReadPids.add(resultIterator.next());
theReadPids.add(resultIterator.next());
}
// add _include to results to support ONC
Set<Include> includes = Collections.singleton(new Include("*", true));
SystemRequestDetails requestDetails = SystemRequestDetails.newSystemRequestAllPartitions();
Set<ResourcePersistentId> includeIds = searchBuilder.loadIncludes(myContext, myEntityManager, myReadPids, includes, false, expandedSpMap.getLastUpdated(), theParams.getJobId(), requestDetails, null);
Set<JpaPid> includeIds = searchBuilder.loadIncludes(myContext, myEntityManager, theReadPids, includes, false, expandedSpMap.getLastUpdated(), theParams.getJobId(), requestDetails, null);
// gets rid of the Patient duplicates
myReadPids.addAll(includeIds.stream().filter((id) -> !id.getResourceType().equals("Patient")).collect(Collectors.toSet()));
theReadPids.addAll(includeIds.stream().filter((id) -> !id.getResourceType().equals("Patient")).collect(Collectors.toSet()));
}
}
@ -504,11 +505,11 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
*
* @return a Set of Strings representing the resource IDs of all members of a group.
*/
private Set<ResourcePersistentId> expandAllPatientPidsFromGroup(ExportPIDIteratorParameters theParams) {
Set<ResourcePersistentId> expandedIds = new HashSet<>();
private Set<JpaPid> expandAllPatientPidsFromGroup(ExportPIDIteratorParameters theParams) {
Set<JpaPid> expandedIds = new HashSet<>();
SystemRequestDetails requestDetails = SystemRequestDetails.newSystemRequestAllPartitions();
IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(theParams.getGroupId()), requestDetails);
ResourcePersistentId pidOrNull = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), group);
JpaPid pidOrNull = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), group);
//Attempt to perform MDM Expansion of membership
if (theParams.isExpandMdm()) {
@ -517,24 +518,24 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor {
//Now manually add the members of the group (its possible even with mdm expansion that some members dont have MDM matches,
//so would be otherwise skipped
List<ResourcePersistentId> membersFromGroupWithFilter = getMembersFromGroupWithFilter(theParams);
List<JpaPid> membersFromGroupWithFilter = getMembersFromGroupWithFilter(theParams);
ourLog.debug("Group with ID [{}] has been expanded to: {}", theParams.getGroupId(), membersFromGroupWithFilter);
expandedIds.addAll(membersFromGroupWithFilter);
return expandedIds;
}
private Set<ResourcePersistentId> performMembershipExpansionViaMdmTable(ResourcePersistentId pidOrNull) {
List<MdmPidTuple> goldenPidTargetPidTuples = myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult(pidOrNull, MdmMatchResultEnum.MATCH);
private Set<JpaPid> performMembershipExpansionViaMdmTable(JpaPid pidOrNull) {
List<MdmPidTuple<JpaPid>> goldenPidTargetPidTuples = myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult(pidOrNull, MdmMatchResultEnum.MATCH);
//Now lets translate these pids into resource IDs
Set<ResourcePersistentId> uniquePids = new HashSet<>();
Set<JpaPid> uniquePids = new HashSet<>();
goldenPidTargetPidTuples.forEach(tuple -> {
uniquePids.add(tuple.getGoldenPid());
uniquePids.add(tuple.getSourcePid());
});
PersistentIdToForcedIdMap pidToForcedIdMap = myIdHelperService.translatePidsToForcedIds(uniquePids);
Map<ResourcePersistentId, Set<ResourcePersistentId>> goldenResourceToSourcePidMap = new HashMap<>();
Map<JpaPid, Set<JpaPid>> goldenResourceToSourcePidMap = new HashMap<>();
extract(goldenPidTargetPidTuples, goldenResourceToSourcePidMap);
populateMdmResourceCache(goldenPidTargetPidTuples);

19
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/cache/ResourceVersionSvcDaoImpl.java vendored
View File

@ -25,12 +25,11 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.util.QueryChunker;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.hl7.fhir.instance.model.api.IIdType;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
@ -60,7 +59,7 @@ public class ResourceVersionSvcDaoImpl implements IResourceVersionSvc {
@Autowired
IResourceTableDao myResourceTableDao;
@Autowired
IIdHelperService myIdHelperService;
IIdHelperService<JpaPid> myIdHelperService;
@Override
@Nonnull
@ -72,8 +71,9 @@ public class ResourceVersionSvcDaoImpl implements IResourceVersionSvc {
ourLog.debug("About to retrieve version map for resource type: {}", theResourceName);
}
List<Long> matchingIds = dao.searchForIds(theSearchParamMap, new SystemRequestDetails().setRequestPartitionId(theRequestPartitionId)).stream()
.map(ResourcePersistentId::getIdAsLong)
List<JpaPid> jpaPids = dao.searchForIds(theSearchParamMap, new SystemRequestDetails().setRequestPartitionId(theRequestPartitionId));
List<Long> matchingIds = jpaPids.stream()
.map(JpaPid::getId)
.collect(Collectors.toList());
List<ResourceTable> allById = new ArrayList<>();
@ -137,16 +137,15 @@ public class ResourceVersionSvcDaoImpl implements IResourceVersionSvc {
return retval;
}
List<ResourcePersistentId> resourcePersistentIds = myIdHelperService.resolveResourcePersistentIdsWithCache(thePartitionId,
theIds.stream().collect(Collectors.toList()));
List<JpaPid> jpaPids = myIdHelperService.resolveResourcePersistentIdsWithCache(thePartitionId, new ArrayList<>(theIds));
// we'll use this map to fetch pids that require versions
HashMap<Long, ResourcePersistentId> pidsToVersionToResourcePid = new HashMap<>();
HashMap<Long, JpaPid> pidsToVersionToResourcePid = new HashMap<>();
// fill in our map
for (ResourcePersistentId pid : resourcePersistentIds) {
for (JpaPid pid : jpaPids) {
if (pid.getVersion() == null) {
pidsToVersionToResourcePid.put(pid.getIdAsLong(), pid);
pidsToVersionToResourcePid.put(pid.getId(), pid);
}
Optional<IIdType> idOp = theIds.stream()
.filter(i -> i.getIdPart().equals(pid.getAssociatedResourceId().getIdPart()))

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/Batch2SupportConfig.java
View File

@ -27,7 +27,6 @@ import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.data.IResourceLinkDao;
import ca.uhn.fhir.jpa.dao.expunge.ResourceTableFKProvider;
import ca.uhn.fhir.jpa.dao.index.IJpaIdHelperService;
import ca.uhn.fhir.jpa.delete.batch2.DeleteExpungeSqlBuilder;
import ca.uhn.fhir.jpa.delete.batch2.DeleteExpungeSvcImpl;
import ca.uhn.fhir.jpa.reindex.Batch2DaoSvcImpl;

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HapiJpaConfig.java
View File

@ -26,7 +26,6 @@ import ca.uhn.fhir.jpa.config.util.ResourceCountCacheUtil;
import ca.uhn.fhir.jpa.config.util.ValidationSupportConfigUtil;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.mdm.MdmLinkDaoJpaImpl;
import ca.uhn.fhir.jpa.dao.search.HSearchSortHelperImpl;
import ca.uhn.fhir.jpa.dao.search.IHSearchSortHelper;
import ca.uhn.fhir.jpa.provider.DaoRegistryResourceSupportedSvc;
@ -35,7 +34,6 @@ import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChain;
import ca.uhn.fhir.mdm.dao.IMdmLinkDao;
import ca.uhn.fhir.rest.api.IResourceSupportedSvc;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
@ -87,9 +85,4 @@ public class HapiJpaConfig {
public ResourceCountCache resourceCountsCache(IFhirSystemDao<?, ?> theSystemDao) {
return ResourceCountCacheUtil.newResourceCountCache(theSystemDao);
}
@Bean
public static IMdmLinkDao mdmLinkDao(){
return new MdmLinkDaoJpaImpl();
}
}

22
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/JpaConfig.java
View File

@ -37,22 +37,26 @@ import ca.uhn.fhir.jpa.dao.expunge.ExpungeOperation;
import ca.uhn.fhir.jpa.dao.expunge.ExpungeService;
import ca.uhn.fhir.jpa.dao.expunge.IExpungeEverythingService;
import ca.uhn.fhir.jpa.dao.expunge.IResourceExpungeService;
import ca.uhn.fhir.jpa.dao.expunge.ResourceExpungeService;
import ca.uhn.fhir.jpa.dao.expunge.JpaResourceExpungeService;
import ca.uhn.fhir.jpa.dao.expunge.ResourceTableFKProvider;
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.JpaMdmLinkImplFactory;
import ca.uhn.fhir.jpa.dao.mdm.MdmLinkDaoJpaImpl;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.jpa.delete.DeleteConflictFinderService;
import ca.uhn.fhir.jpa.delete.DeleteConflictService;
import ca.uhn.fhir.jpa.delete.ThreadSafeResourceDeleterSvc;
import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.graphql.DaoRegistryGraphQLStorageServices;
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
import ca.uhn.fhir.jpa.interceptor.JpaConsentContextServices;
import ca.uhn.fhir.jpa.interceptor.OverridePathBasedReferentialIntegrityForDeletesInterceptor;
import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingRuleBuilder;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
import ca.uhn.fhir.jpa.packages.IHapiPackageCacheManager;
import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc;
@ -131,10 +135,12 @@ import ca.uhn.fhir.jpa.term.config.TermCodeSystemConfig;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.jpa.validation.ResourceLoaderImpl;
import ca.uhn.fhir.jpa.validation.ValidationSettings;
import ca.uhn.fhir.mdm.dao.IMdmLinkDao;
import ca.uhn.fhir.mdm.dao.IMdmLinkImplFactory;
import ca.uhn.fhir.mdm.svc.MdmLinkExpandSvc;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.IDeleteExpungeJobSubmitter;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.server.interceptor.ResponseTerminologyTranslationInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseTerminologyTranslationSvc;
import ca.uhn.fhir.rest.server.interceptor.consent.IConsentContextServices;
@ -299,7 +305,7 @@ public class JpaConfig {
@Bean
@Primary
public IResourceLinkResolver daoResourceLinkResolver() {
return new DaoResourceLinkResolver();
return new DaoResourceLinkResolver<JpaPid>();
}
@Bean
@ -679,7 +685,7 @@ public class JpaConfig {
@Bean
@Scope("prototype")
public ExpungeOperation expungeOperation(String theResourceName, ResourcePersistentId theResourceId, ExpungeOptions theExpungeOptions, RequestDetails theRequestDetails) {
public ExpungeOperation expungeOperation(String theResourceName, IResourcePersistentId theResourceId, ExpungeOptions theExpungeOptions, RequestDetails theRequestDetails) {
return new ExpungeOperation(theResourceName, theResourceId, theExpungeOptions, theRequestDetails);
}
@ -690,7 +696,7 @@ public class JpaConfig {
@Bean
public IResourceExpungeService resourceExpungeService() {
return new ResourceExpungeService();
return new JpaResourceExpungeService();
}
@Bean
@ -791,5 +797,11 @@ public class JpaConfig {
return new ObservationLastNIndexPersistSvc();
}
@Bean
public IMdmLinkDao<JpaPid, MdmLink> mdmLinkDao(){
return new MdmLinkDaoJpaImpl();
}
@Bean
IMdmLinkImplFactory<MdmLink> mdmLinkImplFactory() {return new JpaMdmLinkImplFactory();}
}

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

@ -27,7 +27,6 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IDao;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
import ca.uhn.fhir.jpa.dao.data.IResourceSearchViewDao;
@ -47,7 +46,6 @@ import ca.uhn.fhir.jpa.search.builder.tasks.SearchTask;
import ca.uhn.fhir.jpa.search.builder.tasks.SearchTaskParameters;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
import ca.uhn.fhir.jpa.search.lastn.IElasticsearchSvc;
import ca.uhn.fhir.rest.server.IPagingProvider;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -164,8 +162,7 @@ public class SearchConfig {
return new SearchTask(theParams,
myManagedTxManager,
myContext,
mySearchStrategyFactory,
myInterceptorBroadcaster,
myInterceptorBroadcaster,
mySearchBuilderFactory,
mySearchResultCacheSvc,
myDaoConfig,
@ -181,7 +178,6 @@ public class SearchConfig {
return new SearchContinuationTask(theParams,
myManagedTxManager,
myContext,
mySearchStrategyFactory,
myInterceptorBroadcaster,
mySearchBuilderFactory,
mySearchResultCacheSvc,

26
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -30,13 +30,12 @@ import ca.uhn.fhir.jpa.dao.index.SearchParamWithInlineReferencesExtractor;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.jpa.delete.DeleteConflictService;
import ca.uhn.fhir.jpa.entity.PartitionEntity;
import ca.uhn.fhir.jpa.entity.ResourceSearchView;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
import ca.uhn.fhir.jpa.model.entity.BaseTag;
import ca.uhn.fhir.jpa.model.entity.IBaseResourceEntity;
import ca.uhn.fhir.jpa.model.entity.PartitionablePartitionId;
import ca.uhn.fhir.jpa.model.entity.ResourceEncodingEnum;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryProvenanceEntity;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
@ -60,21 +59,16 @@ import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.jpa.util.QueryChunker;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.api.StorageResponseCodeEnum;
import ca.uhn.fhir.model.api.Tag;
import ca.uhn.fhir.model.api.TagList;
import ca.uhn.fhir.model.base.composite.BaseCodingDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.parser.LenientErrorHandler;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -86,7 +80,6 @@ import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.HapiExtensions;
import ca.uhn.fhir.util.MetaUtil;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.UrlUtil;
import ca.uhn.fhir.util.XmlUtil;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Charsets;
@ -108,7 +101,6 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IDomainResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.BeansException;
@ -205,11 +197,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
protected EntityManager myEntityManager;
@Autowired
protected IIdHelperService myIdHelperService;
protected IIdHelperService<JpaPid> myIdHelperService;
@Autowired
protected IForcedIdDao myForcedIdDao;
@Autowired
protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
protected ISearchCoordinatorSvc<JpaPid> mySearchCoordinatorSvc;
@Autowired
protected ITermReadSvc myTerminologySvc;
@Autowired
@ -1110,7 +1102,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
*/
if (thePerformIndexing) {
if (newParams == null) {
myExpungeService.deleteAllSearchParams(new ResourcePersistentId(entity.getId()));
myExpungeService.deleteAllSearchParams(JpaPid.fromId(entity.getId()));
} else {
// Synchronize search param indexes
@ -1425,16 +1417,14 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
doCallHooks(theTransactionDetails, theRequestDetails, interceptorPointcut, hookParams);
}
protected void addPidToResource(IBasePersistedResource theEntity, IBaseResource theResource) {
protected void addPidToResource(IResourceLookup<JpaPid> theEntity, IBaseResource theResource) {
if (theResource instanceof IAnyResource) {
IDao.RESOURCE_PID.put((IAnyResource) theResource, theEntity.getPersistentId().getIdAsLong());
IDao.RESOURCE_PID.put((IAnyResource) theResource, theEntity.getPersistentId().getId());
} else if (theResource instanceof IResource) {
IDao.RESOURCE_PID.put((IResource) theResource, theEntity.getPersistentId().getIdAsLong());
IDao.RESOURCE_PID.put((IResource) theResource, theEntity.getPersistentId().getId());
}
}
private void validateChildReferenceTargetTypes(IBase theElement, String thePath) {
if (theElement == null) {
return;

93
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
View File

@ -46,6 +46,7 @@ import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.jpa.delete.DeleteConflictUtil;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
import ca.uhn.fhir.jpa.model.entity.BaseTag;
import ca.uhn.fhir.jpa.model.entity.ForcedId;
@ -84,7 +85,7 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.SimplePreResourceAccessDetails;
import ca.uhn.fhir.rest.api.server.SimplePreResourceShowDetails;
import ca.uhn.fhir.rest.api.server.storage.IDeleteExpungeJobSubmitter;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.param.HasParam;
import ca.uhn.fhir.rest.param.HistorySearchDateRangeParam;
@ -163,9 +164,9 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
@Autowired
protected HapiTransactionService myTransactionService;
@Autowired
private MatchResourceUrlService myMatchResourceUrlService;
private MatchResourceUrlService<JpaPid> myMatchResourceUrlService;
@Autowired
private SearchBuilderFactory mySearchBuilderFactory;
private SearchBuilderFactory<JpaPid> mySearchBuilderFactory;
@Autowired
private DaoRegistry myDaoRegistry;
@Autowired
@ -288,12 +289,12 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
entity.setVersion(1);
if (isNotBlank(theMatchUrl) && theProcessMatchUrl) {
Set<ResourcePersistentId> match = myMatchResourceUrlService.processMatchUrl(theMatchUrl, myResourceType, theTransactionDetails, theRequest);
Set<JpaPid> match = myMatchResourceUrlService.processMatchUrl(theMatchUrl, myResourceType, theTransactionDetails, theRequest);
if (match.size() > 1) {
String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "transactionOperationWithMultipleMatchFailure", "CREATE", theMatchUrl, match.size());
throw new PreconditionFailedException(Msg.code(958) + msg);
} else if (match.size() == 1) {
ResourcePersistentId pid = match.iterator().next();
JpaPid pid = match.iterator().next();
Supplier<LazyDaoMethodOutcome.EntityAndResource> entitySupplier = () -> {
return myTxTemplate.execute(tx -> {
@ -308,12 +309,12 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
return myTxTemplate.execute(tx -> {
IIdType retVal = myIdHelperService.translatePidIdToForcedId(myFhirContext, myResourceName, pid);
if (!retVal.hasVersionIdPart()) {
IIdType idWithVersion = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.RESOURCE_CONDITIONAL_CREATE_VERSION, pid.getIdAsLong());
IIdType idWithVersion = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.RESOURCE_CONDITIONAL_CREATE_VERSION, pid.getId());
if (idWithVersion == null) {
Long version = myResourceTableDao.findCurrentVersionByPid(pid.getIdAsLong());
Long version = myResourceTableDao.findCurrentVersionByPid(pid.getId());
if (version != null) {
retVal = myFhirContext.getVersion().newIdType().setParts(retVal.getBaseUrl(), retVal.getResourceType(), retVal.getIdPart(), Long.toString(version));
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.RESOURCE_CONDITIONAL_CREATE_VERSION, pid.getIdAsLong(), retVal);
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.RESOURCE_CONDITIONAL_CREATE_VERSION, pid.getId(), retVal);
}
} else {
retVal = idWithVersion;
@ -364,7 +365,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
ResourceTable updatedEntity = updateEntity(theRequest, theResource, entity, null, thePerformIndexing, false, theTransactionDetails, false, thePerformIndexing);
// Store the resource forced ID if necessary
ResourcePersistentId persistentId = new ResourcePersistentId(updatedEntity.getResourceId());
JpaPid jpaPid = JpaPid.fromId(updatedEntity.getResourceId());
if (resourceHadIdBeforeStorage) {
if (resourceIdWasServerAssigned) {
boolean createForPureNumericIds = true;
@ -393,13 +394,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
theResource.setId(entity.getIdDt());
// Pre-cache the resource ID
persistentId.setAssociatedResourceId(entity.getIdType(myFhirContext));
myIdHelperService.addResolvedPidToForcedId(persistentId, theRequestPartitionId, getResourceName(), entity.getTransientForcedId(), null);
theTransactionDetails.addResolvedResourceId(persistentId.getAssociatedResourceId(), persistentId);
jpaPid.setAssociatedResourceId(entity.getIdType(myFhirContext));
myIdHelperService.addResolvedPidToForcedId(jpaPid, theRequestPartitionId, getResourceName(), entity.getTransientForcedId(), null);
theTransactionDetails.addResolvedResourceId(jpaPid.getAssociatedResourceId(), jpaPid);
// Pre-cache the match URL
if (theMatchUrl != null) {
myMatchResourceUrlService.matchUrlResolved(theTransactionDetails, getResourceName(), theMatchUrl, persistentId);
myMatchResourceUrlService.matchUrlResolved(theTransactionDetails, getResourceName(), theMatchUrl, jpaPid);
}
// Update the version/last updated in the resource so that interceptors get
@ -556,7 +557,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
DaoMethodOutcome outcome = createMethodOutcomeForResourceId(entity.getIdDt().getValue(), MESSAGE_KEY_DELETE_RESOURCE_ALREADY_DELETED, StorageResponseCodeEnum.SUCCESSFUL_DELETE_ALREADY_DELETED);
// used to exist, so we'll set the persistent id
outcome.setPersistentId(new ResourcePersistentId(entity.getResourceId()));
outcome.setPersistentId(JpaPid.fromId(entity.getResourceId()));
outcome.setEntity(entity);
return outcome;
@ -639,7 +640,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
SearchParameterMap paramMap = resourceSearch.getSearchParameterMap();
paramMap.setLoadSynchronous(true);
Set<ResourcePersistentId> resourceIds = myMatchResourceUrlService.search(paramMap, myResourceType, theRequest, null);
Set<JpaPid> resourceIds = myMatchResourceUrlService.search(paramMap, myResourceType, theRequest, null);
if (resourceIds.size() > 1) {
if (!getConfig().isAllowMultipleDelete()) {
@ -670,12 +671,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
@Nonnull
@Override
public DeleteMethodOutcome deletePidList(String theUrl, Collection<ResourcePersistentId> theResourceIds, DeleteConflictList theDeleteConflicts, RequestDetails theRequest) {
public <P extends IResourcePersistentId> DeleteMethodOutcome deletePidList(String theUrl, Collection<P> theResourceIds, DeleteConflictList theDeleteConflicts, RequestDetails theRequest) {
StopWatch w = new StopWatch();
TransactionDetails transactionDetails = new TransactionDetails();
List<ResourceTable> deletedResources = new ArrayList<>();
for (ResourcePersistentId pid : theResourceIds) {
ResourceTable entity = myEntityManager.find(ResourceTable.class, pid.getIdAsLong());
for (P pid : theResourceIds) {
JpaPid jpaPid = (JpaPid)pid;
ResourceTable entity = myEntityManager.find(ResourceTable.class, jpaPid.getId());
deletedResources.add(entity);
T resourceToDelete = myJpaStorageResourceParser.toResource(myResourceType, entity, null, false);
@ -878,10 +880,10 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
throw new PreconditionFailedException(Msg.code(969) + "Can not perform version-specific expunge of resource " + theId.toUnqualified().getValue() + " as this is the current version");
}
return myExpungeService.expunge(getResourceName(), new ResourcePersistentId(entity.getResourceId(), entity.getVersion()), theExpungeOptions, theRequest);
return myExpungeService.expunge(getResourceName(), JpaPid.fromIdAndVersion(entity.getResourceId(), entity.getVersion()), theExpungeOptions, theRequest);
}
return myExpungeService.expunge(getResourceName(), new ResourcePersistentId(entity.getResourceId()), theExpungeOptions, theRequest);
return myExpungeService.expunge(getResourceName(), JpaPid.fromId(entity.getResourceId()), theExpungeOptions, theRequest);
}
@Override
@ -1132,18 +1134,19 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
@Override
@Transactional
public T readByPid(ResourcePersistentId thePid) {
public T readByPid(IResourcePersistentId thePid) {
return readByPid(thePid, false);
}
@Override
@Transactional
public T readByPid(ResourcePersistentId thePid, boolean theDeletedOk) {
public T readByPid(IResourcePersistentId thePid, boolean theDeletedOk) {
StopWatch w = new StopWatch();
JpaPid jpaPid = (JpaPid)thePid;
Optional<ResourceTable> entity = myResourceTableDao.findById(thePid.getIdAsLong());
Optional<ResourceTable> entity = myResourceTableDao.findById(jpaPid.getId());
if (!entity.isPresent()) {
throw new ResourceNotFoundException(Msg.code(975) + "No resource found with PID " + thePid);
throw new ResourceNotFoundException(Msg.code(975) + "No resource found with PID " + jpaPid);
}
if (isDeleted(entity.get()) && !theDeletedOk) {
throw createResourceGoneException(entity.get());
@ -1151,7 +1154,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
T retVal = myJpaStorageResourceParser.toResource(myResourceType, entity.get(), null, false);
ourLog.debug("Processed read on {} in {}ms", thePid, w.getMillis());
ourLog.debug("Processed read on {} in {}ms", jpaPid, w.getMillis());
return retVal;
}
@ -1228,10 +1231,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
@SuppressWarnings("unchecked")
@Override
public void reindex(ResourcePersistentId theResourcePersistentId, RequestDetails theRequest, TransactionDetails theTransactionDetails) {
Optional<ResourceTable> entityOpt = myResourceTableDao.findById(theResourcePersistentId.getIdAsLong());
public void reindex(IResourcePersistentId thePid, RequestDetails theRequest, TransactionDetails theTransactionDetails) {
JpaPid jpaPid = (JpaPid)thePid;
Optional<ResourceTable> entityOpt = myResourceTableDao.findById(jpaPid.getId());
if (!entityOpt.isPresent()) {
ourLog.warn("Unable to find entity with PID: {}", theResourcePersistentId.getId());
ourLog.warn("Unable to find entity with PID: {}", jpaPid.getId());
return;
}
@ -1253,24 +1257,24 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineReadPartitionForRequestForRead(theRequest, getResourceName(), theId);
BaseHasResource entity;
ResourcePersistentId pid = myIdHelperService.resolveResourcePersistentIds(requestPartitionId, getResourceName(), theId.getIdPart());
JpaPid pid = myIdHelperService.resolveResourcePersistentIds(requestPartitionId, getResourceName(), theId.getIdPart());
Set<Integer> readPartitions = null;
if (requestPartitionId.isAllPartitions()) {
entity = myEntityManager.find(ResourceTable.class, pid.getIdAsLong());
entity = myEntityManager.find(ResourceTable.class, pid.getId());
} else {
readPartitions = myRequestPartitionHelperService.toReadPartitions(requestPartitionId);
if (readPartitions.size() == 1) {
if (readPartitions.contains(null)) {
entity = myResourceTableDao.readByPartitionIdNull(pid.getIdAsLong()).orElse(null);
entity = myResourceTableDao.readByPartitionIdNull(pid.getId()).orElse(null);
} else {
entity = myResourceTableDao.readByPartitionId(readPartitions.iterator().next(), pid.getIdAsLong()).orElse(null);
entity = myResourceTableDao.readByPartitionId(readPartitions.iterator().next(), pid.getId()).orElse(null);
}
} else {
if (readPartitions.contains(null)) {
List<Integer> readPartitionsWithoutNull = readPartitions.stream().filter(t -> t != null).collect(Collectors.toList());
entity = myResourceTableDao.readByPartitionIdsOrNull(readPartitionsWithoutNull, pid.getIdAsLong()).orElse(null);
entity = myResourceTableDao.readByPartitionIdsOrNull(readPartitionsWithoutNull, pid.getId()).orElse(null);
} else {
entity = myResourceTableDao.readByPartitionIds(readPartitions, pid.getIdAsLong()).orElse(null);
entity = myResourceTableDao.readByPartitionIds(readPartitions, pid.getId()).orElse(null);
}
}
}
@ -1320,8 +1324,9 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
@Override
protected IBasePersistedResource readEntityLatestVersion(ResourcePersistentId thePersistentId, RequestDetails theRequestDetails, TransactionDetails theTransactionDetails) {
return myEntityManager.find(ResourceTable.class, thePersistentId.getIdAsLong());
protected IBasePersistedResource readEntityLatestVersion(IResourcePersistentId thePersistentId, RequestDetails theRequestDetails, TransactionDetails theTransactionDetails) {
JpaPid jpaPid = (JpaPid)thePersistentId;
return myEntityManager.find(ResourceTable.class, jpaPid.getId());
}
@ -1336,13 +1341,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
private ResourceTable readEntityLatestVersion(IIdType theId, @Nonnull RequestPartitionId theRequestPartitionId, TransactionDetails theTransactionDetails) {
validateResourceTypeAndThrowInvalidRequestException(theId);
ResourcePersistentId persistentId = null;
JpaPid persistentId = null;
if (theTransactionDetails != null) {
if (theTransactionDetails.isResolvedResourceIdEmpty(theId.toUnqualifiedVersionless())) {
throw new ResourceNotFoundException(Msg.code(1997) + theId);
}
if (theTransactionDetails.hasResolvedResourceIds()) {
persistentId = theTransactionDetails.getResolvedResourceId(theId);
persistentId = (JpaPid)theTransactionDetails.getResolvedResourceId(theId);
}
}
@ -1517,7 +1522,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
@Override
public List<ResourcePersistentId> searchForIds(SearchParameterMap theParams, RequestDetails theRequest, @Nullable IBaseResource theConditionalOperationTargetOrNull) {
public List<JpaPid> searchForIds(SearchParameterMap theParams, RequestDetails theRequest, @Nullable IBaseResource theConditionalOperationTargetOrNull) {
TransactionDetails transactionDetails = new TransactionDetails();
return myTransactionService.execute(theRequest, transactionDetails, tx -> {
@ -1530,13 +1535,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
ISearchBuilder builder = mySearchBuilderFactory.newSearchBuilder(this, getResourceName(), getResourceType());
List<ResourcePersistentId> ids = new ArrayList<>();
List<JpaPid> ids = new ArrayList<>();
String uuid = UUID.randomUUID().toString();
RequestPartitionId requestPartitionId = myRequestPartitionHelperService.determineReadPartitionForRequestForSearchType(theRequest, getResourceName(), theParams, theConditionalOperationTargetOrNull);
SearchRuntimeDetails searchRuntimeDetails = new SearchRuntimeDetails(theRequest, uuid);
try (IResultIterator iter = builder.createQuery(theParams, searchRuntimeDetails, theRequest, requestPartitionId)) {
try (IResultIterator<JpaPid> iter = builder.createQuery(theParams, searchRuntimeDetails, theRequest, requestPartitionId)) {
while (iter.hasNext()) {
ids.add(iter.next());
}
@ -1652,12 +1657,12 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
IIdType resourceId;
RestOperationTypeEnum update = RestOperationTypeEnum.UPDATE;
if (isNotBlank(theMatchUrl)) {
Set<ResourcePersistentId> match = myMatchResourceUrlService.processMatchUrl(theMatchUrl, myResourceType, theTransactionDetails, theRequest, theResource);
Set<JpaPid> match = myMatchResourceUrlService.processMatchUrl(theMatchUrl, myResourceType, theTransactionDetails, theRequest, theResource);
if (match.size() > 1) {
String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "transactionOperationWithMultipleMatchFailure", "UPDATE", theMatchUrl, match.size());
throw new PreconditionFailedException(Msg.code(988) + msg);
} else if (match.size() == 1) {
ResourcePersistentId pid = match.iterator().next();
JpaPid pid = match.iterator().next();
entity = myEntityManager.find(ResourceTable.class, pid.getId());
resourceId = entity.getIdDt();
} else {
@ -1666,7 +1671,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
// Pre-cache the match URL
if (outcome.getPersistentId() != null) {
myMatchResourceUrlService.matchUrlResolved(theTransactionDetails, getResourceName(), theMatchUrl, outcome.getPersistentId());
myMatchResourceUrlService.matchUrlResolved(theTransactionDetails, getResourceName(), theMatchUrl, (JpaPid)outcome.getPersistentId());
}
return outcome;

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirSystemDao.java
View File

@ -7,11 +7,10 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.api.model.ExpungeOutcome;
import ca.uhn.fhir.jpa.dao.data.IResourceSearchViewDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
import ca.uhn.fhir.jpa.dao.expunge.ExpungeService;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.search.PersistedJpaBundleProviderFactory;
@ -20,12 +19,11 @@ import ca.uhn.fhir.jpa.util.QueryChunker;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
import ca.uhn.fhir.util.StopWatch;
import com.google.common.annotations.VisibleForTesting;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.transaction.annotation.Propagation;
@ -165,10 +163,10 @@ public abstract class BaseHapiFhirSystemDao<T extends IBaseBundle, MT> extends B
@Override
@Transactional(propagation = Propagation.MANDATORY)
public void preFetchResources(List<ResourcePersistentId> theResolvedIds) {
public <P extends IResourcePersistentId> void preFetchResources(List<P> theResolvedIds) {
List<Long> pids = theResolvedIds
.stream()
.map(t -> t.getIdAsLong())
.map(t -> ((JpaPid) t).getId())
.collect(Collectors.toList());
new QueryChunker<Long>().chunk(pids, ids->{

25
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FulltextSearchSvcImpl.java
View File

@ -30,6 +30,7 @@ import ca.uhn.fhir.jpa.dao.search.ExtendedHSearchResourceProjection;
import ca.uhn.fhir.jpa.dao.search.ExtendedHSearchSearchBuilder;
import ca.uhn.fhir.jpa.dao.search.IHSearchSortHelper;
import ca.uhn.fhir.jpa.dao.search.LastNOperation;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.search.ExtendedHSearchIndexData;
@ -43,7 +44,7 @@ import ca.uhn.fhir.jpa.searchparam.extractor.ResourceIndexedSearchParams;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.rest.server.util.ResourceSearchParams;
import com.google.common.collect.Ordering;
@ -156,7 +157,7 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
// keep this in sync with supportsSomeOf();
private ISearchQueryExecutor doSearch(String theResourceType, SearchParameterMap theParams,
ResourcePersistentId theReferencingPid, Integer theMaxResultsToFetch) {
IResourcePersistentId theReferencingPid, Integer theMaxResultsToFetch) {
int offset = theParams.getOffset() == null ? 0 : theParams.getOffset();
int count = getMaxFetchSize(theParams, theMaxResultsToFetch);
@ -185,7 +186,7 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
private SearchQueryOptionsStep<?, Long, SearchLoadingOptionsStep, ?, ?> getSearchQueryOptionsStep(
String theResourceType, SearchParameterMap theParams, ResourcePersistentId theReferencingPid) {
String theResourceType, SearchParameterMap theParams, IResourcePersistentId theReferencingPid) {
dispatchEvent(IHSearchEventListener.HSearchEventType.SEARCH);
var query= getSearchSession().search(ResourceTable.class)
@ -213,7 +214,7 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
private PredicateFinalStep buildWhereClause(SearchPredicateFactory f, String theResourceType,
SearchParameterMap theParams, ResourcePersistentId theReferencingPid) {
SearchParameterMap theParams, IResourcePersistentId theReferencingPid) {
return f.bool(b -> {
ExtendedHSearchClauseBuilder builder = new ExtendedHSearchClauseBuilder(myFhirContext, myModelConfig, b, f);
@ -261,18 +262,18 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
return Search.session(myEntityManager);
}
private List<ResourcePersistentId> convertLongsToResourcePersistentIds(List<Long> theLongPids) {
private List<IResourcePersistentId> convertLongsToResourcePersistentIds(List<Long> theLongPids) {
return theLongPids.stream()
.map(ResourcePersistentId::new)
.map(JpaPid::fromId)
.collect(Collectors.toList());
}
@Override
public List<ResourcePersistentId> everything(String theResourceName, SearchParameterMap theParams, ResourcePersistentId theReferencingPid) {
public List<IResourcePersistentId> everything(String theResourceName, SearchParameterMap theParams, IResourcePersistentId theReferencingPid) {
validateHibernateSearchIsEnabled();
// todo mb what about max results here?
List<ResourcePersistentId> retVal = toList(doSearch(null, theParams, theReferencingPid, 10_000), 10_000);
List<IResourcePersistentId> retVal = toList(doSearch(null, theParams, theReferencingPid, 10_000), 10_000);
if (theReferencingPid != null) {
retVal.add(theReferencingPid);
}
@ -310,7 +311,7 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
@Transactional()
@Override
public List<ResourcePersistentId> search(String theResourceName, SearchParameterMap theParams) {
public List<IResourcePersistentId> search(String theResourceName, SearchParameterMap theParams) {
validateHibernateSearchIsEnabled();
return toList(doSearch(theResourceName, theParams, null, DEFAULT_MAX_NON_PAGED_SIZE), DEFAULT_MAX_NON_PAGED_SIZE);
}
@ -318,9 +319,9 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
/**
* Adapt our async interface to the legacy concrete List
*/
private List<ResourcePersistentId> toList(ISearchQueryExecutor theSearchResultStream, long theMaxSize) {
private List<IResourcePersistentId> toList(ISearchQueryExecutor theSearchResultStream, long theMaxSize) {
return StreamSupport.stream(Spliterators.spliteratorUnknownSize(theSearchResultStream, 0), false)
.map(ResourcePersistentId::new)
.map(JpaPid::fromId)
.limit(theMaxSize)
.collect(Collectors.toList());
}
@ -356,7 +357,7 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
}
@Override
public List<ResourcePersistentId> lastN(SearchParameterMap theParams, Integer theMaximumResults) {
public List<IResourcePersistentId> lastN(SearchParameterMap theParams, Integer theMaximumResults) {
ensureElastic();
dispatchEvent(IHSearchEventListener.HSearchEventType.SEARCH);
List<Long> pidList = new LastNOperation(getSearchSession(), myFhirContext, myModelConfig, mySearchParamRegistry)

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/HistoryBuilder.java
View File

@ -27,8 +27,8 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.model.PersistentIdToForcedIdMap;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.HistorySearchStyleEnum;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import com.google.common.collect.ImmutableListMultimap;
@ -128,7 +128,7 @@ public class HistoryBuilder {
List<ResourceHistoryTable> tables = query.getResultList();
if (tables.size() > 0) {
ImmutableListMultimap<Long, ResourceHistoryTable> resourceIdToHistoryEntries = Multimaps.index(tables, ResourceHistoryTable::getResourceId);
Set<ResourcePersistentId> pids = resourceIdToHistoryEntries.keySet().stream().map(t-> new ResourcePersistentId(t)).collect(Collectors.toSet());
Set<JpaPid> pids = resourceIdToHistoryEntries.keySet().stream().map(JpaPid::fromId).collect(Collectors.toSet());
PersistentIdToForcedIdMap pidToForcedId = myIdHelperService.translatePidsToForcedIds(pids);
ourLog.trace("Translated IDs: {}", pidToForcedId.getResourcePersistentIdOptionalMap());
@ -137,7 +137,7 @@ public class HistoryBuilder {
String resourceId;
Optional<String> forcedId = pidToForcedId.get(new ResourcePersistentId(nextResourceId));
Optional<String> forcedId = pidToForcedId.get(JpaPid.fromId(nextResourceId));
if (forcedId.isPresent()) {
resourceId = forcedId.get();
} else {

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

@ -26,7 +26,7 @@ import ca.uhn.fhir.jpa.search.autocomplete.ValueSetAutocompleteOptions;
import ca.uhn.fhir.jpa.search.builder.ISearchQueryExecutor;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.extractor.ResourceIndexedSearchParams;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import org.hl7.fhir.instance.model.api.IBaseResource;
import java.util.Collection;
@ -43,7 +43,7 @@ public interface IFulltextSearchSvc {
* @param theParams the full query - modified to return only params unused by the index.
* @return the pid list for the matchign resources.
*/
List<ResourcePersistentId> search(String theResourceName, SearchParameterMap theParams);
<T extends IResourcePersistentId> List<T> search(String theResourceName, SearchParameterMap theParams);
/**
@ -63,7 +63,7 @@ public interface IFulltextSearchSvc {
*/
IBaseResource tokenAutocompleteValueSetSearch(ValueSetAutocompleteOptions theOptions);
List<ResourcePersistentId> everything(String theResourceName, SearchParameterMap theParams, ResourcePersistentId theReferencingPid);
<T extends IResourcePersistentId> List<T> everything(String theResourceName, SearchParameterMap theParams, T theReferencingPid);
boolean isDisabled();
@ -81,7 +81,7 @@ public interface IFulltextSearchSvc {
*/
void reindex(ResourceTable theEntity);
List<ResourcePersistentId> lastN(SearchParameterMap theParams, Integer theMaximumResults);
List<IResourcePersistentId> lastN(SearchParameterMap theParams, Integer theMaximumResults);
/**
* Returns inlined resource stored along with index mappings for matched identifiers

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaResourceDaoCodeSystem.java
View File

@ -36,7 +36,7 @@ import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -88,9 +88,9 @@ public class JpaResourceDaoCodeSystem<T extends IBaseResource> extends BaseHapiF
@Override
public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
List<IIdType> valueSetIds;
List<ResourcePersistentId> ids = searchForIds(new SearchParameterMap(org.hl7.fhir.r4.model.CodeSystem.SP_CODE, new TokenParam(theSystem, theCode)), theRequest);
List<IResourcePersistentId> ids = searchForIds(new SearchParameterMap(org.hl7.fhir.r4.model.CodeSystem.SP_CODE, new TokenParam(theSystem, theCode)), theRequest);
valueSetIds = new ArrayList<>();
for (ResourcePersistentId next : ids) {
for (IResourcePersistentId next : ids) {
IIdType id = myIdHelperService.translatePidIdToForcedId(myFhirContext, "CodeSystem", next);
valueSetIds.add(id);
}

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

@ -31,7 +31,6 @@ import ca.uhn.fhir.rest.param.StringParam;
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.hl7.fhir.r4.model.Composition;
import javax.servlet.http.HttpServletRequest;
import java.util.Collections;

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaResourceDaoObservation.java
View File

@ -24,6 +24,7 @@ import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoObservation;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@ -34,7 +35,6 @@ import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.param.ReferenceOrListParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
@ -152,8 +152,8 @@ public class JpaResourceDaoObservation<T extends IBaseResource> extends BaseHapi
for (IQueryParameterType nextOr : nextPatientList) {
if (nextOr instanceof ReferenceParam) {
ReferenceParam ref = (ReferenceParam) nextOr;
ResourcePersistentId pid = myIdHelperService.resolveResourcePersistentIds(requestPartitionId, ref.getResourceType(), ref.getIdPart());
orderedSubjectReferenceMap.put(pid.getIdAsLong(), nextOr);
JpaPid pid = myIdHelperService.resolveResourcePersistentIds(requestPartitionId, ref.getResourceType(), ref.getIdPart());
orderedSubjectReferenceMap.put(pid.getId(), nextOr);
} else {
throw new IllegalArgumentException(Msg.code(942) + "Invalid token type (expecting ReferenceParam): " + nextOr.getClass());
}

29
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/TransactionProcessor.java
View File

@ -28,16 +28,14 @@ import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.util.StopWatch;
@ -90,7 +88,7 @@ public class TransactionProcessor extends BaseTransactionProcessor {
@Autowired(required = false)
private HapiFhirHibernateJpaDialect myHapiFhirHibernateJpaDialect;
@Autowired
private IIdHelperService myIdHelperService;
private IIdHelperService<JpaPid> myIdHelperService;
@Autowired
private PartitionSettings myPartitionSettings;
@Autowired
@ -98,7 +96,7 @@ public class TransactionProcessor extends BaseTransactionProcessor {
@Autowired
private FhirContext myFhirContext;
@Autowired
private MatchResourceUrlService myMatchResourceUrlService;
private MatchResourceUrlService<JpaPid> myMatchResourceUrlService;
@Autowired
private MatchUrlService myMatchUrlService;
@Autowired
@ -166,12 +164,13 @@ public class TransactionProcessor extends BaseTransactionProcessor {
}
}
}
List<ResourcePersistentId> outcome = myIdHelperService.resolveResourcePersistentIdsWithCache(requestPartitionId, idsToPreResolve);
for (ResourcePersistentId next : outcome) {
List<JpaPid> outcome = myIdHelperService.resolveResourcePersistentIdsWithCache(requestPartitionId, idsToPreResolve)
.stream().collect(Collectors.toList());
for (JpaPid next : outcome) {
foundIds.add(next.getAssociatedResourceId().toUnqualifiedVersionless().getValue());
theTransactionDetails.addResolvedResourceId(next.getAssociatedResourceId(), next);
if (myDaoConfig.getResourceClientIdStrategy() != DaoConfig.ClientIdStrategyEnum.ANY || !next.getAssociatedResourceId().isIdPartValidLong()) {
idsToPreFetch.add(next.getIdAsLong());
idsToPreFetch.add(next.getId());
}
}
for (IIdType next : idsToPreResolve) {
@ -192,18 +191,18 @@ public class TransactionProcessor extends BaseTransactionProcessor {
String requestIfNoneExist = versionAdapter.getEntryIfNoneExist(nextEntry);
String resourceType = myFhirContext.getResourceType(resource);
if ("PUT".equals(verb) && requestUrl != null && requestUrl.contains("?")) {
ResourcePersistentId cachedId = myMatchResourceUrlService.processMatchUrlUsingCacheOnly(resourceType, requestUrl);
JpaPid cachedId = myMatchResourceUrlService.processMatchUrlUsingCacheOnly(resourceType, requestUrl);
if (cachedId != null) {
idsToPreFetch.add(cachedId.getIdAsLong());
idsToPreFetch.add(cachedId.getId());
} else if (SINGLE_PARAMETER_MATCH_URL_PATTERN.matcher(requestUrl).matches()) {
RuntimeResourceDefinition resourceDefinition = myFhirContext.getResourceDefinition(resource);
SearchParameterMap matchUrlSearchMap = myMatchUrlService.translateMatchUrl(requestUrl, resourceDefinition);
searchParameterMapsToResolve.add(new MatchUrlToResolve(requestUrl, matchUrlSearchMap, resourceDefinition));
}
} else if ("POST".equals(verb) && requestIfNoneExist != null && requestIfNoneExist.contains("?")) {
ResourcePersistentId cachedId = myMatchResourceUrlService.processMatchUrlUsingCacheOnly(resourceType, requestIfNoneExist);
JpaPid cachedId = myMatchResourceUrlService.processMatchUrlUsingCacheOnly(resourceType, requestIfNoneExist);
if (cachedId != null) {
idsToPreFetch.add(cachedId.getIdAsLong());
idsToPreFetch.add(cachedId.getId());
} else if (SINGLE_PARAMETER_MATCH_URL_PATTERN.matcher(requestIfNoneExist).matches()) {
RuntimeResourceDefinition resourceDefinition = myFhirContext.getResourceDefinition(resource);
SearchParameterMap matchUrlSearchMap = myMatchUrlService.translateMatchUrl(requestIfNoneExist, resourceDefinition);
@ -277,7 +276,7 @@ public class TransactionProcessor extends BaseTransactionProcessor {
}
IFhirSystemDao<?,?> systemDao = myApplicationContext.getBean(IFhirSystemDao.class);
systemDao.preFetchResources(ResourcePersistentId.fromLongList(idsToPreFetch));
systemDao.preFetchResources(JpaPid.fromLongList(idsToPreFetch));
}
@ -322,8 +321,8 @@ public class TransactionProcessor extends BaseTransactionProcessor {
private void setSearchToResolvedAndPrefetchFoundResourcePid(TransactionDetails theTransactionDetails, List<Long> idsToPreFetch, ResourceIndexedSearchParamToken nextResult, MatchUrlToResolve nextSearchParameterMap) {
ourLog.debug("Matched url {} from database", nextSearchParameterMap.myRequestUrl);
idsToPreFetch.add(nextResult.getResourcePid());
myMatchResourceUrlService.matchUrlResolved(theTransactionDetails, nextSearchParameterMap.myResourceDefinition.getName(), nextSearchParameterMap.myRequestUrl, new ResourcePersistentId(nextResult.getResourcePid()));
theTransactionDetails.addResolvedMatchUrl(nextSearchParameterMap.myRequestUrl, new ResourcePersistentId(nextResult.getResourcePid()));
myMatchResourceUrlService.matchUrlResolved(theTransactionDetails, nextSearchParameterMap.myResourceDefinition.getName(), nextSearchParameterMap.myRequestUrl, JpaPid.fromId(nextResult.getResourcePid()));
theTransactionDetails.addResolvedMatchUrl(nextSearchParameterMap.myRequestUrl, JpaPid.fromId(nextResult.getResourcePid()));
nextSearchParameterMap.setResolved(true);
}

73
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ResourceExpungeService.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/JpaResourceExpungeService.java
View File

@ -45,13 +45,13 @@ import ca.uhn.fhir.jpa.dao.data.IResourceLinkDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
import ca.uhn.fhir.jpa.dao.data.ISearchParamPresentDao;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ForcedId;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import org.apache.commons.lang3.Validate;
@ -74,8 +74,8 @@ import java.util.List;
import java.util.concurrent.atomic.AtomicInteger;
@Service
public class ResourceExpungeService implements IResourceExpungeService {
private static final Logger ourLog = LoggerFactory.getLogger(ResourceExpungeService.class);
public class JpaResourceExpungeService implements IResourceExpungeService<JpaPid> {
private static final Logger ourLog = LoggerFactory.getLogger(JpaResourceExpungeService.class);
@Autowired
private IForcedIdDao myForcedIdDao;
@ -128,7 +128,7 @@ public class ResourceExpungeService implements IResourceExpungeService {
@Override
@Transactional
public List<ResourcePersistentId> findHistoricalVersionsOfNonDeletedResources(String theResourceName, ResourcePersistentId theResourceId, int theRemainingCount) {
public List<JpaPid> findHistoricalVersionsOfNonDeletedResources(String theResourceName, JpaPid theJpaPid, int theRemainingCount) {
if (isEmptyQuery(theRemainingCount)) {
return Collections.EMPTY_LIST;
}
@ -136,11 +136,11 @@ public class ResourceExpungeService implements IResourceExpungeService {
Pageable page = PageRequest.of(0, theRemainingCount);
Slice<Long> ids;
if (theResourceId != null && theResourceId.getId() != null) {
if (theResourceId.getVersion() != null) {
ids = toSlice(myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(theResourceId.getIdAsLong(), theResourceId.getVersion()));
if (theJpaPid != null && theJpaPid.getId() != null) {
if (theJpaPid.getVersion() != null) {
ids = toSlice(myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(theJpaPid.getId(), theJpaPid.getVersion()));
} else {
ids = myResourceHistoryTableDao.findIdsOfPreviousVersionsOfResourceId(page, theResourceId.getIdAsLong());
ids = myResourceHistoryTableDao.findIdsOfPreviousVersionsOfResourceId(page, theJpaPid.getId());
}
} else {
if (theResourceName != null) {
@ -150,12 +150,12 @@ public class ResourceExpungeService implements IResourceExpungeService {
}
}
return ResourcePersistentId.fromLongList(ids.getContent());
return JpaPid.fromLongList(ids.getContent());
}
@Override
@Transactional
public List<ResourcePersistentId> findHistoricalVersionsOfDeletedResources(String theResourceName, ResourcePersistentId theResourceId, int theRemainingCount) {
public List<JpaPid> findHistoricalVersionsOfDeletedResources(String theResourceName, JpaPid theResourceId, int theRemainingCount) {
if (isEmptyQuery(theRemainingCount)) {
return Collections.EMPTY_LIST;
}
@ -163,7 +163,7 @@ public class ResourceExpungeService implements IResourceExpungeService {
Pageable page = PageRequest.of(0, theRemainingCount);
Slice<Long> ids;
if (theResourceId != null) {
ids = myResourceTableDao.findIdsOfDeletedResourcesOfType(page, theResourceId.getIdAsLong(), theResourceName);
ids = myResourceTableDao.findIdsOfDeletedResourcesOfType(page, theResourceId.getId(), theResourceName);
ourLog.info("Expunging {} deleted resources of type[{}] and ID[{}]", ids.getNumberOfElements(), theResourceName, theResourceId);
} else {
if (theResourceName != null) {
@ -174,14 +174,14 @@ public class ResourceExpungeService implements IResourceExpungeService {
ourLog.info("Expunging {} deleted resources (all types)", ids.getNumberOfElements());
}
}
return ResourcePersistentId.fromLongList(ids.getContent());
return JpaPid.fromLongList(ids.getContent());
}
@Override
@Transactional
public void expungeCurrentVersionOfResources(RequestDetails theRequestDetails, List<ResourcePersistentId> theResourceIds, AtomicInteger theRemainingCount) {
for (ResourcePersistentId next : theResourceIds) {
expungeCurrentVersionOfResource(theRequestDetails, next.getIdAsLong(), theRemainingCount);
public void expungeCurrentVersionOfResources(RequestDetails theRequestDetails, List<JpaPid> theResourceIds, AtomicInteger theRemainingCount) {
for (JpaPid next : theResourceIds) {
expungeCurrentVersionOfResource(theRequestDetails,(next).getId(), theRemainingCount);
if (expungeLimitReached(theRemainingCount)) {
return;
}
@ -236,9 +236,9 @@ public class ResourceExpungeService implements IResourceExpungeService {
@Override
@Transactional
public void expungeHistoricalVersionsOfIds(RequestDetails theRequestDetails, List<ResourcePersistentId> theResourceIds, AtomicInteger theRemainingCount) {
for (ResourcePersistentId next : theResourceIds) {
expungeHistoricalVersionsOfId(theRequestDetails, next.getIdAsLong(), theRemainingCount);
public void expungeHistoricalVersionsOfIds(RequestDetails theRequestDetails, List<JpaPid> theResourceIds, AtomicInteger theRemainingCount) {
for (JpaPid next : theResourceIds) {
expungeHistoricalVersionsOfId(theRequestDetails, (next).getId(), theRemainingCount);
if (expungeLimitReached(theRemainingCount)) {
return;
}
@ -247,9 +247,9 @@ public class ResourceExpungeService implements IResourceExpungeService {
@Override
@Transactional
public void expungeHistoricalVersions(RequestDetails theRequestDetails, List<ResourcePersistentId> theHistoricalIds, AtomicInteger theRemainingCount) {
for (ResourcePersistentId next : theHistoricalIds) {
expungeHistoricalVersion(theRequestDetails, next.getIdAsLong(), theRemainingCount);
public void expungeHistoricalVersions(RequestDetails theRequestDetails, List<JpaPid> theHistoricalIds, AtomicInteger theRemainingCount) {
for (JpaPid next : theHistoricalIds) {
expungeHistoricalVersion(theRequestDetails, (next).getId(), theRemainingCount);
if (expungeLimitReached(theRemainingCount)) {
return;
}
@ -266,7 +266,7 @@ public class ResourceExpungeService implements IResourceExpungeService {
ourLog.info("Expunging current version of resource {}", resource.getIdDt().getValue());
deleteAllSearchParams(new ResourcePersistentId(resource.getResourceId()));
deleteAllSearchParams(JpaPid.fromId(resource.getResourceId()));
myResourceTagDao.deleteByResourceId(resource.getId());
@ -282,44 +282,45 @@ public class ResourceExpungeService implements IResourceExpungeService {
@Override
@Transactional
public void deleteAllSearchParams(ResourcePersistentId theResourceId) {
ResourceTable resource = myResourceTableDao.findById(theResourceId.getIdAsLong()).orElse(null);
public void deleteAllSearchParams(JpaPid theResourceId) {
Long theResourceLongId = theResourceId.getId();
ResourceTable resource = myResourceTableDao.findById(theResourceLongId).orElse(null);
if (resource == null || resource.isParamsUriPopulated()) {
myResourceIndexedSearchParamUriDao.deleteByResourceId(theResourceId.getIdAsLong());
myResourceIndexedSearchParamUriDao.deleteByResourceId(theResourceLongId);
}
if (resource == null || resource.isParamsCoordsPopulated()) {
myResourceIndexedSearchParamCoordsDao.deleteByResourceId(theResourceId.getIdAsLong());
myResourceIndexedSearchParamCoordsDao.deleteByResourceId(theResourceLongId);
}
if (resource == null || resource.isParamsDatePopulated()) {
myResourceIndexedSearchParamDateDao.deleteByResourceId(theResourceId.getIdAsLong());
myResourceIndexedSearchParamDateDao.deleteByResourceId(theResourceLongId);
}
if (resource == null || resource.isParamsNumberPopulated()) {
myResourceIndexedSearchParamNumberDao.deleteByResourceId(theResourceId.getIdAsLong());
myResourceIndexedSearchParamNumberDao.deleteByResourceId(theResourceLongId);
}
if (resource == null || resource.isParamsQuantityPopulated()) {
myResourceIndexedSearchParamQuantityDao.deleteByResourceId(theResourceId.getIdAsLong());
myResourceIndexedSearchParamQuantityDao.deleteByResourceId(theResourceLongId);
}
if (resource == null || resource.isParamsQuantityNormalizedPopulated()) {
myResourceIndexedSearchParamQuantityNormalizedDao.deleteByResourceId(theResourceId.getIdAsLong());
myResourceIndexedSearchParamQuantityNormalizedDao.deleteByResourceId(theResourceLongId);
}
if (resource == null || resource.isParamsStringPopulated()) {
myResourceIndexedSearchParamStringDao.deleteByResourceId(theResourceId.getIdAsLong());
myResourceIndexedSearchParamStringDao.deleteByResourceId(theResourceLongId);
}
if (resource == null || resource.isParamsTokenPopulated()) {
myResourceIndexedSearchParamTokenDao.deleteByResourceId(theResourceId.getIdAsLong());
myResourceIndexedSearchParamTokenDao.deleteByResourceId(theResourceLongId);
}
if (resource == null || resource.isParamsComboStringUniquePresent()) {
myResourceIndexedCompositeStringUniqueDao.deleteByResourceId(theResourceId.getIdAsLong());
myResourceIndexedCompositeStringUniqueDao.deleteByResourceId(theResourceLongId);
}
if (resource == null || resource.isParamsComboTokensNonUniquePresent()) {
myResourceIndexedComboTokensNonUniqueDao.deleteByResourceId(theResourceId.getIdAsLong());
myResourceIndexedComboTokensNonUniqueDao.deleteByResourceId(theResourceLongId);
}
if (myDaoConfig.getIndexMissingFields() == DaoConfig.IndexEnabledEnum.ENABLED) {
mySearchParamPresentDao.deleteByResourceId(theResourceId.getIdAsLong());
mySearchParamPresentDao.deleteByResourceId(theResourceLongId);
}
if (resource == null || resource.isHasLinks()) {
myResourceLinkDao.deleteByResourceId(theResourceId.getIdAsLong());
myResourceLinkDao.deleteByResourceId(theResourceLongId);
}
}

97
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IJpaIdHelperService.java
View File

@ -1,97 +0,0 @@
package ca.uhn.fhir.jpa.dao.index;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2022 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.api.svc.IIdHelperService;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.util.List;
import java.util.Set;
/**
* This class is an analog to {@link IIdHelperService} but with additional JPA server methods
* added.
*
* JA 2022-02-17 - I moved these methods out of IdHelperService because I want to reuse
* IdHelperService in storage-engine-neutral batch tasks such as bulk import. These methods
* are all just being used by MDM, so they're JPA specific. I believe it should be possible
* though to just replace all of these calls with equivalents from IdHelperService,
* at which point this interface and its implementation could just go away.
*
* All of the methods here aren't partition aware, so it's not great to use them
* anyhow. The equivalents in {@link IIdHelperService} are probably a bit more
* clunky because you have to convert between {@link Long} and
* {@link ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId} to use them,
* but they also have caching and partition awareness so the tradeoff for that
* extra effort is that they are better.
*/
public interface IJpaIdHelperService extends IIdHelperService {
/**
* @deprecated This method doesn't take a partition ID as input, so it is unsafe. It
* should be reworked to include the partition ID before any new use is incorporated
*/
@Deprecated
@Nonnull
List<Long> getPidsOrThrowException(List<IIdType> theIds);
/**
* @deprecated This method doesn't take a partition ID as input, so it is unsafe. It
* should be reworked to include the partition ID before any new use is incorporated
*/
@Deprecated
@Nullable
Long getPidOrNull(IBaseResource theResource);
/**
* @deprecated This method doesn't take a partition ID as input, so it is unsafe. It
* should be reworked to include the partition ID before any new use is incorporated
*/
@Deprecated
@Nonnull
Long getPidOrThrowException(IIdType theId);
@Nonnull
ResourcePersistentId getPidOrThrowException(@Nonnull IAnyResource theResource);
IIdType resourceIdFromPidOrThrowException(Long thePid);
/**
* 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:
* <p>
* [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.
*/
Set<String> translatePidsToFhirResourceIds(Set<ResourcePersistentId> thePids);
}

145
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java
View File

@ -30,14 +30,16 @@ import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
import ca.uhn.fhir.jpa.model.cross.ResourceLookup;
import ca.uhn.fhir.jpa.model.cross.JpaResourceLookup;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ForcedId;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.search.builder.SearchBuilder;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.jpa.util.QueryChunker;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.BaseResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
@ -92,13 +94,13 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* <p>
* This service is highly optimized in order to minimize the number of DB calls as much as possible,
* since ID resolution is fundamental to many basic operations. This service returns either
* {@link IResourceLookup} or {@link ResourcePersistentId} depending on the method being called.
* {@link IResourceLookup} or {@link BaseResourcePersistentId} depending on the method being called.
* The former involves an extra database join that the latter does not require, so selecting the
* right method here is important.
* </p>
*/
@Service
public class IdHelperService implements IIdHelperService {
public class IdHelperService implements IIdHelperService<JpaPid> {
public static final Predicate[] EMPTY_PREDICATE_ARRAY = new Predicate[0];
public static final String RESOURCE_PID = "RESOURCE_PID";
@Autowired
@ -130,7 +132,7 @@ public class IdHelperService implements IIdHelperService {
*/
@Override
@Nonnull
public IResourceLookup resolveResourceIdentity(@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, String theResourceId) throws ResourceNotFoundException {
public IResourceLookup<JpaPid> resolveResourceIdentity(@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, String theResourceId) throws ResourceNotFoundException {
return resolveResourceIdentity(theRequestPartitionId, theResourceType, theResourceId, false);
}
@ -143,12 +145,12 @@ public class IdHelperService implements IIdHelperService {
*/
@Override
@Nonnull
public IResourceLookup resolveResourceIdentity(@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, String theResourceId, boolean theExcludeDeleted) throws ResourceNotFoundException {
public IResourceLookup<JpaPid> resolveResourceIdentity(@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, String theResourceId, boolean theExcludeDeleted) throws ResourceNotFoundException {
assert myDontCheckActiveTransactionForUnitTest || TransactionSynchronizationManager.isSynchronizationActive();
assert theRequestPartitionId != null;
IdDt id = new IdDt(theResourceType, theResourceId);
Map<String, List<IResourceLookup>> matches = translateForcedIdToPids(theRequestPartitionId,
Map<String, List<IResourceLookup<JpaPid>>> matches = translateForcedIdToPids(theRequestPartitionId,
Collections.singletonList(id),
theExcludeDeleted);
@ -171,25 +173,25 @@ public class IdHelperService implements IIdHelperService {
}
/**
* Returns a mapping of Id -> ResourcePersistentId.
* Returns a mapping of Id -> IResourcePersistentId.
* If any resource is not found, it will throw ResourceNotFound exception (and no map will be returned)
*/
@Override
@Nonnull
public Map<String, ResourcePersistentId> resolveResourcePersistentIds(@Nonnull RequestPartitionId theRequestPartitionId,
public Map<String, JpaPid> resolveResourcePersistentIds(@Nonnull RequestPartitionId theRequestPartitionId,
String theResourceType,
List<String> theIds) {
return resolveResourcePersistentIds(theRequestPartitionId, theResourceType, theIds, false);
}
/**
* Returns a mapping of Id -> ResourcePersistentId.
* Returns a mapping of Id -> IResourcePersistentId.
* If any resource is not found, it will throw ResourceNotFound exception (and no map will be returned)
* Optionally filters out deleted resources.
*/
@Override
@Nonnull
public Map<String, ResourcePersistentId> resolveResourcePersistentIds(@Nonnull RequestPartitionId theRequestPartitionId,
public Map<String, JpaPid> resolveResourcePersistentIds(@Nonnull RequestPartitionId theRequestPartitionId,
String theResourceType,
List<String> theIds,
boolean theExcludeDeleted) {
@ -197,13 +199,13 @@ public class IdHelperService implements IIdHelperService {
Validate.notNull(theIds, "theIds cannot be null");
Validate.isTrue(!theIds.isEmpty(), "theIds must not be empty");
Map<String, ResourcePersistentId> retVals = new HashMap<>();
Map<String, JpaPid> retVals = new HashMap<>();
for (String id : theIds) {
ResourcePersistentId retVal;
JpaPid retVal;
if (!idRequiresForcedId(id)) {
// is already a PID
retVal = new ResourcePersistentId(Long.parseLong(id));
retVal = JpaPid.fromId(Long.parseLong(id));
retVals.put(id, retVal);
} else {
// is a forced id
@ -217,7 +219,7 @@ public class IdHelperService implements IIdHelperService {
retVal = myMemoryCacheService.getThenPutAfterCommit(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key, t -> {
List<IIdType> ids = Collections.singletonList(new IdType(theResourceType, id));
// fetches from cache using a function that checks cache first...
List<ResourcePersistentId> resolvedIds = resolveResourcePersistentIdsWithCache(theRequestPartitionId, ids);
List<JpaPid> resolvedIds = resolveResourcePersistentIdsWithCache(theRequestPartitionId, ids);
if (resolvedIds.isEmpty()) {
throw new ResourceNotFoundException(Msg.code(1100) + ids.get(0));
}
@ -238,7 +240,7 @@ public class IdHelperService implements IIdHelperService {
*/
@Override
@Nonnull
public ResourcePersistentId resolveResourcePersistentIds(@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, String theId) {
public JpaPid resolveResourcePersistentIds(@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, String theId) {
return resolveResourcePersistentIds(theRequestPartitionId, theResourceType, theId, false);
}
@ -249,10 +251,10 @@ public class IdHelperService implements IIdHelperService {
* @throws ResourceNotFoundException If the ID can not be found
*/
@Override
public ResourcePersistentId resolveResourcePersistentIds(@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, String theId, boolean theExcludeDeleted){
public JpaPid resolveResourcePersistentIds(@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, String theId, boolean theExcludeDeleted){
Validate.notNull(theId, "theId must not be null");
Map<String, ResourcePersistentId> retVal = resolveResourcePersistentIds(theRequestPartitionId,
Map<String, JpaPid> retVal = resolveResourcePersistentIds(theRequestPartitionId,
theResourceType,
Collections.singletonList(theId),
theExcludeDeleted);
@ -284,7 +286,7 @@ public class IdHelperService implements IIdHelperService {
*/
@Override
@Nonnull
public List<ResourcePersistentId> resolveResourcePersistentIdsWithCache(RequestPartitionId theRequestPartitionId, List<IIdType> theIds) {
public List<JpaPid> resolveResourcePersistentIdsWithCache(RequestPartitionId theRequestPartitionId, List<IIdType> theIds) {
boolean onlyForcedIds = false;
return resolveResourcePersistentIdsWithCache(theRequestPartitionId, theIds, onlyForcedIds);
}
@ -299,10 +301,10 @@ public class IdHelperService implements IIdHelperService {
*/
@Override
@Nonnull
public List<ResourcePersistentId> resolveResourcePersistentIdsWithCache(RequestPartitionId theRequestPartitionId, List<IIdType> theIds, boolean theOnlyForcedIds) {
public List<JpaPid> resolveResourcePersistentIdsWithCache(RequestPartitionId theRequestPartitionId, List<IIdType> theIds, boolean theOnlyForcedIds) {
assert myDontCheckActiveTransactionForUnitTest || TransactionSynchronizationManager.isSynchronizationActive();
List<ResourcePersistentId> retVal = new ArrayList<>(theIds.size());
List<JpaPid> retVal = new ArrayList<>(theIds.size());
for (IIdType id : theIds) {
if (!id.hasIdPart()) {
@ -316,14 +318,16 @@ public class IdHelperService implements IIdHelperService {
if (myDaoConfig.getResourceClientIdStrategy() != DaoConfig.ClientIdStrategyEnum.ANY) {
if (nextId.isIdPartValidLong()) {
if (!theOnlyForcedIds) {
retVal.add(new ResourcePersistentId(nextId.getIdPartAsLong()).setAssociatedResourceId(nextId));
JpaPid jpaPid = JpaPid.fromId(nextId.getIdPartAsLong());
jpaPid.setAssociatedResourceId(nextId);
retVal.add(jpaPid);
}
continue;
}
}
String key = toForcedIdToPidKey(theRequestPartitionId, nextId.getResourceType(), nextId.getIdPart());
ResourcePersistentId cachedId = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key);
JpaPid cachedId = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key);
if (cachedId != null) {
retVal.add(cachedId);
continue;
@ -337,7 +341,7 @@ public class IdHelperService implements IIdHelperService {
return retVal;
}
private void doResolvePersistentIds(RequestPartitionId theRequestPartitionId, List<IIdType> theIds, List<ResourcePersistentId> theOutputListToPopulate) {
private void doResolvePersistentIds(RequestPartitionId theRequestPartitionId, List<IIdType> theIds, List<JpaPid> theOutputListToPopulate) {
CriteriaBuilder cb = myEntityManager.getCriteriaBuilder();
CriteriaQuery<ForcedId> criteriaQuery = cb.createQuery(ForcedId.class);
Root<ForcedId> from = criteriaQuery.from(ForcedId.class);
@ -365,12 +369,12 @@ public class IdHelperService implements IIdHelperService {
for (ForcedId nextId : results) {
// Check if the nextId has a resource ID. It may have a null resource ID if a commit is still pending.
if (nextId.getResourceId() != null) {
ResourcePersistentId persistentId = new ResourcePersistentId(nextId.getResourceId());
populateAssociatedResourceId(nextId.getResourceType(), nextId.getForcedId(), persistentId);
theOutputListToPopulate.add(persistentId);
JpaPid jpaPid = JpaPid.fromId(nextId.getResourceId());
populateAssociatedResourceId(nextId.getResourceType(), nextId.getForcedId(), jpaPid);
theOutputListToPopulate.add(jpaPid);
String key = toForcedIdToPidKey(theRequestPartitionId, nextId.getResourceType(), nextId.getForcedId());
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key, persistentId);
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key, jpaPid);
}
}
}
@ -401,10 +405,10 @@ public class IdHelperService implements IIdHelperService {
return Optional.empty();
}
private void populateAssociatedResourceId(String nextResourceType, String forcedId, ResourcePersistentId persistentId) {
private void populateAssociatedResourceId(String nextResourceType, String forcedId, JpaPid jpaPid) {
IIdType resourceId = myFhirCtx.getVersion().newIdType();
resourceId.setValue(nextResourceType + "/" + forcedId);
persistentId.setAssociatedResourceId(resourceId);
jpaPid.setAssociatedResourceId(resourceId);
}
/**
@ -412,7 +416,7 @@ public class IdHelperService implements IIdHelperService {
*/
@Nonnull
@Override
public IIdType translatePidIdToForcedId(FhirContext theCtx, String theResourceType, ResourcePersistentId theId) {
public IIdType translatePidIdToForcedId(FhirContext theCtx, String theResourceType, JpaPid theId) {
if (theId.getAssociatedResourceId() != null) {
return theId.getAssociatedResourceId();
}
@ -430,8 +434,8 @@ public class IdHelperService implements IIdHelperService {
}
@Override
public Optional<String> translatePidIdToForcedIdWithCache(ResourcePersistentId theId) {
return myMemoryCacheService.get(MemoryCacheService.CacheEnum.PID_TO_FORCED_ID, theId.getIdAsLong(), pid -> myForcedIdDao.findByResourcePid(pid).map(ForcedId::asTypedFhirResourceId));
public Optional<String> translatePidIdToForcedIdWithCache(JpaPid theId) {
return myMemoryCacheService.get(MemoryCacheService.CacheEnum.PID_TO_FORCED_ID, theId.getId(), pid -> myForcedIdDao.findByResourcePid(pid).map(ForcedId::asTypedFhirResourceId));
}
private ListMultimap<String, String> organizeIdsByResourceType(Collection<IIdType> theIds) {
@ -448,7 +452,7 @@ public class IdHelperService implements IIdHelperService {
return typeToIds;
}
private Map<String, List<IResourceLookup>> translateForcedIdToPids(@Nonnull RequestPartitionId theRequestPartitionId, Collection<IIdType> theId, boolean theExcludeDeleted) {
private Map<String, List<IResourceLookup<JpaPid>>> translateForcedIdToPids(@Nonnull RequestPartitionId theRequestPartitionId, Collection<IIdType> theId, boolean theExcludeDeleted) {
assert theRequestPartitionId != null;
theId.forEach(id -> Validate.isTrue(id.hasIdPart()));
@ -457,7 +461,7 @@ public class IdHelperService implements IIdHelperService {
return new HashMap<>();
}
Map<String, List<IResourceLookup>> retVal = new HashMap<>();
Map<String, List<IResourceLookup<JpaPid>>> retVal = new HashMap<>();
RequestPartitionId requestPartitionId = replaceDefault(theRequestPartitionId);
if (myDaoConfig.getResourceClientIdStrategy() != DaoConfig.ClientIdStrategyEnum.ANY) {
@ -514,7 +518,7 @@ public class IdHelperService implements IIdHelperService {
String forcedId = (String) next[2];
Date deletedAt = (Date) next[3];
ResourceLookup lookup = new ResourceLookup(resourceType, resourcePid, deletedAt);
JpaResourceLookup lookup = new JpaResourceLookup(resourceType, resourcePid, deletedAt);
if (!retVal.containsKey(forcedId)) {
retVal.put(forcedId, new ArrayList<>());
}
@ -546,7 +550,7 @@ public class IdHelperService implements IIdHelperService {
return theRequestPartitionId;
}
private void resolvePids(@Nonnull RequestPartitionId theRequestPartitionId, List<Long> thePidsToResolve, Map<String, List<IResourceLookup>> theTargets) {
private void resolvePids(@Nonnull RequestPartitionId theRequestPartitionId, List<Long> thePidsToResolve, Map<String, List<IResourceLookup<JpaPid>>> theTargets) {
if (!myDaoConfig.isDeleteEnabled()) {
for (Iterator<Long> forcedIdIterator = thePidsToResolve.iterator(); forcedIdIterator.hasNext(); ) {
Long nextPid = forcedIdIterator.next();
@ -577,7 +581,7 @@ public class IdHelperService implements IIdHelperService {
}
lookup
.stream()
.map(t -> new ResourceLookup((String) t[0], (Long) t[1], (Date) t[2]))
.map(t -> new JpaResourceLookup((String) t[0], (Long) t[1], (Date) t[2]))
.forEach(t -> {
String id = t.getPersistentId().toString();
if (!theTargets.containsKey(id)) {
@ -594,9 +598,9 @@ public class IdHelperService implements IIdHelperService {
}
@Override
public PersistentIdToForcedIdMap translatePidsToForcedIds(Set<ResourcePersistentId> theResourceIds) {
public PersistentIdToForcedIdMap translatePidsToForcedIds(Set<JpaPid> theResourceIds) {
assert myDontCheckActiveTransactionForUnitTest || TransactionSynchronizationManager.isSynchronizationActive();
Set<Long> thePids = theResourceIds.stream().map(t -> t.getIdAsLong()).collect(Collectors.toSet());
Set<Long> thePids = theResourceIds.stream().map(JpaPid::getId).collect(Collectors.toSet());
Map<Long, Optional<String>> retVal = new HashMap<>(myMemoryCacheService.getAllPresent(MemoryCacheService.CacheEnum.PID_TO_FORCED_ID, thePids));
List<Long> remainingPids = thePids
@ -623,10 +627,10 @@ public class IdHelperService implements IIdHelperService {
retVal.put(nextResourcePid, Optional.empty());
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.PID_TO_FORCED_ID, nextResourcePid, Optional.empty());
}
Map<ResourcePersistentId, Optional<String>> convertRetVal = new HashMap<>();
Map<IResourcePersistentId, Optional<String>> convertRetVal = new HashMap<>();
retVal.forEach(
(k, v) -> {
convertRetVal.put(new ResourcePersistentId(k), v);
convertRetVal.put(JpaPid.fromId(k), v);
}
);
return new PersistentIdToForcedIdMap(convertRetVal);
@ -636,22 +640,22 @@ public class IdHelperService implements IIdHelperService {
* Pre-cache a PID-to-Resource-ID mapping for later retrieval by {@link #translatePidsToForcedIds(Set)} and related methods
*/
@Override
public void addResolvedPidToForcedId(ResourcePersistentId theResourcePersistentId, @Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, @Nullable String theForcedId, @Nullable Date theDeletedAt) {
public void addResolvedPidToForcedId(JpaPid theJpaPid, @Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, @Nullable String theForcedId, @Nullable Date theDeletedAt) {
if (theForcedId != null) {
if (theResourcePersistentId.getAssociatedResourceId() == null) {
populateAssociatedResourceId(theResourceType, theForcedId, theResourcePersistentId);
if (theJpaPid.getAssociatedResourceId() == null) {
populateAssociatedResourceId(theResourceType, theForcedId, theJpaPid);
}
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.PID_TO_FORCED_ID, theResourcePersistentId.getIdAsLong(), Optional.of(theResourceType + "/" + theForcedId));
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.PID_TO_FORCED_ID, theJpaPid.getId(), Optional.of(theResourceType + "/" + theForcedId));
String key = toForcedIdToPidKey(theRequestPartitionId, theResourceType, theForcedId);
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key, theResourcePersistentId);
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key, theJpaPid);
} else {
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.PID_TO_FORCED_ID, theResourcePersistentId.getIdAsLong(), Optional.empty());
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.PID_TO_FORCED_ID, theJpaPid.getId(), Optional.empty());
}
if (!myDaoConfig.isDeleteEnabled()) {
ResourceLookup lookup = new ResourceLookup(theResourceType, theResourcePersistentId.getIdAsLong(), theDeletedAt);
String nextKey = theResourcePersistentId.toString();
JpaResourceLookup lookup = new JpaResourceLookup(theResourceType, theJpaPid.getId(), theDeletedAt);
String nextKey = theJpaPid.toString();
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, nextKey, lookup);
}
@ -677,47 +681,50 @@ public class IdHelperService implements IIdHelperService {
@Override
@Nonnull
public List<ResourcePersistentId> getPidsOrThrowException(@Nonnull RequestPartitionId theRequestPartitionId, List<IIdType> theIds) {
List<ResourcePersistentId> resourcePersistentIds = resolveResourcePersistentIdsWithCache(theRequestPartitionId, theIds);
public List<JpaPid> getPidsOrThrowException(@Nonnull RequestPartitionId theRequestPartitionId, List<IIdType> theIds) {
List<JpaPid> resourcePersistentIds = resolveResourcePersistentIdsWithCache(theRequestPartitionId, theIds);
return resourcePersistentIds;
}
@Override
@Nullable
public ResourcePersistentId getPidOrNull(@Nonnull RequestPartitionId theRequestPartitionId, IBaseResource theResource) {
ResourcePersistentId retVal = new ResourcePersistentId(theResource.getUserData(RESOURCE_PID));
if (retVal.getId() == null) {
public JpaPid getPidOrNull(@Nonnull RequestPartitionId theRequestPartitionId, IBaseResource theResource) {
Object resourceId = theResource.getUserData(RESOURCE_PID);
JpaPid retVal;
if (resourceId == null) {
IIdType id = theResource.getIdElement();
try {
retVal = resolveResourcePersistentIds(theRequestPartitionId, id.getResourceType(), id.getIdPart());
} catch (ResourceNotFoundException e) {
return null;
retVal = null;
}
} else {
retVal = JpaPid.fromId(Long.parseLong(resourceId.toString()));
}
return retVal;
}
@Override
@Nonnull
public ResourcePersistentId getPidOrThrowException(@Nonnull RequestPartitionId theRequestPartitionId, IIdType theId) {
public JpaPid getPidOrThrowException(@Nonnull RequestPartitionId theRequestPartitionId, IIdType theId) {
List<IIdType> ids = Collections.singletonList(theId);
List<ResourcePersistentId> resourcePersistentIds = resolveResourcePersistentIdsWithCache(theRequestPartitionId, ids);
List<JpaPid> resourcePersistentIds = resolveResourcePersistentIdsWithCache(theRequestPartitionId, ids);
return resourcePersistentIds.get(0);
}
@Override
@Nonnull
public ResourcePersistentId getPidOrThrowException(@Nonnull IAnyResource theResource) {
Object theResourcePID = theResource.getUserData(RESOURCE_PID);
public JpaPid getPidOrThrowException(@Nonnull IAnyResource theResource) {
Long theResourcePID = (Long) theResource.getUserData(RESOURCE_PID);
if (theResourcePID == null) {
throw new IllegalStateException(Msg.code(2108) + String.format("Unable to find %s in the user data for %s with ID %s", RESOURCE_PID, theResource, theResource.getId()));
}
return new ResourcePersistentId(theResourcePID);
return JpaPid.fromId(theResourcePID);
}
@Override
public IIdType resourceIdFromPidOrThrowException(ResourcePersistentId thePid, String theResourceType) {
Optional<ResourceTable> optionalResource = myResourceTableDao.findById(thePid.getIdAsLong());
public IIdType resourceIdFromPidOrThrowException(JpaPid thePid, String theResourceType) {
Optional<ResourceTable> optionalResource = myResourceTableDao.findById(thePid.getId());
if (!optionalResource.isPresent()) {
throw new ResourceNotFoundException(Msg.code(2124) + "Requested resource not found");
}
@ -736,11 +743,21 @@ public class IdHelperService implements IIdHelperService {
* @return A Set of strings representing the FHIR IDs of the pids.
*/
@Override
public Set<String> translatePidsToFhirResourceIds(Set<ResourcePersistentId> thePids) {
public Set<String> translatePidsToFhirResourceIds(Set<JpaPid> thePids) {
assert TransactionSynchronizationManager.isSynchronizationActive();
PersistentIdToForcedIdMap pidToForcedIdMap = translatePidsToForcedIds(thePids);
return pidToForcedIdMap.getResolvedResourceIds();
}
@Override
public JpaPid newPid(Object thePid) {
return JpaPid.fromId((Long) thePid);
}
@Override
public JpaPid newPidFromStringIdAndResourceName(String thePid, String theResourceName) {
return JpaPid.fromIdAndResourceType(Long.parseLong(thePid), theResourceName);
}
}

143
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/JpaIdHelperService.java
View File

@ -1,143 +0,0 @@
package ca.uhn.fhir.jpa.dao.index;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2022 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.i18n.Msg;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.model.PersistentIdToForcedIdMap;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.support.TransactionSynchronizationManager;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.util.Collections;
import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
/**
* See {@link IJpaIdHelperService} for an explanation of this class.
*/
public class JpaIdHelperService extends IdHelperService implements IJpaIdHelperService, IIdHelperService {
@Autowired
protected IResourceTableDao myResourceTableDao;
/**
* @deprecated This method doesn't take a partition ID as input, so it is unsafe. It
* should be reworked to include the partition ID before any new use is incorporated
*/
@Override
@Deprecated
@Nonnull
public List<Long> getPidsOrThrowException(List<IIdType> theIds) {
List<ResourcePersistentId> resourcePersistentIds = super.resolveResourcePersistentIdsWithCache(RequestPartitionId.allPartitions(), theIds);
return resourcePersistentIds.stream().map(ResourcePersistentId::getIdAsLong).collect(Collectors.toList());
}
/**
* @deprecated This method doesn't take a partition ID as input, so it is unsafe. It
* should be reworked to include the partition ID before any new use is incorporated
*/
@Override
@Deprecated
@Nullable
public Long getPidOrNull(IBaseResource theResource) {
IAnyResource anyResource = (IAnyResource) theResource;
Long retVal = (Long) anyResource.getUserData(RESOURCE_PID);
if (retVal == null) {
IIdType id = theResource.getIdElement();
try {
retVal = super.resolveResourcePersistentIds(RequestPartitionId.allPartitions(), id.getResourceType(), id.getIdPart()).getIdAsLong();
} catch (ResourceNotFoundException e) {
return null;
}
}
return retVal;
}
/**
* @deprecated This method doesn't take a partition ID as input, so it is unsafe. It
* should be reworked to include the partition ID before any new use is incorporated
*/
@Override
@Deprecated
@Nonnull
public Long getPidOrThrowException(IIdType theId) {
assert TransactionSynchronizationManager.isSynchronizationActive();
List<IIdType> ids = Collections.singletonList(theId);
List<ResourcePersistentId> resourcePersistentIds = super.resolveResourcePersistentIdsWithCache(RequestPartitionId.allPartitions(), ids);
return resourcePersistentIds.get(0).getIdAsLong();
}
@Override
@Nonnull
public ResourcePersistentId getPidOrThrowException(@Nonnull IAnyResource theResource) {
Long retVal = (Long) theResource.getUserData(RESOURCE_PID);
if (retVal == null) {
throw new IllegalStateException(Msg.code(1102) + String.format("Unable to find %s in the user data for %s with ID %s", RESOURCE_PID, theResource, theResource.getId())
);
}
return new ResourcePersistentId(retVal);
}
@Override
public IIdType resourceIdFromPidOrThrowException(Long thePid) {
Optional<ResourceTable> optionalResource = myResourceTableDao.findById(thePid);
if (!optionalResource.isPresent()) {
throw new ResourceNotFoundException(Msg.code(1103) + "Requested resource not found");
}
return optionalResource.get().getIdDt().toVersionless();
}
/**
* 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:
* <p>
* [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.
*/
@Override
public Set<String> translatePidsToFhirResourceIds(Set<ResourcePersistentId> thePids) {
assert TransactionSynchronizationManager.isSynchronizationActive();
PersistentIdToForcedIdMap pidToForcedIdMap = super.translatePidsToForcedIds(thePids);
return pidToForcedIdMap.getResolvedResourceIds();
}
}

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java
View File

@ -34,6 +34,7 @@ import ca.uhn.fhir.jpa.dao.MatchResourceUrlService;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedComboStringUniqueDao;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedComboStringUnique;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedComboTokenNonUnique;
@ -46,7 +47,6 @@ import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
@ -88,19 +88,19 @@ public class SearchParamWithInlineReferencesExtractor {
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
protected EntityManager myEntityManager;
@Autowired
private MatchResourceUrlService myMatchResourceUrlService;
private MatchResourceUrlService<JpaPid> myMatchResourceUrlService;
@Autowired
private DaoConfig myDaoConfig;
@Autowired
private FhirContext myContext;
@Autowired
private IIdHelperService myIdHelperService;
private IIdHelperService<JpaPid> myIdHelperService;
@Autowired
private ISearchParamRegistry mySearchParamRegistry;
@Autowired
private SearchParamExtractorService mySearchParamExtractorService;
@Autowired
private DaoResourceLinkResolver myDaoResourceLinkResolver;
private DaoResourceLinkResolver<JpaPid> myDaoResourceLinkResolver;
@Autowired
private DaoSearchParamSynchronizer myDaoSearchParamSynchronizer;
@Autowired
@ -350,14 +350,14 @@ public class SearchParamWithInlineReferencesExtractor {
Class<? extends IBaseResource> matchResourceType = matchResourceDef.getImplementingClass();
//Attempt to find the target reference before creating a placeholder
Set<ResourcePersistentId> matches = myMatchResourceUrlService.processMatchUrl(nextIdText, matchResourceType, theTransactionDetails, theRequest);
Set<JpaPid> matches = myMatchResourceUrlService.processMatchUrl(nextIdText, matchResourceType, theTransactionDetails, theRequest);
ResourcePersistentId match;
JpaPid match;
if (matches.isEmpty()) {
Optional<IBasePersistedResource> placeholderOpt = myDaoResourceLinkResolver.createPlaceholderTargetIfConfiguredToDoSo(matchResourceType, nextRef, null, theRequest, theTransactionDetails);
if (placeholderOpt.isPresent()) {
match = placeholderOpt.get().getPersistentId();
match = (JpaPid) placeholderOpt.get().getPersistentId();
match.setAssociatedResourceId(placeholderOpt.get().getIdDt());
theTransactionDetails.addResolvedMatchUrl(nextIdText, match);
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.MATCH_URL, nextIdText, match);

2
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/dao/JpaMdmLinkImplFactory.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/mdm/JpaMdmLinkImplFactory.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.mdm.dao;
package ca.uhn.fhir.jpa.dao.mdm;
/*-
* #%L

81
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/mdm/MdmLinkDaoJpaImpl.java
View File

@ -25,13 +25,13 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.dao.data.IMdmLinkJpaRepository;
import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.mdm.api.IMdmLink;
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.dao.IMdmLinkDao;
import ca.uhn.fhir.mdm.model.MdmPidTuple;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.collections4.ListUtils;
@ -56,81 +56,80 @@ import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
public class MdmLinkDaoJpaImpl implements IMdmLinkDao<MdmLink> {
public class MdmLinkDaoJpaImpl implements IMdmLinkDao<JpaPid, MdmLink> {
@Autowired
IMdmLinkJpaRepository myMdmLinkDao;
@Autowired
protected EntityManager myEntityManager;
@Autowired
private IIdHelperService myIdHelperService;
private IIdHelperService<JpaPid> myIdHelperService;
@Override
public int deleteWithAnyReferenceToPid(ResourcePersistentId thePid) {
return myMdmLinkDao.deleteWithAnyReferenceToPid(thePid.getIdAsLong());
public int deleteWithAnyReferenceToPid(JpaPid thePid) {
return myMdmLinkDao.deleteWithAnyReferenceToPid(thePid.getId());
}
@Override
public int deleteWithAnyReferenceToPidAndMatchResultNot(ResourcePersistentId thePid, MdmMatchResultEnum theMatchResult) {
return myMdmLinkDao.deleteWithAnyReferenceToPidAndMatchResultNot(thePid.getIdAsLong(), theMatchResult);
public int deleteWithAnyReferenceToPidAndMatchResultNot(JpaPid thePid, MdmMatchResultEnum theMatchResult) {
return myMdmLinkDao.deleteWithAnyReferenceToPidAndMatchResultNot(thePid.getId(), theMatchResult);
}
@Override
public List<MdmPidTuple> expandPidsFromGroupPidGivenMatchResult(ResourcePersistentId theGroupPid, MdmMatchResultEnum theMdmMatchResultEnum) {
return myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult(theGroupPid.getIdAsLong(), theMdmMatchResultEnum)
public List<MdmPidTuple<JpaPid>> expandPidsFromGroupPidGivenMatchResult(JpaPid theGroupPid, MdmMatchResultEnum theMdmMatchResultEnum) {
return myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult((theGroupPid).getId(), theMdmMatchResultEnum)
.stream()
.map( theMdmPidTuple -> new MdmPidTuple()
.setSourcePid(new ResourcePersistentId(theMdmPidTuple.getSourcePid()))
.setGoldenPid(new ResourcePersistentId(theMdmPidTuple.getGoldenPid())))
.map(this::daoTupleToMdmTuple)
.collect(Collectors.toList());
}
private MdmPidTuple<JpaPid> daoTupleToMdmTuple(IMdmLinkJpaRepository.MdmPidTuple theMdmPidTuple) {
return MdmPidTuple.fromGoldenAndSource(JpaPid.fromId(theMdmPidTuple.getGoldenPid()), JpaPid.fromId(theMdmPidTuple.getSourcePid()));
}
@Override
public List<MdmPidTuple<JpaPid>> expandPidsBySourcePidAndMatchResult(JpaPid theSourcePid, MdmMatchResultEnum theMdmMatchResultEnum) {
return myMdmLinkDao.expandPidsBySourcePidAndMatchResult((theSourcePid).getId(), theMdmMatchResultEnum)
.stream()
.map(this::daoTupleToMdmTuple)
.collect(Collectors.toList());
}
@Override
public List<MdmPidTuple> expandPidsBySourcePidAndMatchResult(ResourcePersistentId theSourcePid, MdmMatchResultEnum theMdmMatchResultEnum) {
return myMdmLinkDao.expandPidsBySourcePidAndMatchResult(theSourcePid.getIdAsLong(), theMdmMatchResultEnum)
public List<MdmPidTuple<JpaPid>> expandPidsByGoldenResourcePidAndMatchResult(JpaPid theSourcePid, MdmMatchResultEnum theMdmMatchResultEnum) {
return myMdmLinkDao.expandPidsByGoldenResourcePidAndMatchResult((theSourcePid).getId(), theMdmMatchResultEnum)
.stream()
.map( theMdmPidTuple -> new MdmPidTuple()
.setSourcePid(new ResourcePersistentId(theMdmPidTuple.getSourcePid()))
.setGoldenPid(new ResourcePersistentId(theMdmPidTuple.getGoldenPid())))
.map(this::daoTupleToMdmTuple)
.collect(Collectors.toList());
}
@Override
public List<MdmPidTuple> expandPidsByGoldenResourcePidAndMatchResult(ResourcePersistentId theSourcePid, MdmMatchResultEnum theMdmMatchResultEnum) {
return myMdmLinkDao.expandPidsByGoldenResourcePidAndMatchResult(theSourcePid.getIdAsLong(), theMdmMatchResultEnum)
.stream()
.map( theMdmPidTuple -> new MdmPidTuple()
.setSourcePid(new ResourcePersistentId(theMdmPidTuple.getSourcePid()))
.setGoldenPid(new ResourcePersistentId(theMdmPidTuple.getGoldenPid())))
.collect(Collectors.toList());
}
@Override
public List<ResourcePersistentId> findPidByResourceNameAndThreshold(String theResourceName, Date theHighThreshold, Pageable thePageable) {
public List<JpaPid> findPidByResourceNameAndThreshold(String theResourceName, Date theHighThreshold, Pageable thePageable) {
return myMdmLinkDao.findPidByResourceNameAndThreshold(theResourceName,theHighThreshold, thePageable)
.stream()
.map( theResourcePids -> new ResourcePersistentId(theResourcePids))
.map( theResourcePids -> JpaPid.fromId(theResourcePids))
.collect(Collectors.toList());
}
@Override
public List<ResourcePersistentId> findPidByResourceNameAndThresholdAndPartitionId(String theResourceName, Date theHighThreshold, List<Integer> thePartitionIds, Pageable thePageable) {
public List<JpaPid> findPidByResourceNameAndThresholdAndPartitionId(String theResourceName, Date theHighThreshold, List<Integer> thePartitionIds, Pageable thePageable) {
return myMdmLinkDao.findPidByResourceNameAndThresholdAndPartitionId(theResourceName,theHighThreshold, thePartitionIds, thePageable)
.stream()
.map( theResourcePids -> new ResourcePersistentId(theResourcePids))
.map( theResourcePids -> JpaPid.fromId(theResourcePids))
.collect(Collectors.toList());
}
@Override
public List<MdmLink> findAllById(List<ResourcePersistentId> thePids) {
List<Long> theLongPids = thePids.stream().map(theResourcePersistentId -> theResourcePersistentId.getIdAsLong()).collect(Collectors.toList());
public List<MdmLink> findAllById(List<JpaPid> thePids) {
List<Long> theLongPids = thePids.stream().map(JpaPid::getId).collect(Collectors.toList());
return myMdmLinkDao.findAllById(theLongPids);
}
@Override
public Optional<MdmLink> findById(ResourcePersistentId thePid) {
return myMdmLinkDao.findById(thePid.getIdAsLong());
public Optional<MdmLink> findById(JpaPid thePid) {
return myMdmLinkDao.findById(thePid.getId());
}
@Override
public void deleteAll(List<MdmLink> theLinks) {
myMdmLinkDao.deleteAll(theLinks);
}
@ -190,11 +189,11 @@ public class MdmLinkDaoJpaImpl implements IMdmLinkDao<MdmLink> {
List<Predicate> andPredicates = new ArrayList<>();
if (theGoldenResourceId != null) {
Predicate goldenResourcePredicate = criteriaBuilder.equal(from.get("myGoldenResourcePid").as(Long.class), myIdHelperService.getPidOrThrowException(RequestPartitionId.allPartitions(), theGoldenResourceId).getIdAsLong());
Predicate goldenResourcePredicate = criteriaBuilder.equal(from.get("myGoldenResourcePid").as(Long.class), (myIdHelperService.getPidOrThrowException(RequestPartitionId.allPartitions(), theGoldenResourceId)).getId());
andPredicates.add(goldenResourcePredicate);
}
if (theSourceId != null) {
Predicate sourceIdPredicate = criteriaBuilder.equal(from.get("mySourcePid").as(Long.class), myIdHelperService.getPidOrThrowException(RequestPartitionId.allPartitions(), theSourceId).getIdAsLong());
Predicate sourceIdPredicate = criteriaBuilder.equal(from.get("mySourcePid").as(Long.class), (myIdHelperService.getPidOrThrowException(RequestPartitionId.allPartitions(), theSourceId)).getId());
andPredicates.add(sourceIdPredicate);
}
if (theMatchResult != null) {
@ -226,13 +225,13 @@ public class MdmLinkDaoJpaImpl implements IMdmLinkDao<MdmLink> {
}
@Override
public Optional<? extends IMdmLink> findBySourcePidAndMatchResult(ResourcePersistentId theSourcePid, MdmMatchResultEnum theMatch) {
return myMdmLinkDao.findBySourcePidAndMatchResult(theSourcePid.getIdAsLong(), theMatch);
public Optional<MdmLink> findBySourcePidAndMatchResult(JpaPid theSourcePid, MdmMatchResultEnum theMatch) {
return myMdmLinkDao.findBySourcePidAndMatchResult((theSourcePid).getId(), theMatch);
}
@Override
public void deleteLinksWithAnyReferenceToPids(List<ResourcePersistentId> theResourcePersistentIds) {
List<Long> goldenResourcePids = theResourcePersistentIds.stream().map(ResourcePersistentId::getIdAsLong).collect(Collectors.toList());
public void deleteLinksWithAnyReferenceToPids(List<JpaPid> theResourcePersistentIds) {
List<Long> goldenResourcePids = theResourcePersistentIds.stream().map(JpaPid::getId).collect(Collectors.toList());
// Split into chunks of 500 so older versions of Oracle don't run into issues (500 = 1000 / 2 since the dao
// method uses the list twice in the sql predicate)
List<List<Long>> chunks = ListUtils.partition(goldenResourcePids, 500);

19
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/batch2/DeleteExpungeSqlBuilder.java
View File

@ -26,9 +26,8 @@ import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.dao.data.IResourceLinkDao;
import ca.uhn.fhir.jpa.dao.expunge.ResourceForeignKey;
import ca.uhn.fhir.jpa.dao.expunge.ResourceTableFKProvider;
import ca.uhn.fhir.jpa.dao.index.IJpaIdHelperService;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -58,8 +57,8 @@ public class DeleteExpungeSqlBuilder {
@Nonnull
List<String> convertPidsToDeleteExpungeSql(List<ResourcePersistentId> thePersistentIds) {
List<Long> pids = ResourcePersistentId.toLongList(thePersistentIds);
List<String> convertPidsToDeleteExpungeSql(List<JpaPid> theJpaPids) {
List<Long> pids = JpaPid.toLongList(theJpaPids);
validateOkToDeleteAndExpunge(pids);
@ -84,7 +83,7 @@ public class DeleteExpungeSqlBuilder {
return;
}
List<ResourcePersistentId> targetPidsAsResourceIds = ResourcePersistentId.fromLongList(thePids);
List<JpaPid> targetPidsAsResourceIds = JpaPid.fromLongList(thePids);
List<ResourceLink> conflictResourceLinks = Collections.synchronizedList(new ArrayList<>());
findResourceLinksWithTargetPidIn(targetPidsAsResourceIds, targetPidsAsResourceIds, conflictResourceLinks);
@ -97,16 +96,16 @@ public class DeleteExpungeSqlBuilder {
//NB-GGG: We previously instantiated these ID values from firstConflict.getSourceResource().getIdDt(), but in a situation where we
//actually had to run delete conflict checks in multiple partitions, the executor service starts its own sessions on a per thread basis, and by the time
//we arrive here, those sessions are closed. So instead, we resolve them from PIDs, which are eagerly loaded.
String sourceResourceId = myIdHelper.resourceIdFromPidOrThrowException(new ResourcePersistentId(firstConflict.getSourceResourcePid()), firstConflict.getSourceResourceType()).toVersionless().getValue();
String targetResourceId = myIdHelper.resourceIdFromPidOrThrowException(new ResourcePersistentId(firstConflict.getTargetResourcePid()), firstConflict.getTargetResourceType()).toVersionless().getValue();
String sourceResourceId = myIdHelper.resourceIdFromPidOrThrowException(JpaPid.fromId(firstConflict.getSourceResourcePid()), firstConflict.getSourceResourceType()).toVersionless().getValue();
String targetResourceId = myIdHelper.resourceIdFromPidOrThrowException(JpaPid.fromId(firstConflict.getTargetResourcePid()), firstConflict.getTargetResourceType()).toVersionless().getValue();
throw new InvalidRequestException(Msg.code(822) + "DELETE with _expunge=true failed. Unable to delete " +
targetResourceId + " because " + sourceResourceId + " refers to it via the path " + firstConflict.getSourcePath());
}
public void findResourceLinksWithTargetPidIn(List<ResourcePersistentId> theAllTargetPids, List<ResourcePersistentId> theSomeTargetPids, List<ResourceLink> theConflictResourceLinks) {
List<Long> allTargetPidsAsLongs = ResourcePersistentId.toLongList(theAllTargetPids);
List<Long> someTargetPidsAsLongs = ResourcePersistentId.toLongList(theSomeTargetPids);
public void findResourceLinksWithTargetPidIn(List<JpaPid> theAllTargetPids, List<JpaPid> theSomeTargetPids, List<ResourceLink> theConflictResourceLinks) {
List<Long> allTargetPidsAsLongs = JpaPid.toLongList(theAllTargetPids);
List<Long> someTargetPidsAsLongs = JpaPid.toLongList(theSomeTargetPids);
// We only need to find one conflict, so if we found one already in an earlier partition run, we can skip the rest of the searches
if (theConflictResourceLinks.isEmpty()) {
List<ResourceLink> conflictResourceLinks = myResourceLinkDao.findWithTargetPidIn(someTargetPidsAsLongs).stream()

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/batch2/DeleteExpungeSvcImpl.java
View File

@ -22,8 +22,8 @@ package ca.uhn.fhir.jpa.delete.batch2;
import ca.uhn.fhir.jpa.api.svc.IDeleteExpungeSvc;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
@ -49,8 +49,8 @@ public class DeleteExpungeSvcImpl implements IDeleteExpungeSvc {
}
@Override
public void deleteExpunge(List<ResourcePersistentId> thePersistentIds) {
List<String> sqlList = myDeleteExpungeSqlBuilder.convertPidsToDeleteExpungeSql(thePersistentIds);
public void deleteExpunge(List<JpaPid> theJpaPids) {
List<String> sqlList = myDeleteExpungeSqlBuilder.convertPidsToDeleteExpungeSql(theJpaPids);
ourLog.debug("Executing {} delete expunge sql commands", sqlList.size());
long totalDeleted = 0;
@ -60,7 +60,7 @@ public class DeleteExpungeSvcImpl implements IDeleteExpungeSvc {
}
ourLog.info("{} records deleted", totalDeleted);
clearHibernateSearchIndex(thePersistentIds);
clearHibernateSearchIndex(theJpaPids);
// TODO KHS instead of logging progress, produce result chunks that get aggregated into a delete expunge report
}
@ -69,9 +69,9 @@ public class DeleteExpungeSvcImpl implements IDeleteExpungeSvc {
* If we are running with HS enabled, the expunge operation will cause dangling documents because Hibernate Search is not aware of custom SQL queries that delete resources.
* This method clears the Hibernate Search index for the given resources.
*/
private void clearHibernateSearchIndex(List<ResourcePersistentId> thePersistentIds) {
private void clearHibernateSearchIndex(List<JpaPid> thePersistentIds) {
if (myFullTextSearchSvc != null) {
List<Object> objectIds = thePersistentIds.stream().map(ResourcePersistentId::getIdAsLong).collect(Collectors.toList());
List<Object> objectIds = thePersistentIds.stream().map(JpaPid::getId).collect(Collectors.toList());
myFullTextSearchSvc.deleteIndexedDocumentsByTypeAndId(ResourceTable.class, objectIds);
ourLog.info("Cleared Hibernate Search indexes.");
}

35
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/MdmLink.java
View File

@ -20,12 +20,12 @@ package ca.uhn.fhir.jpa.entity;
* #L%
*/
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.BasePartitionable;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.mdm.api.IMdmLink;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.apache.commons.lang3.builder.ToStringBuilder;
import javax.persistence.Column;
@ -57,7 +57,7 @@ import java.util.Date;
}, indexes = {
@Index(name = "IDX_EMPI_MATCH_TGT_VER", columnList = "MATCH_RESULT, TARGET_PID, VERSION")
})
public class MdmLink extends BasePartitionable implements IMdmLink {
public class MdmLink extends BasePartitionable implements IMdmLink<JpaPid> {
public static final int VERSION_LENGTH = 16;
private static final int MATCH_RESULT_LENGTH = 16;
private static final int LINK_SOURCE_LENGTH = 16;
@ -139,37 +139,38 @@ public class MdmLink extends BasePartitionable implements IMdmLink {
private String myMdmSourceType;
@Override
public ResourcePersistentId getId() {
return new ResourcePersistentId(myId);
public JpaPid getId() {
return JpaPid.fromId(myId);
}
@Override
public MdmLink setId(ResourcePersistentId theId) {
myId = theId.getIdAsLong();
public MdmLink setId(JpaPid theId) {
myId = theId.getId();
return this;
}
@Override
public ResourcePersistentId getGoldenResourcePersistenceId() {
return new ResourcePersistentId(myGoldenResourcePid);
public JpaPid getGoldenResourcePersistenceId() {
return JpaPid.fromId(myGoldenResourcePid);
}
@Override
public IMdmLink setGoldenResourcePersistenceId(ResourcePersistentId theGoldenResourcePid) {
setPersonPid(theGoldenResourcePid.getIdAsLong());
public IMdmLink setGoldenResourcePersistenceId(JpaPid theGoldenResourcePid) {
Long longPid = theGoldenResourcePid.getId();
setPersonPid(longPid);
myGoldenResourcePid = theGoldenResourcePid.getIdAsLong();
myGoldenResourcePid = longPid;
return this;
}
@Override
public ResourcePersistentId getSourcePersistenceId() {
return new ResourcePersistentId(mySourcePid);
public JpaPid getSourcePersistenceId() {
return JpaPid.fromId(mySourcePid);
}
@Override
public IMdmLink setSourcePersistenceId(ResourcePersistentId theSourcePid) {
mySourcePid = theSourcePid.getIdAsLong();
public IMdmLink setSourcePersistenceId(JpaPid theSourcePid) {
mySourcePid = theSourcePid.getId();
return this;
}
@ -202,7 +203,7 @@ public class MdmLink extends BasePartitionable implements IMdmLink {
}
/**
* @deprecated Use {@link #setGoldenResourcePersistenceId(ResourcePersistentId)} instead
* @deprecated Use {@link #setGoldenResourcePersistenceId(JpaPid)} instead
*/
@Deprecated
public MdmLink setGoldenResourcePid(Long theGoldenResourcePid) {
@ -228,7 +229,7 @@ public class MdmLink extends BasePartitionable implements IMdmLink {
}
/**
* @deprecated Use {@link #setSourcePersistenceId(ResourcePersistentId)} instead
* @deprecated Use {@link #setSourcePersistenceId(JpaPid)} instead
*/
@Deprecated
public MdmLink setSourcePid(Long theSourcePid) {

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/JpaPreResourceAccessDetails.java
View File

@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.interceptor;
*/
import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
import ca.uhn.fhir.util.ICallable;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -37,12 +37,12 @@ import java.util.List;
@NotThreadSafe
public class JpaPreResourceAccessDetails implements IPreResourceAccessDetails {
private final List<ResourcePersistentId> myResourcePids;
private final List<JpaPid> myResourcePids;
private final boolean[] myBlocked;
private final ICallable<ISearchBuilder> mySearchBuilderSupplier;
private List<IBaseResource> myResources;
public JpaPreResourceAccessDetails(List<ResourcePersistentId> theResourcePids, ICallable<ISearchBuilder> theSearchBuilderSupplier) {
public JpaPreResourceAccessDetails(List<JpaPid> theResourcePids, ICallable<ISearchBuilder> theSearchBuilderSupplier) {
myResourcePids = theResourcePids;
myBlocked = new boolean[myResourcePids.size()];
mySearchBuilderSupplier = theSearchBuilderSupplier;

10
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/cross/ResourceLookup.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/model/cross/JpaResourceLookup.java
View File

@ -20,16 +20,16 @@ package ca.uhn.fhir.jpa.model.cross;
* #L%
*/
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import java.util.Date;
public class ResourceLookup implements IResourceLookup {
public class JpaResourceLookup implements IResourceLookup {
private final String myResourceType;
private final Long myResourcePid;
private final Date myDeletedAt;
public ResourceLookup(String theResourceType, Long theResourcePid, Date theDeletedAt) {
public JpaResourceLookup(String theResourceType, Long theResourcePid, Date theDeletedAt) {
myResourceType = theResourceType;
myResourcePid = theResourcePid;
myDeletedAt = theDeletedAt;
@ -46,7 +46,7 @@ public class ResourceLookup implements IResourceLookup {
}
@Override
public ResourcePersistentId getPersistentId() {
return new ResourcePersistentId(myResourcePid);
public JpaPid getPersistentId() {
return JpaPid.fromId(myResourcePid);
}
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/JpaPackageCache.java
View File

@ -34,6 +34,7 @@ import ca.uhn.fhir.jpa.dao.data.INpmPackageDao;
import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionResourceDao;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.NpmPackageEntity;
import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionEntity;
import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionResourceEntity;
@ -42,7 +43,6 @@ import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
@ -72,6 +72,7 @@ import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Slice;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nonnull;
@ -85,7 +86,6 @@ import javax.persistence.criteria.Join;
import javax.persistence.criteria.JoinType;
import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
import org.springframework.transaction.annotation.Transactional;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
@ -182,7 +182,7 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
private IHapiPackageCacheManager.PackageContents loadPackageContents(NpmPackageVersionEntity thePackageVersion) {
IFhirResourceDao<? extends IBaseBinary> binaryDao = getBinaryDao();
IBaseBinary binary = binaryDao.readByPid(new ResourcePersistentId(thePackageVersion.getPackageBinary().getId()));
IBaseBinary binary = binaryDao.readByPid(JpaPid.fromId(thePackageVersion.getPackageBinary().getId()));
try {
byte[] content = fetchBlobFromBinary(binary);
PackageContents retVal = new PackageContents()
@ -529,7 +529,7 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
private IBaseResource loadPackageEntity(NpmPackageVersionResourceEntity contents) {
try {
ResourcePersistentId binaryPid = new ResourcePersistentId(contents.getResourceBinary().getId());
JpaPid binaryPid = JpaPid.fromId(contents.getResourceBinary().getId());
IBaseBinary binary = getBinaryDao().readByPid(binaryPid);
byte[] resourceContentsBytes= fetchBlobFromBinary(binary);
String resourceContents = new String(resourceContentsBytes, StandardCharsets.UTF_8);

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/Batch2DaoSvcImpl.java
View File

@ -31,13 +31,14 @@ import ca.uhn.fhir.jpa.api.pid.IResourcePidList;
import ca.uhn.fhir.jpa.api.pid.MixedResourcePidList;
import ca.uhn.fhir.jpa.api.svc.IBatch2DaoSvc;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.util.DateRangeUtil;
import org.springframework.beans.factory.annotation.Autowired;
@ -95,7 +96,7 @@ public class Batch2DaoSvcImpl implements IBatch2DaoSvc {
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(resourceType);
SystemRequestDetails request = new SystemRequestDetails();
request.setRequestPartitionId(theRequestPartitionId);
List<ResourcePersistentId> ids = dao.searchForIds(searchParamMap, request);
List<IResourcePersistentId> ids = dao.searchForIds(searchParamMap, request);
Date lastDate = null;
if (ids.size() > 0) {
@ -122,9 +123,9 @@ public class Batch2DaoSvcImpl implements IBatch2DaoSvc {
return new EmptyResourcePidList();
}
List<ResourcePersistentId> ids = content
List<IResourcePersistentId> ids = content
.stream()
.map(t -> new ResourcePersistentId(t[0]))
.map(t -> JpaPid.fromId((Long) t[0]))
.collect(Collectors.toList());
List<String> types = content

29
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProvider.java
View File

@ -33,10 +33,10 @@ import ca.uhn.fhir.jpa.dao.HistoryBuilder;
import ca.uhn.fhir.jpa.dao.HistoryBuilderFactory;
import ca.uhn.fhir.jpa.dao.IJpaStorageResourceParser;
import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.dao.JpaStorageResourceParser;
import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.partition.RequestPartitionHelperSvc;
@ -51,7 +51,6 @@ import ca.uhn.fhir.rest.api.server.IPreResourceShowDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.SimplePreResourceAccessDetails;
import ca.uhn.fhir.rest.api.server.SimplePreResourceShowDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.interceptor.ServerInterceptorUtil;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
@ -91,7 +90,7 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
@Autowired
private IInterceptorBroadcaster myInterceptorBroadcaster;
@Autowired
private SearchBuilderFactory mySearchBuilderFactory;
private SearchBuilderFactory<JpaPid> mySearchBuilderFactory;
@Autowired
private HistoryBuilderFactory myHistoryBuilderFactory;
@Autowired
@ -99,7 +98,7 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
@Autowired
private FhirContext myContext;
@Autowired
private ISearchCoordinatorSvc mySearchCoordinatorSvc;
private ISearchCoordinatorSvc<JpaPid> mySearchCoordinatorSvc;
@Autowired
private ISearchCacheSvc mySearchCacheSvc;
@Autowired
@ -136,18 +135,6 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
mySearchEntity = theSearch;
}
/**
* When HAPI FHIR server is running "for real", a new
* instance of the bundle provider is created to serve
* every HTTP request, so it's ok for us to keep
* state in here and expect that it will go away. But
* in unit tests we keep this object around for longer
* sometimes.
*/
public void clearCachedDataForUnitTest() {
mySearchEntity = null;
}
/**
* Perform a history search
*/
@ -225,7 +212,7 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
final ISearchBuilder sb = mySearchBuilderFactory.newSearchBuilder(dao, resourceName, resourceType);
final List<ResourcePersistentId> pidsSubList = mySearchCoordinatorSvc.getResources(myUuid, theFromIndex, theToIndex, myRequest);
final List<JpaPid> pidsSubList = mySearchCoordinatorSvc.getResources(myUuid, theFromIndex, theToIndex, myRequest);
TransactionTemplate template = new TransactionTemplate(myTxManager);
template.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
@ -413,14 +400,14 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
// Note: Leave as protected, HSPC depends on this
@SuppressWarnings("WeakerAccess")
protected List<IBaseResource> toResourceList(ISearchBuilder theSearchBuilder, List<ResourcePersistentId> thePids) {
protected List<IBaseResource> toResourceList(ISearchBuilder theSearchBuilder, List<JpaPid> thePids) {
List<ResourcePersistentId> includedPidList = new ArrayList<>();
List<JpaPid> includedPidList = new ArrayList<>();
if (mySearchEntity.getSearchType() == SearchTypeEnum.SEARCH) {
Integer maxIncludes = myDaoConfig.getMaximumIncludesToLoadPerPage();
// Load _revincludes
Set<ResourcePersistentId> includedPids = theSearchBuilder.loadIncludes(myContext, myEntityManager, thePids, mySearchEntity.toRevIncludesList(), true, mySearchEntity.getLastUpdated(), myUuid, myRequest, maxIncludes);
Set<JpaPid> includedPids = theSearchBuilder.loadIncludes(myContext, myEntityManager, thePids, mySearchEntity.toRevIncludesList(), true, mySearchEntity.getLastUpdated(), myUuid, myRequest, maxIncludes);
if (maxIncludes != null) {
maxIncludes -= includedPids.size();
}
@ -428,7 +415,7 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
includedPidList.addAll(includedPids);
// Load _includes
Set<ResourcePersistentId> revIncludedPids = theSearchBuilder.loadIncludes(myContext, myEntityManager, thePids, mySearchEntity.toIncludesList(), false, mySearchEntity.getLastUpdated(), myUuid, myRequest, maxIncludes);
Set<JpaPid> revIncludedPids = theSearchBuilder.loadIncludes(myContext, myEntityManager, thePids, mySearchEntity.toIncludesList(), false, mySearchEntity.getLastUpdated(), myUuid, myRequest, maxIncludes);
thePids.addAll(revIncludedPids);
includedPidList.addAll(revIncludedPids);

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaSearchFirstPageBundleProvider.java
View File

@ -22,10 +22,10 @@ package ca.uhn.fhir.jpa.search;
import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.util.QueryParameterUtils;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import ca.uhn.fhir.jpa.search.builder.tasks.SearchTask;
import ca.uhn.fhir.jpa.util.QueryParameterUtils;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
@ -67,7 +67,7 @@ public class PersistedJpaSearchFirstPageBundleProvider extends PersistedJpaBundl
mySearchTask.awaitInitialSync();
ourLog.trace("Fetching search resource PIDs from task: {}", mySearchTask.getClass());
final List<ResourcePersistentId> pids = mySearchTask.getResourcePids(theFromIndex, theToIndex);
final List<JpaPid> pids = mySearchTask.getResourcePids(theFromIndex, theToIndex);
ourLog.trace("Done fetching search resource PIDs");
TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);

26
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
View File

@ -37,6 +37,7 @@ import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
import ca.uhn.fhir.jpa.dao.search.ResourceNotFoundInIndexException;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.search.builder.StorageInterceptorHooksFacade;
@ -55,7 +56,6 @@ import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
@ -96,7 +96,7 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@Component("mySearchCoordinatorSvc")
public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc<JpaPid> {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchCoordinatorSvcImpl.class);
@ -107,7 +107,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
private final ISearchCacheSvc mySearchCacheSvc;
private final ISearchResultCacheSvc mySearchResultCacheSvc;
private final DaoRegistry myDaoRegistry;
private final SearchBuilderFactory mySearchBuilderFactory;
private final SearchBuilderFactory<JpaPid> mySearchBuilderFactory;
private final ISynchronousSearchSvc mySynchronousSearchSvc;
private final PersistedJpaBundleProviderFactory myPersistedJpaBundleProviderFactory;
private final IRequestPartitionHelperSvc myRequestPartitionHelperService;
@ -124,9 +124,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
private final ConcurrentHashMap<String, SearchTask> myIdToSearchTask = new ConcurrentHashMap<>();
private final Consumer<String> myOnRemoveSearchTask = (theId) -> {
myIdToSearchTask.remove(theId);
};
private final Consumer<String> myOnRemoveSearchTask = (theId) -> myIdToSearchTask.remove(theId);
private final StorageInterceptorHooksFacade myStorageInterceptorHooks;
@ -141,7 +139,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
ISearchCacheSvc theSearchCacheSvc,
ISearchResultCacheSvc theSearchResultCacheSvc,
DaoRegistry theDaoRegistry,
SearchBuilderFactory theSearchBuilderFactory,
SearchBuilderFactory<JpaPid> theSearchBuilderFactory,
ISynchronousSearchSvc theSynchronousSearchSvc,
PersistedJpaBundleProviderFactory thePersistedJpaBundleProviderFactory,
IRequestPartitionHelperSvc theRequestPartitionHelperService,
@ -211,7 +209,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
*/
@Override
@Transactional(propagation = Propagation.NEVER)
public List<ResourcePersistentId> getResources(final String theUuid, int theFrom, int theTo, @Nullable RequestDetails theRequestDetails) {
public List<JpaPid> getResources(final String theUuid, int theFrom, int theTo, @Nullable RequestDetails theRequestDetails) {
TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
@ -231,7 +229,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
if (myNeverUseLocalSearchForUnitTests == false) {
if (searchTask != null) {
ourLog.trace("Local search found");
List<ResourcePersistentId> resourcePids = searchTask.getResourcePids(theFrom, theTo);
List<JpaPid> resourcePids = searchTask.getResourcePids(theFrom, theTo);
ourLog.trace("Local search returned {} pids, wanted {}-{} - Search: {}", resourcePids.size(), theFrom, theTo, searchTask.getSearch());
/*
@ -301,7 +299,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
ourLog.trace("Finished looping");
List<ResourcePersistentId> pids = mySearchResultCacheSvc.fetchResultPids(search, theFrom, theTo);
List<JpaPid> pids = mySearchResultCacheSvc.fetchResultPids(search, theFrom, theTo);
if (pids == null) {
throw myExceptionSvc.newUnknownSearchException(theUuid);
}
@ -326,7 +324,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
validateSearch(theParams);
Class<? extends IBaseResource> resourceTypeClass = myContext.getResourceDefinition(theResourceType).getImplementingClass();
final ISearchBuilder sb = mySearchBuilderFactory.newSearchBuilder(theCallingDao, theResourceType, resourceTypeClass);
final ISearchBuilder<JpaPid> sb = mySearchBuilderFactory.newSearchBuilder(theCallingDao, theResourceType, resourceTypeClass);
sb.setFetchSize(mySyncSize);
final Integer loadSynchronousUpTo = getLoadSynchronousUpToOrNull(theCacheControlDirective);
@ -359,7 +357,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
* instead
*/
SearchCacheStatusEnum cacheStatus = SearchCacheStatusEnum.MISS;
if (theCacheControlDirective != null && theCacheControlDirective.isNoCache() == true) {
if (theCacheControlDirective != null && theCacheControlDirective.isNoCache()) {
cacheStatus = SearchCacheStatusEnum.NOT_TRIED;
}
@ -375,7 +373,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
}
}
PersistedJpaSearchFirstPageBundleProvider retVal = submitSearch(theCallingDao, theParams, theResourceType, theRequestDetails, searchUuid, sb, queryString, theRequestPartitionId, search);
PersistedJpaSearchFirstPageBundleProvider retVal = submitSearch(theCallingDao, theParams, theResourceType, theRequestDetails, sb, theRequestPartitionId, search);
retVal.setCacheStatus(cacheStatus);
return retVal;
}
@ -463,7 +461,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
}
@Nonnull
private PersistedJpaSearchFirstPageBundleProvider submitSearch(IDao theCallingDao, SearchParameterMap theParams, String theResourceType, RequestDetails theRequestDetails, String theSearchUuid, ISearchBuilder theSb, String theQueryString, RequestPartitionId theRequestPartitionId, Search theSearch) {
private PersistedJpaSearchFirstPageBundleProvider submitSearch(IDao theCallingDao, SearchParameterMap theParams, String theResourceType, RequestDetails theRequestDetails, ISearchBuilder<JpaPid> theSb, RequestPartitionId theRequestPartitionId, Search theSearch) {
StopWatch w = new StopWatch();
SearchTaskParameters stp = new SearchTaskParameters(

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SynchronousSearchSvcImpl.java
View File

@ -33,6 +33,7 @@ import ca.uhn.fhir.jpa.dao.IResultIterator;
import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
import ca.uhn.fhir.jpa.interceptor.JpaPreResourceAccessDetails;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.IQueryParameterType;
@ -40,7 +41,6 @@ import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.SimpleBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.interceptor.ServerInterceptorUtil;
@ -104,7 +104,7 @@ public class SynchronousSearchSvcImpl implements ISynchronousSearchSvc {
return txTemplate.execute(t -> {
// Load the results synchronously
final List<ResourcePersistentId> pids = new ArrayList<>();
final List<JpaPid> pids = new ArrayList<>();
Long count = 0L;
if (wantCount) {
@ -130,7 +130,7 @@ public class SynchronousSearchSvcImpl implements ISynchronousSearchSvc {
return bundleProvider;
}
try (IResultIterator resultIter = theSb.createQuery(theParams, searchRuntimeDetails, theRequestDetails, theRequestPartitionId)) {
try (IResultIterator<JpaPid> resultIter = theSb.createQuery(theParams, searchRuntimeDetails, theRequestDetails, theRequestPartitionId)) {
while (resultIter.hasNext()) {
pids.add(resultIter.next());
if (theLoadSynchronousUpTo != null && pids.size() >= theLoadSynchronousUpTo) {
@ -170,16 +170,16 @@ public class SynchronousSearchSvcImpl implements ISynchronousSearchSvc {
// _includes
Integer maxIncludes = myDaoConfig.getMaximumIncludesToLoadPerPage();
final Set<ResourcePersistentId> includedPids = theSb.loadIncludes(myContext, myEntityManager, pids, theParams.getRevIncludes(), true, theParams.getLastUpdated(), "(synchronous)", theRequestDetails, maxIncludes);
final Set<JpaPid> includedPids = theSb.loadIncludes(myContext, myEntityManager, pids, theParams.getRevIncludes(), true, theParams.getLastUpdated(), "(synchronous)", theRequestDetails, maxIncludes);
if (maxIncludes != null) {
maxIncludes -= includedPids.size();
}
pids.addAll(includedPids);
List<ResourcePersistentId> includedPidsList = new ArrayList<>(includedPids);
List<JpaPid> includedPidsList = new ArrayList<>(includedPids);
// _revincludes
if (theParams.getEverythingMode() == null && (maxIncludes == null || maxIncludes > 0)) {
Set<ResourcePersistentId> revIncludedPids = theSb.loadIncludes(myContext, myEntityManager, pids, theParams.getIncludes(), false, theParams.getLastUpdated(), "(synchronous)", theRequestDetails, maxIncludes);
Set<JpaPid> revIncludedPids = theSb.loadIncludes(myContext, myEntityManager, pids, theParams.getIncludes(), false, theParams.getLastUpdated(), "(synchronous)", theRequestDetails, maxIncludes);
includedPids.addAll(revIncludedPids);
pids.addAll(revIncludedPids);
includedPidsList.addAll(revIncludedPids);

151
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java
View File

@ -48,6 +48,7 @@ import ca.uhn.fhir.jpa.dao.search.ResourceNotFoundInIndexException;
import ca.uhn.fhir.jpa.entity.ResourceSearchView;
import ca.uhn.fhir.jpa.interceptor.JpaPreResourceAccessDetails;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.IBaseResourceEntity;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.ResourceTag;
@ -80,7 +81,6 @@ import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.StringParam;
@ -135,7 +135,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* The SearchBuilder is responsible for actually forming the SQL query that handles
* searches for resources
*/
public class SearchBuilder implements ISearchBuilder {
public class SearchBuilder implements ISearchBuilder<JpaPid> {
/**
* See loadResourcesByPid
@ -148,7 +148,7 @@ public class SearchBuilder implements ISearchBuilder {
public static final String RESOURCE_ID_ALIAS = "resource_id";
public static final String RESOURCE_VERSION_ALIAS = "resource_version";
private static final Logger ourLog = LoggerFactory.getLogger(SearchBuilder.class);
private static final ResourcePersistentId NO_MORE = new ResourcePersistentId(-1L);
private static final JpaPid NO_MORE = JpaPid.fromId(-1L);
private static final String MY_TARGET_RESOURCE_PID = "myTargetResourcePid";
private static final String MY_SOURCE_RESOURCE_PID = "mySourceResourcePid";
private static final String MY_TARGET_RESOURCE_TYPE = "myTargetResourceType";
@ -168,18 +168,18 @@ public class SearchBuilder implements ISearchBuilder {
private final DaoRegistry myDaoRegistry;
private final IResourceSearchViewDao myResourceSearchViewDao;
private final FhirContext myContext;
private final IIdHelperService myIdHelperService;
private final IIdHelperService<JpaPid> myIdHelperService;
private final DaoConfig myDaoConfig;
private final IDao myCallingDao;
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
protected EntityManager myEntityManager;
private List<ResourcePersistentId> myAlsoIncludePids;
private List<JpaPid> myAlsoIncludePids;
private CriteriaBuilder myCriteriaBuilder;
private SearchParameterMap myParams;
private String mySearchUuid;
private int myFetchSize;
private Integer myMaxResultsToFetch;
private Set<ResourcePersistentId> myPidSet;
private Set<JpaPid> myPidSet;
private boolean myHasNextIteratorQuery = false;
private RequestPartitionId myRequestPartitionId;
@Autowired(required = false)
@ -313,7 +313,7 @@ public class SearchBuilder implements ISearchBuilder {
* @param thePidSet May be null
*/
@Override
public void setPreviouslyAddedResourcePids(@Nonnull List<ResourcePersistentId> thePidSet) {
public void setPreviouslyAddedResourcePids(@Nonnull List<JpaPid> thePidSet) {
myPidSet = new HashSet<>(thePidSet);
}
@ -351,7 +351,7 @@ public class SearchBuilder implements ISearchBuilder {
// Ugh - we have two different return types for now
ISearchQueryExecutor fulltextExecutor = null;
List<ResourcePersistentId> fulltextMatchIds = null;
List<JpaPid> fulltextMatchIds = null;
int resultCount = 0;
if (myParams.isLastN()) {
fulltextMatchIds = executeLastNAgainstIndex(theMaximumResults);
@ -441,7 +441,7 @@ public class SearchBuilder implements ISearchBuilder {
}
}
private List<ResourcePersistentId> executeLastNAgainstIndex(Integer theMaximumResults) {
private List<JpaPid> executeLastNAgainstIndex(Integer theMaximumResults) {
// Can we use our hibernate search generated index on resource to support lastN?:
if (myDaoConfig.isAdvancedHSearchIndexing()) {
if (myFulltextSearchSvc == null) {
@ -461,8 +461,8 @@ public class SearchBuilder implements ISearchBuilder {
}
}
private List<ResourcePersistentId> queryHibernateSearchForEverythingPids() {
ResourcePersistentId pid = null;
private List<JpaPid> queryHibernateSearchForEverythingPids() {
JpaPid pid = null;
if (myParams.get(IAnyResource.SP_RES_ID) != null) {
String idParamValue;
IQueryParameterType idParam = myParams.get(IAnyResource.SP_RES_ID).get(0).get(0);
@ -476,7 +476,7 @@ public class SearchBuilder implements ISearchBuilder {
pid = myIdHelperService.resolveResourcePersistentIds(myRequestPartitionId, myResourceName, idParamValue);
}
List<ResourcePersistentId> pids = myFulltextSearchSvc.everything(myResourceName, myParams, pid);
List<JpaPid> pids = myFulltextSearchSvc.everything(myResourceName, myParams, pid);
return pids;
}
@ -514,7 +514,7 @@ public class SearchBuilder implements ISearchBuilder {
// fetch our target Pids
// this will throw if an id is not found
Map<String, ResourcePersistentId> idToPid = myIdHelperService.resolveResourcePersistentIds(myRequestPartitionId,
Map<String, JpaPid> idToPid = myIdHelperService.resolveResourcePersistentIds(myRequestPartitionId,
myResourceName,
new ArrayList<>(ids));
if (myAlsoIncludePids == null) {
@ -522,9 +522,9 @@ public class SearchBuilder implements ISearchBuilder {
}
// add the pids to targetPids
for (ResourcePersistentId pid : idToPid.values()) {
for (JpaPid pid : idToPid.values()) {
myAlsoIncludePids.add(pid);
theTargetPids.add(pid.getIdAsLong());
theTargetPids.add(pid.getId());
}
}
@ -563,7 +563,7 @@ public class SearchBuilder implements ISearchBuilder {
if (myAlsoIncludePids == null) {
myAlsoIncludePids = new ArrayList<>(output.size());
}
myAlsoIncludePids.addAll(ResourcePersistentId.fromLongList(output));
myAlsoIncludePids.addAll(JpaPid.fromLongList(output));
}
@ -795,8 +795,8 @@ public class SearchBuilder implements ISearchBuilder {
RuntimeSearchParam left = compositeList.get(0);
RuntimeSearchParam right = compositeList.get(1);
createCompositeSort(theQueryStack, myResourceName, left.getParamType(), left.getName(), ascending);
createCompositeSort(theQueryStack, myResourceName, right.getParamType(), right.getName(), ascending);
createCompositeSort(theQueryStack, left.getParamType(), left.getName(), ascending);
createCompositeSort(theQueryStack, right.getParamType(), right.getName(), ascending);
break;
case SPECIAL:
@ -812,7 +812,7 @@ public class SearchBuilder implements ISearchBuilder {
}
private void createCompositeSort(QueryStack theQueryStack, String theResourceName, RestSearchParameterTypeEnum theParamType, String theParamName, boolean theAscending) {
private void createCompositeSort(QueryStack theQueryStack, RestSearchParameterTypeEnum theParamType, String theParamName, boolean theAscending) {
switch (theParamType) {
case STRING:
@ -839,20 +839,20 @@ public class SearchBuilder implements ISearchBuilder {
}
private void doLoadPids(Collection<ResourcePersistentId> thePids, Collection<ResourcePersistentId> theIncludedPids, List<IBaseResource> theResourceListToPopulate, boolean theForHistoryOperation,
Map<ResourcePersistentId, Integer> thePosition) {
private void doLoadPids(Collection<JpaPid> thePids, Collection<JpaPid> theIncludedPids, List<IBaseResource> theResourceListToPopulate, boolean theForHistoryOperation,
Map<JpaPid, Integer> thePosition) {
Map<Long, Long> resourcePidToVersion = null;
for (ResourcePersistentId next : thePids) {
for (JpaPid next : thePids) {
if (next.getVersion() != null && myModelConfig.isRespectVersionsForSearchIncludes()) {
if (resourcePidToVersion == null) {
resourcePidToVersion = new HashMap<>();
}
resourcePidToVersion.put(next.getIdAsLong(), next.getVersion());
resourcePidToVersion.put((next).getId(), next.getVersion());
}
}
List<Long> versionlessPids = ResourcePersistentId.toLongList(thePids);
List<Long> versionlessPids = JpaPid.toLongList(thePids);
if (versionlessPids.size() < getMaximumPageSize()) {
versionlessPids = normalizeIdListForLastNInClause(versionlessPids);
}
@ -870,7 +870,7 @@ public class SearchBuilder implements ISearchBuilder {
Class<? extends IBaseResource> resourceType = myContext.getResourceDefinition(next.getResourceType()).getImplementingClass();
ResourcePersistentId resourceId = new ResourcePersistentId(next.getResourceId());
JpaPid resourceId = JpaPid.fromId(next.getResourceId());
/*
* If a specific version is requested via an include, we'll replace the current version
@ -946,16 +946,16 @@ public class SearchBuilder implements ISearchBuilder {
Collection<ResourceTag> tagList = myResourceTagDao.findByResourceIds(thePidList);
//-- build the map, key = resourceId, value = list of ResourceTag
ResourcePersistentId resourceId;
JpaPid resourceId;
Collection<ResourceTag> tagCol;
for (ResourceTag tag : tagList) {
resourceId = new ResourcePersistentId(tag.getResourceId());
tagCol = tagMap.get(resourceId.getIdAsLong());
resourceId = JpaPid.fromId(tag.getResourceId());
tagCol = tagMap.get(resourceId.getId());
if (tagCol == null) {
tagCol = new ArrayList<>();
tagCol.add(tag);
tagMap.put(resourceId.getIdAsLong(), tagCol);
tagMap.put(resourceId.getId(), tagCol);
} else {
tagCol.add(tag);
}
@ -965,7 +965,7 @@ public class SearchBuilder implements ISearchBuilder {
}
@Override
public void loadResourcesByPid(Collection<ResourcePersistentId> thePids, Collection<ResourcePersistentId> theIncludedPids, List<IBaseResource> theResourceListToPopulate, boolean theForHistoryOperation, RequestDetails theDetails) {
public void loadResourcesByPid(Collection<JpaPid> thePids, Collection<JpaPid> theIncludedPids, List<IBaseResource> theResourceListToPopulate, boolean theForHistoryOperation, RequestDetails theDetails) {
if (thePids.isEmpty()) {
ourLog.debug("The include pids are empty");
// return;
@ -975,8 +975,8 @@ public class SearchBuilder implements ISearchBuilder {
// when running asserts
assert new HashSet<>(thePids).size() == thePids.size() : "PID list contains duplicates: " + thePids;
Map<ResourcePersistentId, Integer> position = new HashMap<>();
for (ResourcePersistentId next : thePids) {
Map<JpaPid, Integer> position = new HashMap<>();
for (JpaPid next : thePids) {
position.put(next, theResourceListToPopulate.size());
theResourceListToPopulate.add(null);
}
@ -994,7 +994,7 @@ public class SearchBuilder implements ISearchBuilder {
}
// We only chunk because some jdbc drivers can't handle long param lists.
new QueryChunker<ResourcePersistentId>().chunk(thePids, t -> doLoadPids(t, theIncludedPids, theResourceListToPopulate, theForHistoryOperation, position));
new QueryChunker<JpaPid>().chunk(thePids, t -> doLoadPids(t, theIncludedPids, theResourceListToPopulate, theForHistoryOperation, position));
}
/**
@ -1006,7 +1006,7 @@ public class SearchBuilder implements ISearchBuilder {
* @param thePids the pids to check for versioned references
* @return can we fetch from Hibernate Search?
*/
private boolean isLoadingFromElasticSearchSupported(Collection<ResourcePersistentId> thePids) {
private boolean isLoadingFromElasticSearchSupported(Collection<JpaPid> thePids) {
// is storage enabled?
return myDaoConfig.isStoreResourceInHSearchIndex() &&
myDaoConfig.isAdvancedHSearchIndexing() &&
@ -1016,11 +1016,11 @@ public class SearchBuilder implements ISearchBuilder {
myContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3);
}
private List<IBaseResource> loadResourcesFromElasticSearch(Collection<ResourcePersistentId> thePids) {
private List<IBaseResource> loadResourcesFromElasticSearch(Collection<JpaPid> thePids) {
// Do we use the fulltextsvc via hibernate-search to load resources or be backwards compatible with older ES only impl
// to handle lastN?
if (myDaoConfig.isAdvancedHSearchIndexing() && myDaoConfig.isStoreResourceInHSearchIndex()) {
List<Long> pidList = thePids.stream().map(ResourcePersistentId::getIdAsLong).collect(Collectors.toList());
List<Long> pidList = thePids.stream().map(pid -> (pid).getId()).collect(Collectors.toList());
List<IBaseResource> resources = myFulltextSearchSvc.getResources(pidList);
return resources;
@ -1035,10 +1035,10 @@ public class SearchBuilder implements ISearchBuilder {
/**
* THIS SHOULD RETURN HASHSET and not just Set because we add to it later
* so it can't be Collections.emptySet() or some such thing.
* The ResourcePersistentId returned will have resource type populated.
* The JpaPid returned will have resource type populated.
*/
@Override
public Set<ResourcePersistentId> loadIncludes(FhirContext theContext, EntityManager theEntityManager, Collection<ResourcePersistentId> theMatches, Collection<Include> theIncludes,
public Set<JpaPid> loadIncludes(FhirContext theContext, EntityManager theEntityManager, Collection<JpaPid> theMatches, Collection<Include> theIncludes,
boolean theReverseMode, DateRangeParam theLastUpdated, String theSearchIdOrDescription, RequestDetails theRequest, Integer theMaxCount) {
if (theMatches.size() == 0) {
return new HashSet<>();
@ -1054,9 +1054,9 @@ public class SearchBuilder implements ISearchBuilder {
findVersionFieldName = MY_TARGET_RESOURCE_VERSION;
}
List<ResourcePersistentId> nextRoundMatches = new ArrayList<>(theMatches);
HashSet<ResourcePersistentId> allAdded = new HashSet<>();
HashSet<ResourcePersistentId> original = new HashSet<>(theMatches);
List<JpaPid> nextRoundMatches = new ArrayList<>(theMatches);
HashSet<JpaPid> allAdded = new HashSet<>();
HashSet<JpaPid> original = new HashSet<>(theMatches);
ArrayList<Include> includes = new ArrayList<>(theIncludes);
int roundCounts = 0;
@ -1066,7 +1066,7 @@ public class SearchBuilder implements ISearchBuilder {
do {
roundCounts++;
HashSet<ResourcePersistentId> pidsToInclude = new HashSet<>();
HashSet<JpaPid> pidsToInclude = new HashSet<>();
for (Iterator<Include> iter = includes.iterator(); iter.hasNext(); ) {
Include nextInclude = iter.next();
@ -1112,10 +1112,10 @@ public class SearchBuilder implements ISearchBuilder {
}
String sql = sqlBuilder.toString();
List<Collection<ResourcePersistentId>> partitions = partition(nextRoundMatches, getMaximumPageSize());
for (Collection<ResourcePersistentId> nextPartition : partitions) {
List<Collection<JpaPid>> partitions = partition(nextRoundMatches, getMaximumPageSize());
for (Collection<JpaPid> nextPartition : partitions) {
TypedQuery<?> q = theEntityManager.createQuery(sql, Object[].class);
q.setParameter("target_pids", ResourcePersistentId.toLongList(nextPartition));
q.setParameter("target_pids", JpaPid.toLongList(nextPartition));
if (wantResourceType != null) {
q.setParameter("want_resource_type", wantResourceType);
}
@ -1138,8 +1138,7 @@ public class SearchBuilder implements ISearchBuilder {
}
if (resourceLink != null) {
ResourcePersistentId pid = new ResourcePersistentId(resourceLink, version);
pid.setResourceType(resourceType);
JpaPid pid = JpaPid.fromIdAndVersionAndResourceType(resourceLink, version, resourceType);
pidsToInclude.add(pid);
}
}
@ -1231,11 +1230,11 @@ public class SearchBuilder implements ISearchBuilder {
String sql = resourceIdBasedQuery + " UNION " + resourceUrlBasedQuery;
List<Collection<ResourcePersistentId>> partitions = partition(nextRoundMatches, getMaximumPageSize());
for (Collection<ResourcePersistentId> nextPartition : partitions) {
List<Collection<JpaPid>> partitions = partition(nextRoundMatches, getMaximumPageSize());
for (Collection<JpaPid> nextPartition : partitions) {
Query q = theEntityManager.createNativeQuery(sql, Tuple.class);
q.setParameter("src_path", nextPath);
q.setParameter("target_pids", ResourcePersistentId.toLongList(nextPartition));
q.setParameter("target_pids", JpaPid.toLongList(nextPartition));
if (targetResourceType != null) {
q.setParameter("target_resource_type", targetResourceType);
} else if (haveTargetTypesDefinedByParam) {
@ -1253,7 +1252,7 @@ public class SearchBuilder implements ISearchBuilder {
if (findVersionFieldName != null && result.get(RESOURCE_VERSION_ALIAS) != null) {
resourceVersion = NumberUtils.createLong(String.valueOf(result.get(RESOURCE_VERSION_ALIAS)));
}
pidsToInclude.add(new ResourcePersistentId(resourceId, resourceVersion));
pidsToInclude.add(JpaPid.fromIdAndVersion(resourceId, resourceVersion));
}
}
}
@ -1268,7 +1267,7 @@ public class SearchBuilder implements ISearchBuilder {
}
nextRoundMatches.clear();
for (ResourcePersistentId next : pidsToInclude) {
for (JpaPid next : pidsToInclude) {
if (original.contains(next) == false && allAdded.contains(next) == false) {
nextRoundMatches.add(next);
}
@ -1292,7 +1291,7 @@ public class SearchBuilder implements ISearchBuilder {
if (allAdded.size() > 0) {
if (CompositeInterceptorBroadcaster.hasHooks(Pointcut.STORAGE_PREACCESS_RESOURCES, myInterceptorBroadcaster, theRequest)) {
List<ResourcePersistentId> includedPidList = new ArrayList<>(allAdded);
List<JpaPid> includedPidList = new ArrayList<>(allAdded);
JpaPreResourceAccessDetails accessDetails = new JpaPreResourceAccessDetails(includedPidList, () -> this);
HookParams params = new HookParams()
.add(IPreResourceAccessDetails.class, accessDetails)
@ -1302,7 +1301,7 @@ public class SearchBuilder implements ISearchBuilder {
for (int i = includedPidList.size() - 1; i >= 0; i--) {
if (accessDetails.isDontReturnResourceAtIndex(i)) {
ResourcePersistentId value = includedPidList.remove(i);
JpaPid value = includedPidList.remove(i);
if (value != null) {
allAdded.remove(value);
}
@ -1314,14 +1313,14 @@ public class SearchBuilder implements ISearchBuilder {
return allAdded;
}
private List<Collection<ResourcePersistentId>> partition(Collection<ResourcePersistentId> theNextRoundMatches, int theMaxLoad) {
private List<Collection<JpaPid>> partition(Collection<JpaPid> theNextRoundMatches, int theMaxLoad) {
if (theNextRoundMatches.size() <= theMaxLoad) {
return Collections.singletonList(theNextRoundMatches);
} else {
List<Collection<ResourcePersistentId>> retVal = new ArrayList<>();
Collection<ResourcePersistentId> current = null;
for (ResourcePersistentId next : theNextRoundMatches) {
List<Collection<JpaPid>> retVal = new ArrayList<>();
Collection<JpaPid> current = null;
for (JpaPid next : theNextRoundMatches) {
if (current == null) {
current = new ArrayList<>(theMaxLoad);
retVal.add(current);
@ -1482,14 +1481,14 @@ public class SearchBuilder implements ISearchBuilder {
return myResourceName;
}
public class IncludesIterator extends BaseIterator<ResourcePersistentId> implements Iterator<ResourcePersistentId> {
public class IncludesIterator extends BaseIterator<JpaPid> implements Iterator<JpaPid> {
private final RequestDetails myRequest;
private final Set<ResourcePersistentId> myCurrentPids;
private Iterator<ResourcePersistentId> myCurrentIterator;
private ResourcePersistentId myNext;
private final Set<JpaPid> myCurrentPids;
private Iterator<JpaPid> myCurrentIterator;
private JpaPid myNext;
IncludesIterator(Set<ResourcePersistentId> thePidSet, RequestDetails theRequest) {
IncludesIterator(Set<JpaPid> thePidSet, RequestDetails theRequest) {
myCurrentPids = new HashSet<>(thePidSet);
myCurrentIterator = null;
myRequest = theRequest;
@ -1500,7 +1499,7 @@ public class SearchBuilder implements ISearchBuilder {
if (myCurrentIterator == null) {
Set<Include> includes = Collections.singleton(new Include("*", true));
Set<ResourcePersistentId> newPids = loadIncludes(myContext, myEntityManager, myCurrentPids, includes, false, getParams().getLastUpdated(), mySearchUuid, myRequest, null);
Set<JpaPid> newPids = loadIncludes(myContext, myEntityManager, myCurrentPids, includes, false, getParams().getLastUpdated(), mySearchUuid, myRequest, null);
myCurrentIterator = newPids.iterator();
}
@ -1520,16 +1519,16 @@ public class SearchBuilder implements ISearchBuilder {
}
@Override
public ResourcePersistentId next() {
public JpaPid next() {
fetchNext();
ResourcePersistentId retVal = myNext;
JpaPid retVal = myNext;
myNext = null;
return retVal;
}
}
private final class QueryIterator extends BaseIterator<ResourcePersistentId> implements IResultIterator {
private final class QueryIterator extends BaseIterator<JpaPid> implements IResultIterator<JpaPid> {
private final SearchRuntimeDetails mySearchRuntimeDetails;
private final RequestDetails myRequest;
@ -1539,7 +1538,7 @@ public class SearchBuilder implements ISearchBuilder {
private final Integer myOffset;
private boolean myFirst = true;
private IncludesIterator myIncludesIterator;
private ResourcePersistentId myNext;
private JpaPid myNext;
private ISearchQueryExecutor myResultsIterator;
private boolean myFetchIncludesForEverythingOperation;
private int mySkipCount = 0;
@ -1591,8 +1590,8 @@ public class SearchBuilder implements ISearchBuilder {
if (myNext == null) {
for (Iterator<ResourcePersistentId> myPreResultsIterator = myAlsoIncludePids.iterator(); myPreResultsIterator.hasNext(); ) {
ResourcePersistentId next = myPreResultsIterator.next();
for (Iterator<JpaPid> myPreResultsIterator = myAlsoIncludePids.iterator(); myPreResultsIterator.hasNext(); ) {
JpaPid next = myPreResultsIterator.next();
if (next != null)
if (myPidSet.add(next)) {
myNext = next;
@ -1616,7 +1615,7 @@ public class SearchBuilder implements ISearchBuilder {
}
if (nextLong != null) {
ResourcePersistentId next = new ResourcePersistentId(nextLong);
JpaPid next = JpaPid.fromId(nextLong);
if (myPidSet.add(next)) {
myNext = next;
myNonSkipCount++;
@ -1655,7 +1654,7 @@ public class SearchBuilder implements ISearchBuilder {
}
if (myIncludesIterator != null) {
while (myIncludesIterator.hasNext()) {
ResourcePersistentId next = myIncludesIterator.next();
JpaPid next = myIncludesIterator.next();
if (next != null)
if (myPidSet.add(next)) {
myNext = next;
@ -1740,9 +1739,9 @@ public class SearchBuilder implements ISearchBuilder {
}
@Override
public ResourcePersistentId next() {
public JpaPid next() {
fetchNext();
ResourcePersistentId retVal = myNext;
JpaPid retVal = myNext;
myNext = null;
Validate.isTrue(!NO_MORE.equals(retVal), "No more elements");
return retVal;
@ -1759,8 +1758,8 @@ public class SearchBuilder implements ISearchBuilder {
}
@Override
public Collection<ResourcePersistentId> getNextResultBatch(long theBatchSize) {
Collection<ResourcePersistentId> batch = new ArrayList<>();
public Collection<JpaPid> getNextResultBatch(long theBatchSize) {
Collection<JpaPid> batch = new ArrayList<>();
while (this.hasNext() && batch.size() < theBatchSize) {
batch.add(this.next());
}

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchQueryExecutors.java
View File

@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.search.builder;
* #L%
*/
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import org.apache.commons.lang3.Validate;
import javax.annotation.Nonnull;
@ -93,18 +93,18 @@ public class SearchQueryExecutors {
}
}
static public ISearchQueryExecutor from(Iterator<ResourcePersistentId> theIterator) {
return new ResourcePersistentIdQueryAdaptor(theIterator);
static public ISearchQueryExecutor from(Iterator<JpaPid> theIterator) {
return new JpaPidQueryAdaptor(theIterator);
}
static public ISearchQueryExecutor from(Iterable<ResourcePersistentId> theIterable) {
return new ResourcePersistentIdQueryAdaptor(theIterable.iterator());
static public ISearchQueryExecutor from(Iterable<JpaPid> theIterable) {
return new JpaPidQueryAdaptor(theIterable.iterator());
}
static class ResourcePersistentIdQueryAdaptor implements ISearchQueryExecutor {
final Iterator<ResourcePersistentId> myIterator;
static class JpaPidQueryAdaptor implements ISearchQueryExecutor {
final Iterator<JpaPid> myIterator;
ResourcePersistentIdQueryAdaptor(Iterator<ResourcePersistentId> theIterator) {
JpaPidQueryAdaptor(Iterator<JpaPid> theIterator) {
myIterator = theIterator;
}
@ -119,8 +119,8 @@ public class SearchQueryExecutors {
@Override
public Long next() {
ResourcePersistentId next = myIterator.next();
return next==null?null:next.getIdAsLong();
JpaPid next = myIterator.next();
return next == null ? null : next.getId();
}
}

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceIdPredicateBuilder.java
View File

@ -23,10 +23,10 @@ package ca.uhn.fhir.jpa.search.builder.predicate;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
import ca.uhn.fhir.jpa.util.QueryParameterUtils;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
import ca.uhn.fhir.jpa.util.QueryParameterUtils;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.TokenParamModifier;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
@ -49,7 +49,7 @@ public class ResourceIdPredicateBuilder extends BasePredicateBuilder {
private static final Logger ourLog = LoggerFactory.getLogger(ResourceIdPredicateBuilder.class);
@Autowired
private IIdHelperService myIdHelperService;
private IIdHelperService<JpaPid> myIdHelperService;
/**
* Constructor
@ -62,12 +62,12 @@ public class ResourceIdPredicateBuilder extends BasePredicateBuilder {
@Nullable
public Condition createPredicateResourceId(@Nullable DbColumn theSourceJoinColumn, String theResourceName, List<List<IQueryParameterType>> theValues, SearchFilterParser.CompareOperation theOperation, RequestPartitionId theRequestPartitionId) {
Set<ResourcePersistentId> allOrPids = null;
Set<JpaPid> allOrPids = null;
SearchFilterParser.CompareOperation defaultOperation = SearchFilterParser.CompareOperation.eq;
boolean allIdsAreForcedIds = true;
for (List<? extends IQueryParameterType> nextValue : theValues) {
Set<ResourcePersistentId> orPids = new HashSet<>();
Set<JpaPid> orPids = new HashSet<>();
boolean haveValue = false;
for (IQueryParameterType next : nextValue) {
String value = next.getValueAsQueryToken(getFhirContext());
@ -83,7 +83,7 @@ public class ResourceIdPredicateBuilder extends BasePredicateBuilder {
haveValue = true;
try {
boolean excludeDeleted = true;
ResourcePersistentId pid = myIdHelperService.resolveResourcePersistentIds(theRequestPartitionId, theResourceName, valueAsId.getIdPart(), excludeDeleted);
JpaPid pid = myIdHelperService.resolveResourcePersistentIds(theRequestPartitionId, theResourceName, valueAsId.getIdPart(), excludeDeleted);
orPids.add(pid);
} catch (ResourceNotFoundException e) {
// This is not an error in a search, it just results in no matches
@ -117,7 +117,7 @@ public class ResourceIdPredicateBuilder extends BasePredicateBuilder {
SearchFilterParser.CompareOperation operation = defaultIfNull(theOperation, defaultOperation);
assert operation == SearchFilterParser.CompareOperation.eq || operation == SearchFilterParser.CompareOperation.ne;
List<Long> resourceIds = ResourcePersistentId.toLongList(allOrPids);
List<Long> resourceIds = JpaPid.toLongList(allOrPids);
if (theSourceJoinColumn == null) {
BaseJoiningPredicateBuilder queryRootTable = super.getOrCreateQueryRootTable(!allIdsAreForcedIds);
Condition predicate;

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceLinkPredicateBuilder.java
View File

@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.search.builder.predicate;
* #L%
*/
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.ConfigurationException;
@ -28,6 +27,7 @@ import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
import ca.uhn.fhir.context.RuntimeChildResourceDefinition;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
@ -38,15 +38,16 @@ import ca.uhn.fhir.jpa.api.dao.IDao;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.dao.BaseStorageDao;
import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
import ca.uhn.fhir.jpa.util.QueryParameterUtils;
import ca.uhn.fhir.jpa.search.builder.QueryStack;
import ca.uhn.fhir.jpa.search.builder.models.MissingQueryParameterPredicateParams;
import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.ResourceMetaParams;
import ca.uhn.fhir.jpa.searchparam.util.JpaParamUtil;
import ca.uhn.fhir.jpa.util.QueryParameterUtils;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.parser.DataFormatException;
@ -54,7 +55,6 @@ import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.CompositeParam;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.NumberParam;
@ -96,9 +96,6 @@ import java.util.ListIterator;
import java.util.Set;
import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.util.QueryParameterUtils.toAndPredicate;
import static ca.uhn.fhir.jpa.util.QueryParameterUtils.toEqualToOrInPredicate;
import static ca.uhn.fhir.jpa.util.QueryParameterUtils.toOrPredicate;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.trim;
@ -238,8 +235,8 @@ public class ResourceLinkPredicateBuilder
inverse = true;
}
List<ResourcePersistentId> targetPids = myIdHelperService.resolveResourcePersistentIdsWithCache(theRequestPartitionId, targetIds);
List<Long> targetPidList = ResourcePersistentId.toLongList(targetPids);
List<JpaPid> targetPids = myIdHelperService.resolveResourcePersistentIdsWithCache(theRequestPartitionId, targetIds);
List<Long> targetPidList = JpaPid.toLongList(targetPids);
if (targetPidList.isEmpty() && targetQualifiedUrls.isEmpty()) {
setMatchNothing();

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/sql/SearchQueryBuilder.java
View File

@ -25,6 +25,7 @@ import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.search.builder.QueryStack;
import ca.uhn.fhir.jpa.search.builder.predicate.BaseJoiningPredicateBuilder;
@ -45,7 +46,6 @@ import ca.uhn.fhir.jpa.search.builder.predicate.StringPredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.TagPredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.TokenPredicateBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.UriPredicateBuilder;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.ParamPrefixEnum;
@ -680,14 +680,14 @@ public class SearchQueryBuilder {
addPredicate(predicate);
}
public void excludeResourceIdsPredicate(Set<ResourcePersistentId> theExsitinghPidSetToExclude) {
public void excludeResourceIdsPredicate(Set<JpaPid> theExistingPidSetToExclude) {
// Do nothing if it's empty
if (theExsitinghPidSetToExclude == null || theExsitinghPidSetToExclude.isEmpty())
if (theExistingPidSetToExclude == null || theExistingPidSetToExclude.isEmpty())
return;
List<Long> excludePids = ResourcePersistentId.toLongList(theExsitinghPidSetToExclude);
List<Long> excludePids = JpaPid.toLongList(theExistingPidSetToExclude);
ourLog.trace("excludePids = " + excludePids);
DbColumn resourceIdColumn = getOrCreateFirstPredicateBuilder().getResourceIdColumn();

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/tasks/SearchContinuationTask.java
View File

@ -24,12 +24,11 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import ca.uhn.fhir.jpa.search.ExceptionService;
import ca.uhn.fhir.jpa.search.SearchStrategyFactory;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.IPagingProvider;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import org.springframework.transaction.PlatformTransactionManager;
@ -47,7 +46,6 @@ public class SearchContinuationTask extends SearchTask {
SearchTaskParameters theCreationParams,
PlatformTransactionManager theManagedTxManager,
FhirContext theContext,
SearchStrategyFactory theSearchStrategyFactory,
IInterceptorBroadcaster theInterceptorBroadcaster,
SearchBuilderFactory theSearchBuilderFactory,
ISearchResultCacheSvc theSearchResultCacheSvc,
@ -60,7 +58,6 @@ public class SearchContinuationTask extends SearchTask {
theCreationParams,
theManagedTxManager,
theContext,
theSearchStrategyFactory,
theInterceptorBroadcaster,
theSearchBuilderFactory,
theSearchResultCacheSvc,
@ -78,7 +75,7 @@ public class SearchContinuationTask extends SearchTask {
TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
txTemplate.afterPropertiesSet();
txTemplate.execute(t -> {
List<ResourcePersistentId> previouslyAddedResourcePids = mySearchResultCacheSvc.fetchAllResultPids(getSearch());
List<JpaPid> previouslyAddedResourcePids = mySearchResultCacheSvc.fetchAllResultPids(getSearch());
if (previouslyAddedResourcePids == null) {
throw myExceptionSvc.newUnknownSearchException(getSearch().getUuid());
}

22
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/tasks/SearchTask.java
View File

@ -33,9 +33,9 @@ import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.interceptor.JpaPreResourceAccessDetails;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import ca.uhn.fhir.jpa.search.SearchStrategyFactory;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@ -43,7 +43,6 @@ import ca.uhn.fhir.jpa.util.QueryParameterUtils;
import ca.uhn.fhir.jpa.util.SearchParameterMapCalculator;
import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.IPagingProvider;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@ -102,10 +101,10 @@ public class SearchTask implements Callable<Void> {
private final SearchParameterMap myParams;
private final IDao myCallingDao;
private final String myResourceType;
private final ArrayList<ResourcePersistentId> mySyncedPids = new ArrayList<>();
private final ArrayList<JpaPid> mySyncedPids = new ArrayList<>();
private final CountDownLatch myInitialCollectionLatch = new CountDownLatch(1);
private final CountDownLatch myCompletionLatch;
private final ArrayList<ResourcePersistentId> myUnsyncedPids = new ArrayList<>();
private final ArrayList<JpaPid> myUnsyncedPids = new ArrayList<>();
private final RequestDetails myRequest;
private final RequestPartitionId myRequestPartitionId;
private final SearchRuntimeDetails mySearchRuntimeDetails;
@ -116,7 +115,7 @@ public class SearchTask implements Callable<Void> {
private int myCountSavedThisPass = 0;
private int myCountBlockedThisPass = 0;
private boolean myAdditionalPrefetchThresholdsRemaining;
private List<ResourcePersistentId> myPreviouslyAddedResourcePids;
private List<JpaPid> myPreviouslyAddedResourcePids;
private Integer myMaxResultsToFetch;
private final Consumer<String> myOnRemove;
@ -130,7 +129,7 @@ public class SearchTask implements Callable<Void> {
protected final PlatformTransactionManager myManagedTxManager;
protected final FhirContext myContext;
private final IInterceptorBroadcaster myInterceptorBroadcaster;
private final SearchBuilderFactory mySearchBuilderFactory;
private final SearchBuilderFactory<JpaPid> mySearchBuilderFactory;
protected final ISearchResultCacheSvc mySearchResultCacheSvc;
private final DaoConfig myDaoConfig;
private final ISearchCacheSvc mySearchCacheSvc;
@ -143,7 +142,6 @@ public class SearchTask implements Callable<Void> {
SearchTaskParameters theCreationParams,
PlatformTransactionManager theManagedTxManager,
FhirContext theContext,
SearchStrategyFactory theSearchStrategyFactory,
IInterceptorBroadcaster theInterceptorBroadcaster,
SearchBuilderFactory theSearchBuilderFactory,
ISearchResultCacheSvc theSearchResultCacheSvc,
@ -215,7 +213,7 @@ public class SearchTask implements Callable<Void> {
return myInitialCollectionLatch;
}
public void setPreviouslyAddedResourcePids(List<ResourcePersistentId> thePreviouslyAddedResourcePids) {
public void setPreviouslyAddedResourcePids(List<JpaPid> thePreviouslyAddedResourcePids) {
myPreviouslyAddedResourcePids = thePreviouslyAddedResourcePids;
myCountSavedTotal = myPreviouslyAddedResourcePids.size();
}
@ -226,7 +224,7 @@ public class SearchTask implements Callable<Void> {
}
@Nonnull
public List<ResourcePersistentId> getResourcePids(int theFromIndex, int theToIndex) {
public List<JpaPid> getResourcePids(int theFromIndex, int theToIndex) {
ourLog.debug("Requesting search PIDs from {}-{}", theFromIndex, theToIndex);
boolean keepWaiting;
@ -268,7 +266,7 @@ public class SearchTask implements Callable<Void> {
ourLog.debug("Proceeding, as we have {} results", mySyncedPids.size());
ArrayList<ResourcePersistentId> retVal = new ArrayList<>();
ArrayList<JpaPid> retVal = new ArrayList<>();
synchronized (mySyncedPids) {
QueryParameterUtils.verifySearchHasntFailedOrThrowInternalErrorException(mySearch);
@ -308,7 +306,7 @@ public class SearchTask implements Callable<Void> {
doSaveSearch();
}
ArrayList<ResourcePersistentId> unsyncedPids = myUnsyncedPids;
ArrayList<JpaPid> unsyncedPids = myUnsyncedPids;
int countBlocked = 0;
// Interceptor call: STORAGE_PREACCESS_RESOURCES
@ -634,7 +632,7 @@ public class SearchTask implements Callable<Void> {
* This is an odd implementation behaviour, but the change
* for this will require a lot more handling at higher levels
*/
try (IResultIterator resultIterator = sb.createQuery(myParams, mySearchRuntimeDetails, myRequest, myRequestPartitionId)) {
try (IResultIterator<JpaPid> resultIterator = sb.createQuery(myParams, mySearchRuntimeDetails, myRequest, myRequestPartitionId)) {
assert (resultIterator != null);
/*

18
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/cache/DatabaseSearchResultCacheSvcImpl.java vendored
View File

@ -20,18 +20,18 @@ package ca.uhn.fhir.jpa.search.cache;
* #L%
*/
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.entity.SearchResult;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import com.google.common.collect.Lists;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Pageable;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import java.util.Collections;
import java.util.List;
@ -45,7 +45,7 @@ public class DatabaseSearchResultCacheSvcImpl implements ISearchResultCacheSvc {
@Override
@Transactional(propagation = Propagation.REQUIRED)
public List<ResourcePersistentId> fetchResultPids(Search theSearch, int theFrom, int theTo) {
public List<JpaPid> fetchResultPids(Search theSearch, int theFrom, int theTo) {
final Pageable page = toPage(theFrom, theTo);
if (page == null) {
return Collections.emptyList();
@ -57,28 +57,28 @@ public class DatabaseSearchResultCacheSvcImpl implements ISearchResultCacheSvc {
ourLog.debug("fetchResultPids for range {}-{} returned {} pids", theFrom, theTo, retVal.size());
return ResourcePersistentId.fromLongList(retVal);
return JpaPid.fromLongList(retVal);
}
@Override
@Transactional(propagation = Propagation.REQUIRED)
public List<ResourcePersistentId> fetchAllResultPids(Search theSearch) {
public List<JpaPid> fetchAllResultPids(Search theSearch) {
List<Long> retVal = mySearchResultDao.findWithSearchPidOrderIndependent(theSearch.getId());
ourLog.trace("fetchAllResultPids returned {} pids", retVal.size());
return ResourcePersistentId.fromLongList(retVal);
return JpaPid.fromLongList(retVal);
}
@Override
@Transactional(propagation = Propagation.REQUIRED)
public void storeResults(Search theSearch, List<ResourcePersistentId> thePreviouslyStoredResourcePids, List<ResourcePersistentId> theNewResourcePids) {
public void storeResults(Search theSearch, List<JpaPid> thePreviouslyStoredResourcePids, List<JpaPid> theNewResourcePids) {
List<SearchResult> resultsToSave = Lists.newArrayList();
ourLog.debug("Storing {} results with {} previous for search", theNewResourcePids.size(), thePreviouslyStoredResourcePids.size());
int order = thePreviouslyStoredResourcePids.size();
for (ResourcePersistentId nextPid : theNewResourcePids) {
for (JpaPid nextPid : theNewResourcePids) {
SearchResult nextResult = new SearchResult(theSearch);
nextResult.setResourcePid(nextPid.getIdAsLong());
nextResult.setResourcePid(nextPid.getId());
nextResult.setOrder(order);
resultsToSave.add(nextResult);
ourLog.trace("Saving ORDER[{}] Resource {}", order, nextResult.getResourcePid());

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/cache/ISearchResultCacheSvc.java vendored
View File

@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.search.cache;
* #L%
*/
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import javax.annotation.Nullable;
import java.util.List;
@ -32,7 +32,7 @@ public interface ISearchResultCacheSvc {
* @param thePreviouslyStoredResourcePids A list of resource PIDs that have previously been saved to this search
* @param theNewResourcePids A list of new resoure PIDs to add to this search (these ones have not been previously saved)
*/
void storeResults(Search theSearch, List<ResourcePersistentId> thePreviouslyStoredResourcePids, List<ResourcePersistentId> theNewResourcePids);
void storeResults(Search theSearch, List<JpaPid> thePreviouslyStoredResourcePids, List<JpaPid> theNewResourcePids);
/**
* Fetch a sunset of the search result IDs from the cache
@ -44,7 +44,7 @@ public interface ISearchResultCacheSvc {
* have been removed from the cache for some reason, such as expiry or manual purge)
*/
@Nullable
List<ResourcePersistentId> fetchResultPids(Search theSearch, int theFrom, int theTo);
List<JpaPid> fetchResultPids(Search theSearch, int theFrom, int theTo);
/**
* Fetch all result PIDs for a given search with no particular order required
@ -54,6 +54,6 @@ public interface ISearchResultCacheSvc {
* have been removed from the cache for some reason, such as expiry or manual purge)
*/
@Nullable
List<ResourcePersistentId> fetchAllResultPids(Search theSearch);
List<JpaPid> fetchAllResultPids(Search theSearch);
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/ElasticsearchSvcImpl.java
View File

@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.search.lastn;
* #L%
*/
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.dao.TolerantJsonParser;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.IBaseResourceEntity;
@ -32,7 +32,7 @@ import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.util.LastNParameterHelper;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.ParamPrefixEnum;
import ca.uhn.fhir.rest.param.ReferenceParam;
@ -752,7 +752,7 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
}
@Override
public List<IBaseResource> getObservationResources(Collection<ResourcePersistentId> thePids) {
public List<IBaseResource> getObservationResources(Collection<? extends IResourcePersistentId> thePids) {
SearchRequest searchRequest = buildObservationResourceSearchRequest(thePids);
try {
SearchResponse observationDocumentResponse = executeSearchRequest(searchRequest);
@ -780,7 +780,7 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
}
}
private SearchRequest buildObservationResourceSearchRequest(Collection<ResourcePersistentId> thePids) {
private SearchRequest buildObservationResourceSearchRequest(Collection<? extends IResourcePersistentId> thePids) {
SearchRequest searchRequest = new SearchRequest(OBSERVATION_INDEX);
SearchSourceBuilder searchSourceBuilder = new SearchSourceBuilder();
// Query

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/IElasticsearchSvc.java
View File

@ -24,7 +24,7 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.search.lastn.json.CodeJson;
import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import org.hl7.fhir.instance.model.api.IBaseResource;
import java.io.IOException;
@ -96,6 +96,6 @@ public interface IElasticsearchSvc {
* @param thePids
* @return Resources list or empty if nothing found
*/
List<IBaseResource> getObservationResources(Collection<ResourcePersistentId> thePids);
List<IBaseResource> getObservationResources(Collection<? extends IResourcePersistentId> thePids);
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexer.java
View File

@ -20,18 +20,18 @@ package ca.uhn.fhir.jpa.search.reindex;
* #L%
*/
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ForcedId;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
@ -84,7 +84,7 @@ public class ResourceReindexer {
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(theResourceTable.getResourceType());
long expectedVersion = theResourceTable.getVersion();
IBaseResource resource = dao.readByPid(new ResourcePersistentId(theResourceTable.getId()), true);
IBaseResource resource = dao.readByPid(JpaPid.fromId(theResourceTable.getId()), true);
if (resource == null) {
throw new InternalErrorException(Msg.code(1171) + "Could not find resource version " + theResourceTable.getIdDt().toUnqualified().getValue() + " in database");

19
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java
View File

@ -40,6 +40,7 @@ import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.entity.TermConceptProperty;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
@ -48,7 +49,7 @@ import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.ObjectUtil;
@ -107,7 +108,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
@Autowired
protected ITermConceptDesignationDao myConceptDesignationDao;
@Autowired
protected IIdHelperService myIdHelperService;
protected IIdHelperService<JpaPid> myIdHelperService;
@Autowired
private ITermConceptParentChildLinkDao myConceptParentChildLinkDao;
@Autowired
@ -278,7 +279,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
Long pid = (Long)theCodeSystem.getUserData(RESOURCE_PID_KEY);
assert pid != null;
ResourcePersistentId codeSystemResourcePid = new ResourcePersistentId(pid);
JpaPid codeSystemResourcePid = JpaPid.fromId(pid);
/*
* If this is a not-present codesystem and codesystem version already exists, we don't want to
@ -321,8 +322,8 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
// Note that this creates the TermCodeSystem and TermCodeSystemVersion entities if needed
IIdType csId = myTerminologyVersionAdapterSvc.createOrUpdateCodeSystem(theCodeSystemResource, theRequest);
ResourcePersistentId codeSystemResourcePid = myIdHelperService.resolveResourcePersistentIds(RequestPartitionId.allPartitions(), csId.getResourceType(), csId.getIdPart());
ResourceTable resource = myResourceTableDao.getOne(codeSystemResourcePid.getIdAsLong());
JpaPid codeSystemResourcePid = myIdHelperService.resolveResourcePersistentIds(RequestPartitionId.allPartitions(), csId.getResourceType(), csId.getIdPart());
ResourceTable resource = myResourceTableDao.getOne(codeSystemResourcePid.getId());
ourLog.info("CodeSystem resource has ID: {}", csId.getValue());
@ -339,7 +340,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
@Override
@Transactional
public void storeNewCodeSystemVersion(ResourcePersistentId theCodeSystemResourcePid, String theSystemUri,
public void storeNewCodeSystemVersion(IResourcePersistentId theCodeSystemResourcePid, String theSystemUri,
String theSystemName, String theCodeSystemVersionId, TermCodeSystemVersion theCodeSystemVersion,
ResourceTable theCodeSystemResourceTable, RequestDetails theRequestDetails) {
assert TransactionSynchronizationManager.isActualTransactionActive();
@ -352,7 +353,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
TermCodeSystem codeSystem = getOrCreateDistinctTermCodeSystem(theCodeSystemResourcePid, theSystemUri, theSystemName, theCodeSystemVersionId, theCodeSystemResourceTable);
List<TermCodeSystemVersion> existing = myCodeSystemVersionDao.findByCodeSystemResourcePid(theCodeSystemResourcePid.getIdAsLong());
List<TermCodeSystemVersion> existing = myCodeSystemVersionDao.findByCodeSystemResourcePid(((JpaPid)theCodeSystemResourcePid).getId());
for (TermCodeSystemVersion next : existing) {
if (Objects.equals(next.getCodeSystemVersionId(), theCodeSystemVersionId) && myConceptDao.countByCodeSystemVersion(next.getPid()) == 0) {
@ -629,10 +630,10 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
}
@Nonnull
private TermCodeSystem getOrCreateDistinctTermCodeSystem(ResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, ResourceTable theCodeSystemResourceTable) {
private TermCodeSystem getOrCreateDistinctTermCodeSystem(IResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, ResourceTable theCodeSystemResourceTable) {
TermCodeSystem codeSystem = myCodeSystemDao.findByCodeSystemUri(theSystemUri);
if (codeSystem == null) {
codeSystem = myCodeSystemDao.findByResourcePid(theCodeSystemResourcePid.getIdAsLong());
codeSystem = myCodeSystemDao.findByResourcePid(((JpaPid)theCodeSystemResourcePid).getId());
if (codeSystem == null) {
codeSystem = new TermCodeSystem();
}

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermConceptMappingSvcImpl.java
View File

@ -36,11 +36,11 @@ import ca.uhn.fhir.jpa.entity.TermConceptMap;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroup;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.api.ITermConceptMappingSvc;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.jpa.util.ScrollableResultsIterator;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
@ -107,7 +107,7 @@ public class TermConceptMappingSvcImpl implements ITermConceptMappingSvc {
@Autowired
private MemoryCacheService myMemoryCacheService;
@Autowired
private IIdHelperService myIdHelperService;
private IIdHelperService<JpaPid> myIdHelperService;
@Override
@Transactional
@ -362,8 +362,8 @@ public class TermConceptMappingSvcImpl implements ITermConceptMappingSvc {
if (translationQuery.hasResourceId()) {
IIdType resourceId = translationQuery.getResourceId();
ResourcePersistentId resourcePid = myIdHelperService.getPidOrThrowException(RequestPartitionId.defaultPartition(), resourceId);
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myResourcePid"), resourcePid.getIdAsLong()));
JpaPid resourcePid = myIdHelperService.getPidOrThrowException(RequestPartitionId.defaultPartition(), resourceId);
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myResourcePid"), resourcePid.getId()));
}
Predicate outerPredicate = criteriaBuilder.and(predicates.toArray(new Predicate[0]));
@ -491,8 +491,8 @@ public class TermConceptMappingSvcImpl implements ITermConceptMappingSvc {
if (translationQuery.hasResourceId()) {
IIdType resourceId = translationQuery.getResourceId();
ResourcePersistentId resourcePid = myIdHelperService.getPidOrThrowException(RequestPartitionId.defaultPartition(), resourceId);
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myResourcePid"), resourcePid.getIdAsLong()));
JpaPid resourcePid = myIdHelperService.getPidOrThrowException(RequestPartitionId.defaultPartition(), resourceId);
predicates.add(criteriaBuilder.equal(conceptMapJoin.get("myResourcePid"), resourcePid.getId()));
}
Predicate outerPredicate = criteriaBuilder.and(predicates.toArray(new Predicate[0]));

26
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcImpl.java
View File

@ -39,8 +39,6 @@ import ca.uhn.fhir.jpa.config.util.ConnectionPoolInfoProvider;
import ca.uhn.fhir.jpa.config.util.IConnectionPoolInfoProvider;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.IJpaStorageResourceParser;
import ca.uhn.fhir.jpa.dao.IStorageResourceParser;
import ca.uhn.fhir.jpa.dao.JpaStorageResourceParser;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
@ -63,6 +61,7 @@ import ca.uhn.fhir.jpa.entity.TermConceptPropertyTypeEnum;
import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ForcedId;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.sched.HapiJob;
@ -76,7 +75,6 @@ import ca.uhn.fhir.jpa.term.api.ReindexTerminologyResult;
import ca.uhn.fhir.jpa.term.ex.ExpansionTooCostlyException;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
@ -255,7 +253,7 @@ public class TermReadSvcImpl implements ITermReadSvc {
@Autowired(required = false)
private ITermDeferredStorageSvc myDeferredStorageSvc;
@Autowired
private IIdHelperService myIdHelperService;
private IIdHelperService<JpaPid> myIdHelperService;
@Autowired
private ApplicationContext myApplicationContext;
private volatile IValidationSupport myJpaValidationSupport;
@ -1606,11 +1604,11 @@ public class TermReadSvcImpl implements ITermReadSvc {
}
private Optional<TermValueSet> fetchValueSetEntity(ValueSet theValueSet) {
ResourcePersistentId valueSetResourcePid = getValueSetResourcePersistentId(theValueSet);
return myTermValueSetDao.findByResourcePid(valueSetResourcePid.getIdAsLong());
JpaPid valueSetResourcePid = getValueSetResourcePersistentId(theValueSet);
return myTermValueSetDao.findByResourcePid(valueSetResourcePid.getId());
}
private ResourcePersistentId getValueSetResourcePersistentId(ValueSet theValueSet) {
private JpaPid getValueSetResourcePersistentId(ValueSet theValueSet) {
return myIdHelperService.resolveResourcePersistentIds(RequestPartitionId.allPartitions(), theValueSet.getIdElement().getResourceType(), theValueSet.getIdElement().getIdPart());
}
@ -1620,13 +1618,13 @@ public class TermReadSvcImpl implements ITermReadSvc {
assert TransactionSynchronizationManager.isSynchronizationActive();
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet.hasId(), "ValueSet.id is required");
ResourcePersistentId valueSetResourcePid = getValueSetResourcePersistentId(theValueSet);
JpaPid valueSetResourcePid = getValueSetResourcePersistentId(theValueSet);
List<TermValueSetConcept> concepts = new ArrayList<>();
if (isNotBlank(theCode)) {
if (theValidationOptions.isInferSystem()) {
concepts.addAll(myValueSetConceptDao.findByValueSetResourcePidAndCode(valueSetResourcePid.getIdAsLong(), theCode));
concepts.addAll(myValueSetConceptDao.findByValueSetResourcePidAndCode(valueSetResourcePid.getId(), theCode));
} else if (isNotBlank(theSystem)) {
concepts.addAll(findByValueSetResourcePidSystemAndCode(valueSetResourcePid, theSystem, theCode));
}
@ -1647,7 +1645,7 @@ public class TermReadSvcImpl implements ITermReadSvc {
return null;
}
TermValueSet valueSetEntity = myTermValueSetDao.findByResourcePid(valueSetResourcePid.getIdAsLong()).orElseThrow(IllegalStateException::new);
TermValueSet valueSetEntity = myTermValueSetDao.findByResourcePid(valueSetResourcePid.getId()).orElseThrow(IllegalStateException::new);
String timingDescription = toHumanReadableExpansionTimestamp(valueSetEntity);
String msg = myContext.getLocalizer().getMessage(TermReadSvcImpl.class, "validationPerformedAgainstPreExpansion", timingDescription);
@ -1696,7 +1694,7 @@ public class TermReadSvcImpl implements ITermReadSvc {
.setMessage("Unable to validate code " + theSystem + "#" + theCode + theAppend);
}
private List<TermValueSetConcept> findByValueSetResourcePidSystemAndCode(ResourcePersistentId theResourcePid, String theSystem, String theCode) {
private List<TermValueSetConcept> findByValueSetResourcePidSystemAndCode(JpaPid theResourcePid, String theSystem, String theCode) {
assert TransactionSynchronizationManager.isSynchronizationActive();
List<TermValueSetConcept> retVal = new ArrayList<>();
@ -1705,9 +1703,11 @@ public class TermReadSvcImpl implements ITermReadSvc {
if (versionIndex >= 0) {
String systemUrl = theSystem.substring(0, versionIndex);
String systemVersion = theSystem.substring(versionIndex + 1);
optionalTermValueSetConcept = myValueSetConceptDao.findByValueSetResourcePidSystemAndCodeWithVersion(theResourcePid.getIdAsLong(), systemUrl, systemVersion, theCode);
optionalTermValueSetConcept = myValueSetConceptDao.findByValueSetResourcePidSystemAndCodeWithVersion(
theResourcePid.getId(), systemUrl, systemVersion, theCode);
} else {
optionalTermValueSetConcept = myValueSetConceptDao.findByValueSetResourcePidSystemAndCode(theResourcePid.getIdAsLong(), theSystem, theCode);
optionalTermValueSetConcept = myValueSetConceptDao.findByValueSetResourcePidSystemAndCode(
theResourcePid.getId(), theSystem, theCode);
}
optionalTermValueSetConcept.ifPresent(retVal::add);
return retVal;

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermCodeSystemStorageSvc.java
View File

@ -26,12 +26,12 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.UploadStatistics;
import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ValueSet;
import org.springframework.transaction.annotation.Transactional;
import java.util.List;
/**
@ -50,16 +50,16 @@ public interface ITermCodeSystemStorageSvc {
(boolean) theRequestDetails.getUserData().getOrDefault(MAKE_LOADING_VERSION_CURRENT, Boolean.TRUE);
}
void storeNewCodeSystemVersion(ResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName,
String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable,
RequestDetails theRequestDetails);
void storeNewCodeSystemVersion(IResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName,
String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable,
RequestDetails theRequestDetails);
/**
* Default implementation supports previous signature of method which was added RequestDetails parameter
*/
@Transactional
default void storeNewCodeSystemVersion(ResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName,
String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable) {
default void storeNewCodeSystemVersion(IResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName,
String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable) {
storeNewCodeSystemVersion(theCodeSystemResourcePid, theSystemUri, theSystemName, theSystemVersionId,
theCodeSystemVersion, theCodeSystemResourceTable, null);

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/QueryParameterUtils.java
View File

@ -25,12 +25,12 @@ import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.entity.SearchInclude;
import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.ParamPrefixEnum;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
@ -194,7 +194,7 @@ public class QueryParameterUtils {
return lastUpdatedPredicates;
}
public static List<ResourcePersistentId> filterResourceIdsByLastUpdated(EntityManager theEntityManager, final DateRangeParam theLastUpdated, Collection<ResourcePersistentId> thePids) {
public static List<JpaPid> filterResourceIdsByLastUpdated(EntityManager theEntityManager, final DateRangeParam theLastUpdated, Collection<JpaPid> thePids) {
if (thePids.isEmpty()) {
return Collections.emptyList();
}
@ -204,12 +204,13 @@ public class QueryParameterUtils {
cq.select(from.get("myId").as(Long.class));
List<Predicate> lastUpdatedPredicates = createLastUpdatedPredicates(theLastUpdated, builder, from);
lastUpdatedPredicates.add(from.get("myId").as(Long.class).in(ResourcePersistentId.toLongList(thePids)));
List<Long> longIds = thePids.stream().map(JpaPid::getId).collect(Collectors.toList());
lastUpdatedPredicates.add(from.get("myId").as(Long.class).in(longIds));
cq.where(toPredicateArray(lastUpdatedPredicates));
TypedQuery<Long> query = theEntityManager.createQuery(cq);
return ResourcePersistentId.fromLongList(query.getResultList());
return query.getResultList().stream().map(JpaPid::fromId).collect(Collectors.toList());
}
public static void verifySearchHasntFailedOrThrowInternalErrorException(Search theSearch) {

87
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/export/svc/JpaBulkExportProcessorTest.java
View File

@ -13,6 +13,7 @@ import ca.uhn.fhir.jpa.dao.IResultIterator;
import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
import ca.uhn.fhir.jpa.dao.mdm.MdmExpansionCacheSvc;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@ -21,10 +22,8 @@ import ca.uhn.fhir.mdm.dao.IMdmLinkDao;
import ca.uhn.fhir.mdm.model.MdmPidTuple;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.HasOrListParam;
import ca.uhn.fhir.rest.param.HasParam;
import ch.qos.logback.classic.spi.ILoggingEvent;
import ca.uhn.fhir.rest.api.server.storage.BaseResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.Group;
@ -34,7 +33,6 @@ import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource;
import org.mockito.ArgumentMatcher;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.Spy;
@ -52,7 +50,6 @@ import java.util.List;
import java.util.Optional;
import java.util.Set;
import static ca.uhn.fhir.rest.api.Constants.PARAM_HAS;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
@ -60,9 +57,7 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
import static org.mockito.AdditionalMatchers.not;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.anyList;
import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.argThat;
import static org.mockito.ArgumentMatchers.eq;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
@ -72,11 +67,11 @@ public class JpaBulkExportProcessorTest {
private class ListResultIterator implements IResultIterator {
private List<ResourcePersistentId> myList;
private List<IResourcePersistentId> myList;
private int index;
public ListResultIterator(List<ResourcePersistentId> theList) {
public ListResultIterator(List<IResourcePersistentId> theList) {
myList = theList;
}
@ -91,7 +86,7 @@ public class JpaBulkExportProcessorTest {
}
@Override
public Collection<ResourcePersistentId> getNextResultBatch(long theBatchSize) {
public Collection<IResourcePersistentId> getNextResultBatch(long theBatchSize) {
return null;
}
@ -106,7 +101,7 @@ public class JpaBulkExportProcessorTest {
}
@Override
public ResourcePersistentId next() {
public IResourcePersistentId next() {
return myList.get(index++);
}
}
@ -163,17 +158,7 @@ public class JpaBulkExportProcessorTest {
}
private MdmPidTuple createTuple(long theGroupId, long theGoldenId) {
return new MdmPidTuple() {
@Override
public ResourcePersistentId getGoldenPid() {
return new ResourcePersistentId(theGoldenId);
}
@Override
public ResourcePersistentId getSourcePid() {
return new ResourcePersistentId(theGroupId);
}
};
return MdmPidTuple.fromGoldenAndSource(JpaPid.fromId(theGoldenId), JpaPid.fromId(theGroupId));
}
@Test
@ -186,8 +171,8 @@ public class JpaBulkExportProcessorTest {
List<SearchParameterMap> maps = new ArrayList<>();
maps.add(map);
ResourcePersistentId pid = new ResourcePersistentId("Patient/123");
ResourcePersistentId pid2 = new ResourcePersistentId("Observation/123");
JpaPid pid = JpaPid.fromId(123L);
JpaPid pid2 = JpaPid.fromId(456L);
ListResultIterator resultIterator = new ListResultIterator(
Arrays.asList(pid, pid2)
);
@ -215,7 +200,7 @@ public class JpaBulkExportProcessorTest {
.thenReturn(resultIterator);
// test
Iterator<ResourcePersistentId> pidIterator = myProcessor.getResourcePidIterator(parameters);
Iterator<JpaPid> pidIterator = myProcessor.getResourcePidIterator(parameters);
// verify
assertNotNull(pidIterator);
@ -252,19 +237,19 @@ public class JpaBulkExportProcessorTest {
ExportPIDIteratorParameters parameters = createExportParameters(BulkDataExportOptions.ExportStyle.GROUP);
parameters.setResourceType("Patient");
ResourcePersistentId groupId = new ResourcePersistentId(Long.parseLong(parameters.getGroupId()));
JpaPid groupId = JpaPid.fromId(Long.parseLong(parameters.getGroupId()));
long groupGoldenPid = 4567l;
Group groupResource = new Group();
groupResource.setId(parameters.getGroupId());
List<IPrimitiveType> patientTypes = createPatientTypes();
List<ResourcePersistentId> pids = new ArrayList<>();
List<IResourcePersistentId> pids = new ArrayList<>();
for (IPrimitiveType type : patientTypes) {
pids.add(new ResourcePersistentId(((IdDt) type).getIdPartAsLong()));
pids.add(JpaPid.fromId(((IdDt) type).getIdPartAsLong()));
}
MdmPidTuple tuple = createTuple(groupId.getIdAsLong(), groupGoldenPid);
MdmPidTuple tuple = createTuple(groupId.getId(), groupGoldenPid);
IFhirResourceDao<Group> groupDao = mock(IFhirResourceDao.class);
parameters.setExpandMdm(theMdm); // set mdm expansion
@ -297,32 +282,32 @@ public class JpaBulkExportProcessorTest {
.thenReturn(groupResource);
when(myIdHelperService.translatePidsToForcedIds(any(Set.class)))
.thenAnswer(params -> {
Set<ResourcePersistentId> uniqPids = params.getArgument(0);
HashMap<ResourcePersistentId, Optional<String>> answer = new HashMap<>();
for (ResourcePersistentId l : uniqPids) {
Set<IResourcePersistentId> uniqPids = params.getArgument(0);
HashMap<IResourcePersistentId, Optional<String>> answer = new HashMap<>();
for (IResourcePersistentId l : uniqPids) {
answer.put(l, Optional.empty());
}
return new PersistentIdToForcedIdMap(answer);
});
when(myIdHelperService.getPidOrNull(any(), any(Group.class)))
.thenReturn(groupId);
when(myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult(any(ResourcePersistentId.class), eq(MdmMatchResultEnum.MATCH)))
when(myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult(any(BaseResourcePersistentId.class), eq(MdmMatchResultEnum.MATCH)))
.thenReturn(Collections.singletonList(tuple));
when(myMdmExpansionCacheSvc.hasBeenPopulated())
.thenReturn(false); // does not matter, since if false, it then goes and populates
}
// test
Iterator<ResourcePersistentId> pidIterator = myProcessor.getResourcePidIterator(parameters);
Iterator<JpaPid> pidIterator = myProcessor.getResourcePidIterator(parameters);
// verify
assertNotNull(pidIterator);
int count = 0;
assertTrue(pidIterator.hasNext());
while (pidIterator.hasNext()) {
ResourcePersistentId pid = pidIterator.next();
long idAsLong = pid.getIdAsLong();
boolean existing = pids.contains(new ResourcePersistentId(idAsLong));
JpaPid pid = pidIterator.next();
long idAsLong = pid.getId();
boolean existing = pids.contains(JpaPid.fromId(idAsLong));
if (!existing) {
assertTrue(theMdm);
assertEquals(groupGoldenPid, idAsLong);
@ -341,18 +326,18 @@ public class JpaBulkExportProcessorTest {
ExportPIDIteratorParameters parameters = createExportParameters(BulkDataExportOptions.ExportStyle.GROUP);
parameters.setResourceType("Observation");
ResourcePersistentId groupId = new ResourcePersistentId(Long.parseLong(parameters.getGroupId()));
JpaPid groupId = JpaPid.fromId(Long.parseLong(parameters.getGroupId()));
Group groupResource = new Group();
groupResource.setId(parameters.getGroupId());
long groupGoldenPid = 4567l;
ResourcePersistentId pid = new ResourcePersistentId("Patient/123");
ResourcePersistentId pid2 = new ResourcePersistentId("Observation/123");
JpaPid pid = JpaPid.fromId(123L);
JpaPid pid2 = JpaPid.fromId(456L);
ListResultIterator resultIterator = new ListResultIterator(
Arrays.asList(pid, pid2)
);
MdmPidTuple tuple = createTuple(groupId.getIdAsLong(), groupGoldenPid);
MdmPidTuple tuple = createTuple(groupId.getId(), groupGoldenPid);
List<IPrimitiveType> patientTypes = createPatientTypes();
IFhirResourceDao<Group> groupDao = mock(IFhirResourceDao.class);
@ -387,13 +372,13 @@ public class JpaBulkExportProcessorTest {
.thenReturn(resultIterator);
if (theMdm) {
when(myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult(any(ResourcePersistentId.class), eq(MdmMatchResultEnum.MATCH)))
when(myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult(any(BaseResourcePersistentId.class), eq(MdmMatchResultEnum.MATCH)))
.thenReturn(Collections.singletonList(tuple));
when(myIdHelperService.translatePidsToForcedIds(any(Set.class)))
.thenAnswer(params -> {
Set<ResourcePersistentId> uniqPids = params.getArgument(0);
HashMap<ResourcePersistentId, Optional<String>> answer = new HashMap<>();
for (ResourcePersistentId l : uniqPids) {
Set<IResourcePersistentId> uniqPids = params.getArgument(0);
HashMap<IResourcePersistentId, Optional<String>> answer = new HashMap<>();
for (IResourcePersistentId l : uniqPids) {
answer.put(l, Optional.empty());
}
return new PersistentIdToForcedIdMap(answer);
@ -401,7 +386,7 @@ public class JpaBulkExportProcessorTest {
}
// test
Iterator<ResourcePersistentId> pidIterator = myProcessor.getResourcePidIterator(parameters);
Iterator<JpaPid> pidIterator = myProcessor.getResourcePidIterator(parameters);
// verify
assertNotNull(pidIterator, "PID iterator null for mdm = " + theMdm);
@ -414,8 +399,8 @@ public class JpaBulkExportProcessorTest {
ExportPIDIteratorParameters parameters = createExportParameters(BulkDataExportOptions.ExportStyle.SYSTEM);
parameters.setResourceType("Patient");
ResourcePersistentId pid = new ResourcePersistentId("Patient/123");
ResourcePersistentId pid2 = new ResourcePersistentId("Observation/123");
JpaPid pid = JpaPid.fromId(123L);
JpaPid pid2 = JpaPid.fromId(456L);
ListResultIterator resultIterator = new ListResultIterator(
Arrays.asList(pid, pid2)
);
@ -444,14 +429,14 @@ public class JpaBulkExportProcessorTest {
)).thenReturn(resultIterator);
// test
Iterator<ResourcePersistentId> iterator = myProcessor.getResourcePidIterator(parameters);
Iterator<JpaPid> iterator = myProcessor.getResourcePidIterator(parameters);
// verify
assertNotNull(iterator);
assertTrue(iterator.hasNext());
int count = 0;
while (iterator.hasNext()) {
ResourcePersistentId ret = iterator.next();
IResourcePersistentId ret = iterator.next();
assertTrue(
ret.equals(pid) || ret.equals(pid2)
);

2
hapi-fhir-jpaserver-cql/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-elastic-test-utilities/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

6
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNIT.java
View File

@ -1,10 +1,10 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.search.builder.SearchBuilder;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.TokenParam;
import org.hl7.fhir.instance.model.api.IIdType;
@ -135,10 +135,10 @@ public class FhirResourceDaoR4SearchLastNIT extends BaseR4SearchLastN {
}
void verifyResourcesLoadedFromElastic(List<IIdType> theObservationIds, List<String> theResults) {
List<ResourcePersistentId> expectedArgumentPids = ResourcePersistentId.fromLongList(
List<JpaPid> expectedArgumentPids = JpaPid.fromLongList(
theObservationIds.stream().map(IIdType::getIdPartAsLong).collect(Collectors.toList())
);
ArgumentCaptor<List<ResourcePersistentId>> actualPids = ArgumentCaptor.forClass(List.class);
ArgumentCaptor<List<JpaPid>> actualPids = ArgumentCaptor.forClass(List.class);
verify(myElasticsearchSvc, times(1)).getObservationResources(actualPids.capture());
assertThat(actualPids.getValue(), is(expectedArgumentPids));

7
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchIT.java
View File

@ -17,6 +17,7 @@ import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@ -35,7 +36,7 @@ import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.StringOrListParam;
import ca.uhn.fhir.rest.param.StringParam;
@ -880,7 +881,7 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest impl
TermConcept childCA = new TermConcept(cs, "childCA").setDisplay("Child CA");
parentC.addChild(childCA, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(JpaPid.fromId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
return codeSystem;
}
@ -939,7 +940,7 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest impl
SearchParameterMap map = new SearchParameterMap();
map.add("code", new TokenParam().setSystem("http://example.com"));
List<ResourcePersistentId> bp = myObservationDao.searchForIds(map, new ServletRequestDetails());
List<IResourcePersistentId> bp = myObservationDao.searchForIds(map, new ServletRequestDetails());
assertNotNull(bp);
assertEquals(600, bp.size());

4
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyElasticsearchIT.java
View File

@ -11,11 +11,11 @@ import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticHSearch;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.test.utilities.docker.RequiresDocker;
@ -120,7 +120,7 @@ public class FhirResourceDaoR4TerminologyElasticsearchIT extends BaseJpaTest {
concept = new TermConcept(cs, "LA9999-7");
cs.getConcepts().add(concept);
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(JpaPid.fromId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
ValueSet valueSet = new ValueSet();
valueSet.setUrl(URL_MY_VALUE_SET);

4
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4ElasticsearchIT.java
View File

@ -15,6 +15,7 @@ import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
@ -23,7 +24,6 @@ import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
@ -171,7 +171,7 @@ public class ValueSetExpansionR4ElasticsearchIT extends BaseJpaTest {
TermConcept parentB = new TermConcept(cs, "ParentB");
cs.getConcepts().add(parentB);
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(JpaPid.fromId(table.getId()), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
}

37
hapi-fhir-jpaserver-mdm/pom.xml
View File

@ -6,10 +6,11 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.2-SNAPSHOT</version>
<version>6.3.3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<!-- Note that even though this project has jpaserver in the name, it is not require a hapi-fhir jpa database to be available -->
<artifactId>hapi-fhir-jpaserver-mdm</artifactId>
<packaging>jar</packaging>
@ -25,17 +26,18 @@
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-jpa</artifactId>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-base</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-storage-mdm</artifactId>
<version>${project.version}</version>
</dependency>
<!-- test -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-base</artifactId>
<version>${project.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-test-utilities</artifactId>
@ -117,6 +119,29 @@
</dependency>
</dependencies>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<executions>
<execution>
<id>enforce-banned-dependencies</id>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<bannedDependencies>
<excludes>
<!-- It is important that this project not depend on jpaserver-base -->
<exclude>ca.uhn.hapi.fhir:hapi-fhir-jpaserver-base:${project.version}:jar:compile</exclude>
</excludes>
</bannedDependencies>
</rules>
<fail>true</fail>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>

18
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/config/MdmSubmitterConfig.java
View File

@ -21,17 +21,13 @@ package ca.uhn.fhir.jpa.mdm.config;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.mdm.MdmLinkDaoJpaImpl;
import ca.uhn.fhir.jpa.mdm.dao.JpaMdmLinkImplFactory;
import ca.uhn.fhir.jpa.mdm.interceptor.MdmSubmitterInterceptorLoader;
import ca.uhn.fhir.mdm.dao.IMdmLinkImplFactory;
import ca.uhn.fhir.mdm.svc.MdmChannelSubmitterSvcImpl;
import ca.uhn.fhir.mdm.dao.IMdmLinkDao;
import ca.uhn.fhir.mdm.svc.MdmSearchParamSvc;
import ca.uhn.fhir.mdm.svc.MdmSubmitSvcImpl;
import ca.uhn.fhir.jpa.subscription.channel.api.IChannelFactory;
import ca.uhn.fhir.mdm.api.IMdmChannelSubmitterSvc;
import ca.uhn.fhir.mdm.api.IMdmSubmitSvc;
import ca.uhn.fhir.mdm.svc.MdmChannelSubmitterSvcImpl;
import ca.uhn.fhir.mdm.svc.MdmSearchParamSvc;
import ca.uhn.fhir.mdm.svc.MdmSubmitSvcImpl;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@ -61,12 +57,4 @@ public class MdmSubmitterConfig {
IMdmSubmitSvc mdmSubmitService() {
return new MdmSubmitSvcImpl();
}
@Bean
IMdmLinkDao mdmLinkDao(){
return new MdmLinkDaoJpaImpl();
}
@Bean
IMdmLinkImplFactory mdmLinkImplFactory() {return new JpaMdmLinkImplFactory();}
}

123
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/dao/MdmLinkDaoSvc.java
View File

@ -34,7 +34,7 @@ import ca.uhn.fhir.mdm.dao.MdmLinkFactory;
import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
@ -52,22 +52,22 @@ import java.util.Date;
import java.util.List;
import java.util.Optional;
public class MdmLinkDaoSvc {
public class MdmLinkDaoSvc<P extends IResourcePersistentId, M extends IMdmLink<P>> {
private static final Logger ourLog = Logs.getMdmTroubleshootingLog();
@Autowired
private IMdmLinkDao myMdmLinkDao;
private IMdmLinkDao<P, M> myMdmLinkDao;
@Autowired
private MdmLinkFactory myMdmLinkFactory;
private MdmLinkFactory<M> myMdmLinkFactory;
@Autowired
private IIdHelperService myIdHelperService;
private IIdHelperService<P> myIdHelperService;
@Autowired
private FhirContext myFhirContext;
@Transactional
public IMdmLink createOrUpdateLinkEntity(IAnyResource theGoldenResource, IAnyResource theSourceResource, MdmMatchOutcome theMatchOutcome, MdmLinkSourceEnum theLinkSource, @Nullable MdmTransactionContext theMdmTransactionContext) {
IMdmLink mdmLink = getOrCreateMdmLinkByGoldenResourceAndSourceResource(theGoldenResource, theSourceResource);
public M createOrUpdateLinkEntity(IAnyResource theGoldenResource, IAnyResource theSourceResource, MdmMatchOutcome theMatchOutcome, MdmLinkSourceEnum theLinkSource, @Nullable MdmTransactionContext theMdmTransactionContext) {
M mdmLink = getOrCreateMdmLinkByGoldenResourceAndSourceResource(theGoldenResource, theSourceResource);
mdmLink.setLinkSource(theLinkSource);
mdmLink.setMatchResult(theMatchOutcome.getMatchResultEnum());
// Preserve these flags for link updates
@ -93,16 +93,16 @@ public class MdmLinkDaoSvc {
}
@Nonnull
public IMdmLink getOrCreateMdmLinkByGoldenResourceAndSourceResource(
public M getOrCreateMdmLinkByGoldenResourceAndSourceResource(
IAnyResource theGoldenResource, IAnyResource theSourceResource
) {
ResourcePersistentId goldenResourcePid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theGoldenResource);
ResourcePersistentId sourceResourcePid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theSourceResource);
Optional<? extends IMdmLink> oExisting = getLinkByGoldenResourcePidAndSourceResourcePid(goldenResourcePid, sourceResourcePid);
P goldenResourcePid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theGoldenResource);
P sourceResourcePid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theSourceResource);
Optional<M> oExisting = getLinkByGoldenResourcePidAndSourceResourcePid(goldenResourcePid, sourceResourcePid);
if (oExisting.isPresent()) {
return oExisting.get();
} else {
IMdmLink newLink = myMdmLinkFactory.newMdmLink();
M newLink = myMdmLinkFactory.newMdmLink();
newLink.setGoldenResourcePersistenceId(goldenResourcePid);
newLink.setSourcePersistenceId(sourceResourcePid);
return newLink;
@ -111,14 +111,15 @@ public class MdmLinkDaoSvc {
/**
* Given a golden resource Pid and source Pid, return the mdm link that matches these criterias if exists
* @deprecated This was deprecated in favour of using ResourcePersistenceId rather than longs
*
* @param theGoldenResourcePid
* @param theSourceResourcePid
* @return
* @deprecated This was deprecated in favour of using ResourcePersistenceId rather than longs
*/
@Deprecated
public Optional<? extends IMdmLink> getLinkByGoldenResourcePidAndSourceResourcePid(Long theGoldenResourcePid, Long theSourceResourcePid) {
return getLinkByGoldenResourcePidAndSourceResourcePid(new ResourcePersistentId(theGoldenResourcePid), new ResourcePersistentId(theSourceResourcePid));
public Optional<M> getLinkByGoldenResourcePidAndSourceResourcePid(Long theGoldenResourcePid, Long theSourceResourcePid) {
return getLinkByGoldenResourcePidAndSourceResourcePid(myIdHelperService.newPid(theGoldenResourcePid), myIdHelperService.newPid(theSourceResourcePid));
}
/**
@ -128,16 +129,16 @@ public class MdmLinkDaoSvc {
* @return The {@link IMdmLink} entity that matches these criteria if exists
*/
@SuppressWarnings("unchecked")
public Optional<? extends IMdmLink> getLinkByGoldenResourcePidAndSourceResourcePid(ResourcePersistentId theGoldenResourcePid, ResourcePersistentId theSourceResourcePid) {
public Optional<M> getLinkByGoldenResourcePidAndSourceResourcePid(P theGoldenResourcePid, P theSourceResourcePid) {
if (theSourceResourcePid == null || theGoldenResourcePid == null) {
return Optional.empty();
}
IMdmLink link = myMdmLinkFactory.newMdmLink();
M link = myMdmLinkFactory.newMdmLink();
link.setSourcePersistenceId(theSourceResourcePid);
link.setGoldenResourcePersistenceId(theGoldenResourcePid);
//TODO - replace the use of example search
Example<? extends IMdmLink> example = Example.of(link);
Example<M> example = Example.of(link);
return myMdmLinkDao.findOne(example);
}
@ -149,11 +150,11 @@ public class MdmLinkDaoSvc {
* @param theMatchResult the Match Result of the relationship
* @return a list of {@link IMdmLink} entities matching these criteria.
*/
public List<? extends IMdmLink> getMdmLinksBySourcePidAndMatchResult(ResourcePersistentId theSourcePid, MdmMatchResultEnum theMatchResult) {
IMdmLink exampleLink = myMdmLinkFactory.newMdmLink();
public List<M> getMdmLinksBySourcePidAndMatchResult(P theSourcePid, MdmMatchResultEnum theMatchResult) {
M exampleLink = myMdmLinkFactory.newMdmLink();
exampleLink.setSourcePersistenceId(theSourcePid);
exampleLink.setMatchResult(theMatchResult);
Example<? extends IMdmLink> example = Example.of(exampleLink);
Example<M> example = Example.of(exampleLink);
return myMdmLinkDao.findAll(example);
}
@ -166,7 +167,7 @@ public class MdmLinkDaoSvc {
*/
@Deprecated
@Transactional
public Optional<? extends IMdmLink> getMatchedLinkForSourcePid(ResourcePersistentId theSourcePid) {
public Optional<M> getMatchedLinkForSourcePid(P theSourcePid) {
return myMdmLinkDao.findBySourcePidAndMatchResult(theSourcePid, MdmMatchResultEnum.MATCH);
}
@ -177,25 +178,25 @@ public class MdmLinkDaoSvc {
* @param theSourceResource The IBaseResource representing the source you wish to find the matching link for.
* @return the {@link IMdmLink} that contains the Match information for the source.
*/
public Optional<? extends IMdmLink> getMatchedLinkForSource(IBaseResource theSourceResource) {
public Optional<M> getMatchedLinkForSource(IBaseResource theSourceResource) {
return getMdmLinkWithMatchResult(theSourceResource, MdmMatchResultEnum.MATCH);
}
public Optional<? extends IMdmLink> getPossibleMatchedLinkForSource(IBaseResource theSourceResource) {
public Optional<M> getPossibleMatchedLinkForSource(IBaseResource theSourceResource) {
return getMdmLinkWithMatchResult(theSourceResource, MdmMatchResultEnum.POSSIBLE_MATCH);
}
@Nonnull
private Optional<? extends IMdmLink> getMdmLinkWithMatchResult(IBaseResource theSourceResource, MdmMatchResultEnum theMatchResult) {
ResourcePersistentId pid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theSourceResource);
private Optional<M> getMdmLinkWithMatchResult(IBaseResource theSourceResource, MdmMatchResultEnum theMatchResult) {
P pid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theSourceResource);
if (pid == null) {
return Optional.empty();
}
IMdmLink exampleLink = myMdmLinkFactory.newMdmLink();
M exampleLink = myMdmLinkFactory.newMdmLink();
exampleLink.setSourcePersistenceId(pid);
exampleLink.setMatchResult(theMatchResult);
Example<? extends IMdmLink> example = Example.of(exampleLink);
Example<M> example = Example.of(exampleLink);
return myMdmLinkDao.findOne(example);
}
@ -207,18 +208,18 @@ public class MdmLinkDaoSvc {
* @param theMatchResult The MatchResult you are looking for.
* @return an Optional {@link IMdmLink} containing the matched link if it exists.
*/
public Optional<? extends IMdmLink> getMdmLinksByGoldenResourcePidSourcePidAndMatchResult(Long theGoldenResourcePid,
public Optional<M> getMdmLinksByGoldenResourcePidSourcePidAndMatchResult(Long theGoldenResourcePid,
Long theSourcePid, MdmMatchResultEnum theMatchResult) {
return getMdmLinksByGoldenResourcePidSourcePidAndMatchResult(new ResourcePersistentId(theGoldenResourcePid), new ResourcePersistentId(theSourcePid), theMatchResult);
return getMdmLinksByGoldenResourcePidSourcePidAndMatchResult(myIdHelperService.newPid(theGoldenResourcePid), myIdHelperService.newPid(theSourcePid), theMatchResult);
}
public Optional<? extends IMdmLink> getMdmLinksByGoldenResourcePidSourcePidAndMatchResult(ResourcePersistentId theGoldenResourcePid,
ResourcePersistentId theSourcePid, MdmMatchResultEnum theMatchResult) {
IMdmLink exampleLink = myMdmLinkFactory.newMdmLink();
public Optional<M> getMdmLinksByGoldenResourcePidSourcePidAndMatchResult(P theGoldenResourcePid,
P theSourcePid, MdmMatchResultEnum theMatchResult) {
M exampleLink = myMdmLinkFactory.newMdmLink();
exampleLink.setGoldenResourcePersistenceId(theGoldenResourcePid);
exampleLink.setSourcePersistenceId(theSourcePid);
exampleLink.setMatchResult(theMatchResult);
Example<? extends IMdmLink> example = Example.of(exampleLink);
Example<M> example = Example.of(exampleLink);
return myMdmLinkDao.findOne(example);
}
@ -227,22 +228,22 @@ public class MdmLinkDaoSvc {
*
* @return A list of {@link IMdmLink} that hold potential duplicate golden resources.
*/
public List<? extends IMdmLink> getPossibleDuplicates() {
IMdmLink exampleLink = myMdmLinkFactory.newMdmLink();
public List<M> getPossibleDuplicates() {
M exampleLink = myMdmLinkFactory.newMdmLink();
exampleLink.setMatchResult(MdmMatchResultEnum.POSSIBLE_DUPLICATE);
Example<? extends IMdmLink> example = Example.of(exampleLink);
Example<M> example = Example.of(exampleLink);
return myMdmLinkDao.findAll(example);
}
@Transactional
public Optional<? extends IMdmLink> findMdmLinkBySource(IBaseResource theSourceResource) {
@Nullable ResourcePersistentId pid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theSourceResource);
public Optional<M> findMdmLinkBySource(IBaseResource theSourceResource) {
@Nullable P pid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theSourceResource);
if (pid == null) {
return Optional.empty();
}
IMdmLink exampleLink = myMdmLinkFactory.newMdmLink();
M exampleLink = myMdmLinkFactory.newMdmLink();
exampleLink.setSourcePersistenceId(pid);
Example<? extends IMdmLink> example = Example.of(exampleLink);
Example<M> example = Example.of(exampleLink);
return myMdmLinkDao.findOne(example);
}
@ -253,7 +254,7 @@ public class MdmLinkDaoSvc {
* @param theMdmLink the {@link IMdmLink} to delete.
*/
@Transactional(propagation = Propagation.REQUIRES_NEW)
public void deleteLink(IMdmLink theMdmLink) {
public void deleteLink(M theMdmLink) {
myMdmLinkDao.validateMdmLink(theMdmLink);
myMdmLinkDao.delete(theMdmLink);
}
@ -265,14 +266,14 @@ public class MdmLinkDaoSvc {
* @return A list of all {@link IMdmLink} entities in which theGoldenResource is the source Golden Resource
*/
@Transactional
public List<? extends IMdmLink> findMdmLinksByGoldenResource(IBaseResource theGoldenResource) {
ResourcePersistentId pid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theGoldenResource);
public List<M> findMdmLinksByGoldenResource(IBaseResource theGoldenResource) {
P pid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theGoldenResource);
if (pid == null) {
return Collections.emptyList();
}
IMdmLink exampleLink = myMdmLinkFactory.newMdmLink();
M exampleLink = myMdmLinkFactory.newMdmLink();
exampleLink.setGoldenResourcePersistenceId(pid);
Example<? extends IMdmLink> example = Example.of(exampleLink);
Example<M> example = Example.of(exampleLink);
return myMdmLinkDao.findAll(example);
}
@ -282,8 +283,8 @@ public class MdmLinkDaoSvc {
* @param theMdmLink the link to save.
* @return the persisted {@link IMdmLink} entity.
*/
public IMdmLink save(IMdmLink theMdmLink) {
IMdmLink mdmLink = myMdmLinkDao.validateMdmLink(theMdmLink);
public M save(M theMdmLink) {
M mdmLink = myMdmLinkDao.validateMdmLink(theMdmLink);
if (mdmLink.getCreated() == null) {
mdmLink.setCreated(new Date());
}
@ -303,7 +304,7 @@ public class MdmLinkDaoSvc {
* @param thePartitionId List of partitions ID being searched, where the link's partition must be in the list.
* @return a list of {@link IMdmLink} entities which match the example.
*/
public Page<? extends IMdmLink> executeTypedQuery(IIdType theGoldenResourceId, IIdType theSourceId, MdmMatchResultEnum theMatchResult, MdmLinkSourceEnum theLinkSource, MdmPageRequest thePageRequest, List<Integer> thePartitionId) {
public Page<M> executeTypedQuery(IIdType theGoldenResourceId, IIdType theSourceId, MdmMatchResultEnum theMatchResult, MdmLinkSourceEnum theLinkSource, MdmPageRequest thePageRequest, List<Integer> thePartitionId) {
return myMdmLinkDao.search(theGoldenResourceId, theSourceId, theMatchResult, theLinkSource, thePageRequest, thePartitionId);
}
@ -315,14 +316,14 @@ public class MdmLinkDaoSvc {
* @return all links for the source.
*/
@Transactional
public List<? extends IMdmLink> findMdmLinksBySourceResource(IBaseResource theSourceResource) {
ResourcePersistentId pid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theSourceResource);
public List<M> findMdmLinksBySourceResource(IBaseResource theSourceResource) {
P pid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theSourceResource);
if (pid == null) {
return Collections.emptyList();
}
IMdmLink exampleLink = myMdmLinkFactory.newMdmLink();
M exampleLink = myMdmLinkFactory.newMdmLink();
exampleLink.setSourcePersistenceId(pid);
Example<? extends IMdmLink> example = Example.of(exampleLink);
Example<M> example = Example.of(exampleLink);
return myMdmLinkDao.findAll(example);
}
@ -333,15 +334,15 @@ public class MdmLinkDaoSvc {
* @param theGoldenResource the source resource to find links for.
* @return all links for the source.
*/
public List<? extends IMdmLink> findMdmMatchLinksByGoldenResource(IBaseResource theGoldenResource) {
ResourcePersistentId pid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theGoldenResource);
public List<M> findMdmMatchLinksByGoldenResource(IBaseResource theGoldenResource) {
P pid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theGoldenResource);
if (pid == null) {
return Collections.emptyList();
}
IMdmLink exampleLink = myMdmLinkFactory.newMdmLink();
M exampleLink = myMdmLinkFactory.newMdmLink();
exampleLink.setGoldenResourcePersistenceId(pid);
exampleLink.setMatchResult(MdmMatchResultEnum.MATCH);
Example<? extends IMdmLink> example = Example.of(exampleLink);
Example<M> example = Example.of(exampleLink);
return myMdmLinkDao.findAll(example);
}
@ -355,16 +356,16 @@ public class MdmLinkDaoSvc {
return myMdmLinkFactory.newMdmLink();
}
public Optional<? extends IMdmLink> getMatchedOrPossibleMatchedLinkForSource(IAnyResource theResource) {
public Optional<M> getMatchedOrPossibleMatchedLinkForSource(IAnyResource theResource) {
// TODO KHS instead of two queries, just do one query with an OR
Optional<? extends IMdmLink> retval = getMatchedLinkForSource(theResource);
Optional<M> retval = getMatchedLinkForSource(theResource);
if (!retval.isPresent()) {
retval = getPossibleMatchedLinkForSource(theResource);
}
return retval;
}
public Optional<? extends IMdmLink> getLinkByGoldenResourceAndSourceResource(@Nullable IAnyResource theGoldenResource, @Nullable IAnyResource theSourceResource) {
public Optional<M> getLinkByGoldenResourceAndSourceResource(@Nullable IAnyResource theGoldenResource, @Nullable IAnyResource theSourceResource) {
if (theGoldenResource == null || theSourceResource == null) {
return Optional.empty();
}
@ -374,7 +375,7 @@ public class MdmLinkDaoSvc {
}
@Transactional(propagation = Propagation.MANDATORY)
public void deleteLinksWithAnyReferenceToPids(List<ResourcePersistentId> theGoldenResourcePids) {
public void deleteLinksWithAnyReferenceToPids(List<P> theGoldenResourcePids) {
myMdmLinkDao.deleteLinksWithAnyReferenceToPids(theGoldenResourcePids);
}
}

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

@ -36,7 +36,7 @@ import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.mdm.util.GoldenResourceHelper;
import ca.uhn.fhir.mdm.util.MdmResourceUtil;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IIdType;
@ -178,7 +178,7 @@ public class GoldenResourceMergerSvcImpl implements IGoldenResourceMergerSvc {
List<? extends IMdmLink> toLinks = myMdmLinkDaoSvc.findMdmLinksByGoldenResource(theToResource);
List<IMdmLink> toDelete = new ArrayList<>();
ResourcePersistentId goldenResourcePid = myIdHelperService.resolveResourcePersistentIds(
IResourcePersistentId goldenResourcePid = myIdHelperService.resolveResourcePersistentIds(
getPartitionIdForResource(theToResource),
theToResource.getIdElement().getResourceType(),
theToResource.getIdElement().getIdPart()

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

@ -35,7 +35,7 @@ import ca.uhn.fhir.mdm.api.MdmConstants;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.util.DateRangeUtil;
@ -77,7 +77,7 @@ public class GoldenResourceSearchSvcImpl implements IGoldenResourceSearchSvc {
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(theResourceType);
SystemRequestDetails request = new SystemRequestDetails();
request.setRequestPartitionId(theRequestPartitionId);
List<ResourcePersistentId> ids = dao.searchForIds(searchParamMap, request);
List<IResourcePersistentId> ids = dao.searchForIds(searchParamMap, request);
Date lastDate = null;
if (ids.size() > 0) {

1
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/IMdmModelConverterSvc.java
View File

@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.mdm.svc;
* #L%
*/
import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.mdm.api.IMdmLink;
import ca.uhn.fhir.mdm.api.MdmLinkJson;

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

@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.mdm.svc;
* #L%
*/
import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc;
import ca.uhn.fhir.jpa.mdm.svc.candidate.MatchedGoldenResourceCandidate;
import ca.uhn.fhir.jpa.mdm.svc.candidate.MdmGoldenResourceFindingSvc;
@ -35,7 +34,7 @@ import ca.uhn.fhir.mdm.model.CanonicalEID;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.mdm.util.EIDHelper;
import ca.uhn.fhir.mdm.util.GoldenResourceHelper;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
@ -168,7 +167,7 @@ public class MdmEidUpdateService {
if (theExistingMatchOrPossibleMatchLink.isPresent()) {
IMdmLink mdmLink = theExistingMatchOrPossibleMatchLink.get();
ResourcePersistentId existingGoldenResourcePid = mdmLink.getGoldenResourcePersistenceId();
IResourcePersistentId existingGoldenResourcePid = mdmLink.getGoldenResourcePersistenceId();
myExistingGoldenResource = myMdmResourceDaoSvc.readGoldenResourceByPid(existingGoldenResourcePid, resourceType);
myRemainsMatchedToSameGoldenResource = candidateIsSameAsMdmLinkGoldenResource(mdmLink, theMatchedGoldenResourceCandidate);
} else {

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

@ -37,7 +37,7 @@ import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.mdm.util.MdmResourceUtil;
import ca.uhn.fhir.mdm.util.MessageHelper;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.slf4j.Logger;
@ -71,8 +71,8 @@ public class MdmLinkCreateSvcImpl implements IMdmLinkCreateSvc {
validateCreateLinkRequest(theGoldenResource, theSourceResource, sourceType);
ResourcePersistentId goldenResourceId = myIdHelperService.getPidOrThrowException(theGoldenResource);
ResourcePersistentId targetId = myIdHelperService.getPidOrThrowException(theSourceResource);
IResourcePersistentId goldenResourceId = myIdHelperService.getPidOrThrowException(theGoldenResource);
IResourcePersistentId targetId = myIdHelperService.getPidOrThrowException(theSourceResource);
// check if the golden resource and the source resource are in the same partition, throw error if not
myMdmPartitionHelper.validateResourcesInSamePartition(theGoldenResource, theSourceResource);

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

@ -31,18 +31,17 @@ import ca.uhn.fhir.mdm.api.MdmMatchOutcome;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
import javax.annotation.Nonnull;
import org.springframework.transaction.annotation.Transactional;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
/**
* This class is in charge of managing MdmLinks between Golden Resources and source resources
@ -79,8 +78,8 @@ public class MdmLinkSvcImpl implements IMdmLinkSvc {
}
private boolean goldenResourceLinkedAsNoMatch(IAnyResource theGoldenResource, IAnyResource theSourceResource) {
ResourcePersistentId goldenResourceId = myIdHelperService.getPidOrThrowException(theGoldenResource);
ResourcePersistentId sourceId = myIdHelperService.getPidOrThrowException(theSourceResource);
IResourcePersistentId goldenResourceId = myIdHelperService.getPidOrThrowException(theGoldenResource);
IResourcePersistentId sourceId = myIdHelperService.getPidOrThrowException(theSourceResource);
// TODO perf collapse into one query
return myMdmLinkDaoSvc.getMdmLinksByGoldenResourcePidSourcePidAndMatchResult(goldenResourceId, sourceId, MdmMatchResultEnum.NO_MATCH).isPresent() ||
myMdmLinkDaoSvc.getMdmLinksByGoldenResourcePidSourcePidAndMatchResult(sourceId, goldenResourceId, MdmMatchResultEnum.NO_MATCH).isPresent();
@ -102,7 +101,7 @@ public class MdmLinkSvcImpl implements IMdmLinkSvc {
@Override
@Transactional
public void deleteLinksWithAnyReferenceTo(List<ResourcePersistentId> theGoldenResourceIds) {
public void deleteLinksWithAnyReferenceTo(List<IResourcePersistentId> theGoldenResourceIds) {
myMdmLinkDaoSvc.deleteLinksWithAnyReferenceToPids(theGoldenResourceIds);
}

14
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkUpdaterSvcImpl.java
View File

@ -38,7 +38,7 @@ import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.mdm.util.MdmResourceUtil;
import ca.uhn.fhir.mdm.util.MessageHelper;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import org.hl7.fhir.instance.model.api.IAnyResource;
@ -80,8 +80,8 @@ public class MdmLinkUpdaterSvcImpl implements IMdmLinkUpdaterSvc {
validateUpdateLinkRequest(theGoldenResource, theSourceResource, theMatchResult, sourceType);
ResourcePersistentId goldenResourceId = myIdHelperService.getPidOrThrowException(theGoldenResource);
ResourcePersistentId sourceResourceId = myIdHelperService.getPidOrThrowException(theSourceResource);
IResourcePersistentId goldenResourceId = myIdHelperService.getPidOrThrowException(theGoldenResource);
IResourcePersistentId sourceResourceId = myIdHelperService.getPidOrThrowException(theSourceResource);
// check if the golden resource and the source resource are in the same partition, throw error if not
myMdmPartitionHelper.validateResourcesInSamePartition(theGoldenResource, theSourceResource);
@ -130,12 +130,12 @@ public class MdmLinkUpdaterSvcImpl implements IMdmLinkUpdaterSvc {
* doesn't exist, because a resource mustn't be a MATCH to more than one golden resource
*/
private void validateNoMatchPresentWhenAcceptingPossibleMatch(IAnyResource theSourceResource,
ResourcePersistentId theGoldenResourceId, MdmMatchResultEnum theMatchResult) {
IResourcePersistentId theGoldenResourceId, MdmMatchResultEnum theMatchResult) {
// if theMatchResult != MATCH, we are not accepting POSSIBLE_MATCH so there is nothing to validate
if (theMatchResult != MdmMatchResultEnum.MATCH) { return; }
ResourcePersistentId sourceResourceId = myIdHelperService.getPidOrThrowException(theSourceResource);
IResourcePersistentId sourceResourceId = myIdHelperService.getPidOrThrowException(theSourceResource);
List<? extends IMdmLink> mdmLinks = myMdmLinkDaoSvc
.getMdmLinksBySourcePidAndMatchResult(sourceResourceId, MdmMatchResultEnum.MATCH);
@ -184,8 +184,8 @@ public class MdmLinkUpdaterSvcImpl implements IMdmLinkUpdaterSvc {
public void notDuplicateGoldenResource(IAnyResource theGoldenResource, IAnyResource theTargetGoldenResource, MdmTransactionContext theMdmContext) {
validateNotDuplicateGoldenResourceRequest(theGoldenResource, theTargetGoldenResource);
ResourcePersistentId goldenResourceId = myIdHelperService.getPidOrThrowException(theGoldenResource);
ResourcePersistentId targetId = myIdHelperService.getPidOrThrowException(theTargetGoldenResource);
IResourcePersistentId goldenResourceId = myIdHelperService.getPidOrThrowException(theGoldenResource);
IResourcePersistentId targetId = myIdHelperService.getPidOrThrowException(theTargetGoldenResource);
Optional<? extends IMdmLink> oMdmLink = myMdmLinkDaoSvc.getLinkByGoldenResourcePidAndSourceResourcePid(goldenResourceId, targetId);
if (oMdmLink.isEmpty()) {

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

@ -30,14 +30,14 @@ import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.mdm.util.GoldenResourceHelper;
import ca.uhn.fhir.mdm.util.MdmResourceUtil;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.server.TransactionLogMessages;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
import java.util.ArrayList;
import java.util.List;
@ -93,7 +93,7 @@ public class MdmMatchLinkSvc {
private void handleMdmWithMultipleCandidates(IAnyResource theResource, CandidateList theCandidateList, MdmTransactionContext theMdmTransactionContext) {
MatchedGoldenResourceCandidate firstMatch = theCandidateList.getFirstMatch();
ResourcePersistentId sampleGoldenResourcePid = firstMatch.getCandidateGoldenResourcePid();
IResourcePersistentId sampleGoldenResourcePid = firstMatch.getCandidateGoldenResourcePid();
boolean allSameGoldenResource = theCandidateList.stream()
.allMatch(candidate -> candidate.getCandidateGoldenResourcePid().equals(sampleGoldenResourcePid));

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

@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.mdm.svc;
* #L%
*/
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
@ -33,7 +33,7 @@ import ca.uhn.fhir.mdm.api.MdmConstants;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.hl7.fhir.instance.model.api.IAnyResource;
@ -77,7 +77,7 @@ public class MdmResourceDaoSvc {
resourceDao.removeTag(theGoldenResource.getIdElement(), TagTypeEnum.TAG, MdmConstants.SYSTEM_GOLDEN_RECORD_STATUS, MdmConstants.CODE_GOLDEN_RECORD, requestDetails);
}
public IAnyResource readGoldenResourceByPid(ResourcePersistentId theGoldenResourcePid, String theResourceType) {
public IAnyResource readGoldenResourceByPid(IResourcePersistentId theGoldenResourcePid, String theResourceType) {
IFhirResourceDao resourceDao = myDaoRegistry.getResourceDao(theResourceType);
return (IAnyResource) resourceDao.readByPid(theGoldenResourcePid);
}

7
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/FindCandidateByEidSvc.java
View File

@ -21,7 +21,6 @@ package ca.uhn.fhir.jpa.mdm.svc.candidate;
*/
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc;
import ca.uhn.fhir.jpa.mdm.svc.MdmResourceDaoSvc;
import ca.uhn.fhir.mdm.api.IMdmLink;
@ -30,7 +29,7 @@ import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.mdm.model.CanonicalEID;
import ca.uhn.fhir.mdm.util.EIDHelper;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
@ -66,7 +65,7 @@ public class FindCandidateByEidSvc extends BaseCandidateFinder {
if (isNoMatch(foundGoldenResource, theIncomingResource)) {
continue;
}
ResourcePersistentId pidOrNull = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), foundGoldenResource);
IResourcePersistentId pidOrNull = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), foundGoldenResource);
MatchedGoldenResourceCandidate mpc = new MatchedGoldenResourceCandidate(pidOrNull, MdmMatchOutcome.EID_MATCH);
ourLog.debug("Incoming Resource {} matched Golden Resource {} by EID {}", theIncomingResource.getIdElement().toUnqualifiedVersionless(), foundGoldenResource.getIdElement().toUnqualifiedVersionless(), eid);
@ -82,7 +81,7 @@ public class FindCandidateByEidSvc extends BaseCandidateFinder {
if (oLink.isEmpty()) {
return false;
}
MdmLink link = (MdmLink) oLink.get();
IMdmLink link = oLink.get();
return link.isNoMatch();
}

14
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/FindCandidateByExampleSvc.java
View File

@ -30,7 +30,7 @@ import ca.uhn.fhir.mdm.api.MatchedTarget;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
@ -43,14 +43,14 @@ import java.util.Optional;
import java.util.stream.Collectors;
@Service
public class FindCandidateByExampleSvc extends BaseCandidateFinder {
public class FindCandidateByExampleSvc<P extends IResourcePersistentId> extends BaseCandidateFinder {
private static final Logger ourLog = Logs.getMdmTroubleshootingLog();
@Autowired
IIdHelperService myIdHelperService;
IIdHelperService<P> myIdHelperService;
@Autowired
private FhirContext myFhirContext;
@Autowired
private MdmLinkDaoSvc myMdmLinkDaoSvc;
private MdmLinkDaoSvc<P, IMdmLink<P>> myMdmLinkDaoSvc;
@Autowired
private IMdmMatchFinderSvc myMdmMatchFinderSvc;
@ -66,7 +66,7 @@ public class FindCandidateByExampleSvc extends BaseCandidateFinder {
protected List<MatchedGoldenResourceCandidate> findMatchGoldenResourceCandidates(IAnyResource theTarget) {
List<MatchedGoldenResourceCandidate> retval = new ArrayList<>();
List<ResourcePersistentId> goldenResourcePidsToExclude = getNoMatchGoldenResourcePids(theTarget);
List<P> goldenResourcePidsToExclude = getNoMatchGoldenResourcePids(theTarget);
List<MatchedTarget> matchedCandidates = myMdmMatchFinderSvc.getMatchedTargets(myFhirContext.getResourceType(theTarget), theTarget, (RequestPartitionId) theTarget.getUserData(Constants.RESOURCE_PARTITION_ID));
@ -113,8 +113,8 @@ public class FindCandidateByExampleSvc extends BaseCandidateFinder {
return retval;
}
private List<ResourcePersistentId> getNoMatchGoldenResourcePids(IBaseResource theBaseResource) {
ResourcePersistentId targetPid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theBaseResource);
private List<P> getNoMatchGoldenResourcePids(IBaseResource theBaseResource) {
P targetPid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theBaseResource);
return myMdmLinkDaoSvc.getMdmLinksBySourcePidAndMatchResult(targetPid, MdmMatchResultEnum.NO_MATCH)
.stream()
.map(IMdmLink::getGoldenResourcePersistenceId)

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

@ -21,10 +21,9 @@ package ca.uhn.fhir.jpa.mdm.svc.candidate;
*/
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.mdm.api.IMdmLink;
import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.slf4j.Logger;
import org.springframework.stereotype.Service;
@ -38,7 +37,7 @@ public class FindCandidateByLinkSvc extends BaseCandidateFinder {
private static final Logger ourLog = Logs.getMdmTroubleshootingLog();
/**
* Attempt to find a currently matching Golden Resource, based on the presence of an {@link MdmLink} entity.
* Attempt to find a currently matching Golden Resource, based on the presence of an {@link IMdmLink} entity.
*
* @param theTarget the {@link IAnyResource} that we want to find candidate Golden Resources for.
* @return an Optional list of {@link MatchedGoldenResourceCandidate} indicating matches.
@ -47,11 +46,11 @@ public class FindCandidateByLinkSvc extends BaseCandidateFinder {
protected List<MatchedGoldenResourceCandidate> findMatchGoldenResourceCandidates(IAnyResource theTarget) {
List<MatchedGoldenResourceCandidate> retval = new ArrayList<>();
ResourcePersistentId targetPid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theTarget);
IResourcePersistentId targetPid = myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theTarget);
if (targetPid != null) {
Optional<? extends IMdmLink> oLink = myMdmLinkDaoSvc.getMatchedLinkForSourcePid(targetPid);
if (oLink.isPresent()) {
ResourcePersistentId goldenResourcePid = oLink.get().getGoldenResourcePersistenceId();
IResourcePersistentId goldenResourcePid = oLink.get().getGoldenResourcePersistenceId();
ourLog.debug("Resource previously linked. Using existing link.");
retval.add(new MatchedGoldenResourceCandidate(goldenResourcePid, oLink.get()));
}

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

@ -22,25 +22,24 @@ package ca.uhn.fhir.jpa.mdm.svc.candidate;
import ca.uhn.fhir.mdm.api.IMdmLink;
import ca.uhn.fhir.mdm.api.MdmMatchOutcome;
import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
public class MatchedGoldenResourceCandidate {
private final ResourcePersistentId myCandidateGoldenResourcePid;
private final IResourcePersistentId myCandidateGoldenResourcePid;
private final MdmMatchOutcome myMdmMatchOutcome;
public MatchedGoldenResourceCandidate(ResourcePersistentId theCandidate, MdmMatchOutcome theMdmMatchOutcome) {
public MatchedGoldenResourceCandidate(IResourcePersistentId theCandidate, MdmMatchOutcome theMdmMatchOutcome) {
myCandidateGoldenResourcePid = theCandidate;
myMdmMatchOutcome = theMdmMatchOutcome;
}
public MatchedGoldenResourceCandidate(ResourcePersistentId theGoldenResourcePid, IMdmLink theMdmLink) {
public MatchedGoldenResourceCandidate(IResourcePersistentId theGoldenResourcePid, IMdmLink theMdmLink) {
myCandidateGoldenResourcePid = theGoldenResourcePid;
myMdmMatchOutcome = new MdmMatchOutcome(theMdmLink.getVector(), theMdmLink.getScore()).setMatchResultEnum(theMdmLink.getMatchResult());
}
public ResourcePersistentId getCandidateGoldenResourcePid() {
public IResourcePersistentId getCandidateGoldenResourcePid() {
return myCandidateGoldenResourcePid;
}

8
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/MdmCandidateSearchSvc.java
View File

@ -20,15 +20,15 @@ package ca.uhn.fhir.jpa.mdm.svc.candidate;
* #L%
*/
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.mdm.api.IMdmSettings;
import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.mdm.rules.json.MdmFilterSearchParamJson;
import ca.uhn.fhir.mdm.rules.json.MdmResourceSearchParamJson;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
@ -75,7 +75,7 @@ public class MdmCandidateSearchSvc {
*/
@Transactional
public Collection<IAnyResource> findCandidates(String theResourceType, IAnyResource theResource, RequestPartitionId theRequestPartitionId) {
Map<ResourcePersistentId, IAnyResource> matchedPidsToResources = new HashMap<>();
Map<IResourcePersistentId, IAnyResource> matchedPidsToResources = new HashMap<>();
List<MdmFilterSearchParamJson> filterSearchParams = myMdmSettings.getMdmRules().getCandidateFilterSearchParams();
List<String> filterCriteria = buildFilterQuery(filterSearchParams, theResourceType);
List<MdmResourceSearchParamJson> candidateSearchParams = myMdmSettings.getMdmRules().getCandidateSearchParams();
@ -120,7 +120,7 @@ public class MdmCandidateSearchSvc {
* 4. Store all results in `theMatchedPidsToResources`
*/
@SuppressWarnings("rawtypes")
private void searchForIdsAndAddToMap(String theResourceType, IAnyResource theResource, Map<ResourcePersistentId, IAnyResource> theMatchedPidsToResources, List<String> theFilterCriteria, MdmResourceSearchParamJson resourceSearchParam, RequestPartitionId theRequestPartitionId) {
private void searchForIdsAndAddToMap(String theResourceType, IAnyResource theResource, Map<IResourcePersistentId, IAnyResource> theMatchedPidsToResources, List<String> theFilterCriteria, MdmResourceSearchParamJson resourceSearchParam, RequestPartitionId theRequestPartitionId) {
//1.
Optional<String> oResourceCriteria = myMdmCandidateSearchCriteriaBuilderSvc.buildResourceQueryString(theResourceType, theResource, theFilterCriteria, resourceSearchParam);
if (!oResourceCriteria.isPresent()) {

4
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/candidate/MdmGoldenResourceFindingSvc.java
View File

@ -22,7 +22,7 @@ package ca.uhn.fhir.jpa.mdm.svc.candidate;
import ca.uhn.fhir.jpa.mdm.svc.MdmResourceDaoSvc;
import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
@ -77,7 +77,7 @@ public class MdmGoldenResourceFindingSvc {
}
public IAnyResource getGoldenResourceFromMatchedGoldenResourceCandidate(MatchedGoldenResourceCandidate theMatchedGoldenResourceCandidate, String theResourceType) {
ResourcePersistentId goldenResourcePid = theMatchedGoldenResourceCandidate.getCandidateGoldenResourcePid();
IResourcePersistentId goldenResourcePid = theMatchedGoldenResourceCandidate.getCandidateGoldenResourcePid();
return myMdmResourceDaoSvc.readGoldenResourceByPid(goldenResourcePid, theResourceType);
}
}

16
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/BaseMdmR4Test.java
View File

@ -19,6 +19,7 @@ import ca.uhn.fhir.jpa.mdm.matcher.IsPossibleMatchWith;
import ca.uhn.fhir.jpa.mdm.matcher.IsSameGoldenResourceAs;
import ca.uhn.fhir.jpa.mdm.svc.MdmMatchLinkSvc;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.partition.IPartitionLookupSvc;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@ -38,7 +39,6 @@ import ca.uhn.fhir.mdm.util.MdmResourceUtil;
import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import org.apache.commons.lang3.StringUtils;
@ -113,11 +113,11 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test {
@Autowired
protected MdmResourceMatcherSvc myMdmResourceMatcherSvc;
@Autowired
protected IMdmLinkDao myMdmLinkDao;
protected IMdmLinkDao<JpaPid, MdmLink> myMdmLinkDao;
@Autowired
protected MdmLinkDaoSvc myMdmLinkDaoSvc;
protected MdmLinkDaoSvc<JpaPid, MdmLink> myMdmLinkDaoSvc;
@Autowired
protected IIdHelperService myIdHelperService;
protected IIdHelperService<JpaPid> myIdHelperService;
@Autowired
protected IMdmSettings myMdmSettings;
@Autowired
@ -361,10 +361,10 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test {
String resourceType = theBaseResource.getIdElement().getResourceType();
IFhirResourceDao relevantDao = myDaoRegistry.getResourceDao(resourceType);
Optional<? extends IMdmLink> matchedLinkForTargetPid = myMdmLinkDaoSvc.getMatchedLinkForSourcePid(runInTransaction(() -> myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theBaseResource)));
Optional<MdmLink> matchedLinkForTargetPid = myMdmLinkDaoSvc.getMatchedLinkForSourcePid(runInTransaction(() -> myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), theBaseResource)));
if (matchedLinkForTargetPid.isPresent()) {
Long goldenResourcePid = matchedLinkForTargetPid.get().getGoldenResourcePersistenceId().getIdAsLong();
return (T) relevantDao.readByPid(new ResourcePersistentId(goldenResourcePid));
JpaPid jpaPid = matchedLinkForTargetPid.get().getGoldenResourcePersistenceId();
return (T) relevantDao.readByPid(jpaPid);
} else {
return null;
}
@ -372,7 +372,7 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test {
protected <T extends IBaseResource> T getTargetResourceFromMdmLink(IMdmLink theMdmLink, String theResourceType) {
IFhirResourceDao resourceDao = myDaoRegistry.getResourceDao(theResourceType);
return (T) resourceDao.readByPid(new ResourcePersistentId(theMdmLink.getGoldenResourcePersistenceId().getIdAsLong()));
return (T) resourceDao.readByPid(theMdmLink.getGoldenResourcePersistenceId());
}
protected Patient addExternalEID(Patient thePatient, String theEID) {

2
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/config/TestMdmConfigR4.java
View File

@ -1,10 +1,8 @@
package ca.uhn.fhir.jpa.mdm.config;
import ca.uhn.fhir.jpa.mdm.dao.JpaMdmLinkImplFactory;
import ca.uhn.fhir.jpa.mdm.helper.MdmHelperR4;
import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
import ca.uhn.fhir.mdm.dao.IMdmLinkImplFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Import;

17
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/dao/MdmLinkDaoSvcTest.java
View File

@ -1,16 +1,15 @@
package ca.uhn.fhir.jpa.mdm.dao;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.dao.data.IMdmLinkJpaRepository;
import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.util.TestUtil;
import ca.uhn.fhir.mdm.api.IMdmLink;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.model.MdmPidTuple;
import ca.uhn.fhir.mdm.rules.json.MdmRulesJson;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.Test;
@ -45,11 +44,11 @@ public class MdmLinkDaoSvcTest extends BaseMdmR4Test {
@Test
public void testUpdate() {
IMdmLink createdLink = myMdmLinkDaoSvc.save(createResourcesAndBuildTestMDMLink());
MdmLink createdLink = myMdmLinkDaoSvc.save(createResourcesAndBuildTestMDMLink());
assertThat(createdLink.getLinkSource(), is(MdmLinkSourceEnum.MANUAL));
TestUtil.sleepOneClick();
createdLink.setLinkSource(MdmLinkSourceEnum.AUTO);
IMdmLink updatedLink = myMdmLinkDaoSvc.save(createdLink);
MdmLink updatedLink = myMdmLinkDaoSvc.save(createdLink);
assertNotEquals(updatedLink.getCreated(), updatedLink.getUpdated());
}
@ -80,14 +79,14 @@ public class MdmLinkDaoSvcTest extends BaseMdmR4Test {
List<Long> expectedExpandedPids = mdmLinks.stream().map(MdmLink::getSourcePid).collect(Collectors.toList());
//SUT
List<MdmPidTuple> lists = runInTransaction(()->myMdmLinkDao.expandPidsBySourcePidAndMatchResult(new ResourcePersistentId(mdmLinks.get(0).getSourcePid()), MdmMatchResultEnum.MATCH));
List<MdmPidTuple<JpaPid>> lists = runInTransaction(() -> myMdmLinkDao.expandPidsBySourcePidAndMatchResult(JpaPid.fromId(mdmLinks.get(0).getSourcePid()), MdmMatchResultEnum.MATCH));
assertThat(lists, hasSize(10));
lists.stream()
.forEach(tuple -> {
assertThat(tuple.getGoldenPid().getIdAsLong(), is(equalTo(golden.getIdElement().getIdPartAsLong())));
assertThat(tuple.getSourcePid().getIdAsLong(), is(in(expectedExpandedPids)));
assertThat(tuple.getGoldenPid().getId(), is(equalTo(myIdHelperService.getPidOrThrowException(golden).getId())));
assertThat(tuple.getSourcePid().getId(), is(in(expectedExpandedPids)));
});
}
@ -99,9 +98,9 @@ public class MdmLinkDaoSvcTest extends BaseMdmR4Test {
mdmLink.setMatchResult(theMdmMatchResultEnum);
mdmLink.setCreated(new Date());
mdmLink.setUpdated(new Date());
mdmLink.setGoldenResourcePersistenceId(new ResourcePersistentId(thePatientPid));
mdmLink.setGoldenResourcePersistenceId(JpaPid.fromId(thePatientPid));
mdmLink.setSourcePersistenceId(runInTransaction(()->myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), patient)));
MdmLink saved= (MdmLink) myMdmLinkDao.save(mdmLink);
MdmLink saved= myMdmLinkDao.save(mdmLink);
return saved;
}
}

24
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/helper/MdmLinkHelper.java
View File

@ -8,6 +8,7 @@ import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc;
import ca.uhn.fhir.jpa.mdm.helper.testmodels.MDMLinkResults;
import ca.uhn.fhir.jpa.mdm.helper.testmodels.MDMState;
import ca.uhn.fhir.jpa.mdm.helper.testmodels.MdmTestLinkExpression;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmMatchOutcome;
@ -16,7 +17,6 @@ import ca.uhn.fhir.mdm.dao.IMdmLinkDao;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.mdm.util.MdmResourceUtil;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.Patient;
import org.slf4j.Logger;
@ -49,10 +49,10 @@ public class MdmLinkHelper {
@Autowired
private IFhirResourceDao<Patient> myPatientDao;
@Autowired
private MdmLinkDaoSvc myMdmLinkDaoSvc;
private MdmLinkDaoSvc<JpaPid, MdmLink> myMdmLinkDaoSvc;
@SuppressWarnings("rawtypes")
@Autowired
private IMdmLinkDao myMdmLinkDao;
private IMdmLinkDao<JpaPid, MdmLink> myMdmLinkDao;
@Autowired
private IdHelperService myIdHelperService;
@ -81,7 +81,7 @@ public class MdmLinkHelper {
* These links will be returned in an MDMLinkResults object, in case
* they are needed.
*/
public MDMLinkResults setup(MDMState<Patient> theState) {
public MDMLinkResults setup(MDMState<Patient, JpaPid> theState) {
MDMLinkResults results = new MDMLinkResults();
List<MdmTestLinkExpression> inputExpressions = theState.getParsedInputState();
@ -122,7 +122,7 @@ public class MdmLinkHelper {
return results;
}
private void createIfNeeded(MDMState<Patient> theState, String thePatientId) {
private void createIfNeeded(MDMState<Patient, JpaPid> theState, String thePatientId) {
Patient patient = theState.getParameter(thePatientId);
if (patient == null) {
// if it doesn't exist, create it
@ -131,7 +131,7 @@ public class MdmLinkHelper {
}
}
private Patient createPatientAndTags(String theId, MDMState<Patient> theState) {
private Patient createPatientAndTags(String theId, MDMState<Patient, JpaPid> theState) {
Patient patient = new Patient();
patient.setActive(true); // all mdm patients must be active
@ -150,11 +150,11 @@ public class MdmLinkHelper {
DaoMethodOutcome outcome = myPatientDao.update(patient,
SystemRequestDetails.forAllPartitions());
Patient outputPatient = (Patient) outcome.getResource();
theState.addPID(theId, outcome.getPersistentId());
theState.addPID(theId, (JpaPid) outcome.getPersistentId());
return outputPatient;
}
public void validateResults(MDMState<Patient> theState) {
public void validateResults(MDMState<Patient, JpaPid> theState) {
List<MdmTestLinkExpression> expectedOutputStates = theState.getParsedOutputState();
StringBuilder outputStateSB = new StringBuilder();
@ -222,9 +222,9 @@ public class MdmLinkHelper {
MdmLink theLink,
Patient theResource,
Side theSide,
MDMState<Patient> theState
MDMState<Patient, JpaPid> theState
) {
ResourcePersistentId resourcePid = theState.getPID(theResource.getIdElement().getIdPart());
JpaPid resourcePid = theState.getPID(theResource.getIdElement().getIdPart());
long linkPid;
if (theSide == Side.LHS) {
@ -235,10 +235,10 @@ public class MdmLinkHelper {
linkPid = theLink.getSourcePid();
}
return linkPid == resourcePid.getIdAsLong();
return linkPid == resourcePid.getId();
}
private String createStateFromLink(MdmLink theLink, MDMState<Patient> theState) {
private String createStateFromLink(MdmLink theLink, MDMState<Patient, JpaPid> theState) {
String LHS = "";
String RHS = "";
for (Map.Entry<String, Patient> set : theState.getParameterToValue().entrySet()) {

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