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updating partition interceptor to allow multiple patient ids (#5326) 

* updating partition interceptor to allow multiple patient ids

* spotless

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
This commit is contained in:
TipzCM 2023-09-22 13:23:43 -04:00 committed by GitHub
parent cfa5e2ef65
commit 0049319751
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GPG Key ID: 4AEE18F83AFDEB23
8 changed files with 183 additions and 48 deletions
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6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5235-allow-search-on-multiple-patient-ids-in-partitioned-environment.yaml Normal file
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@ -0,0 +1,6 @@
---
type: add
issue: 5235
title: "Changes have been made to allow searching on multiple patient _ids
when in a patient_id partitioned environment.
"

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java
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@ -162,7 +162,6 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
boolean theExcludeDeleted)
throws ResourceNotFoundException {
assert myDontCheckActiveTransactionForUnitTest || TransactionSynchronizationManager.isSynchronizationActive();
assert theRequestPartitionId != null;
if (theResourceId.contains("/")) {
theResourceId = theResourceId.substring(theResourceId.indexOf("/") + 1);
@ -510,8 +509,6 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
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()));
if (theId.isEmpty()) {

56
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/BaseMdmR4Test.java
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@ -183,6 +183,17 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test {
@Nonnull
protected Patient createPatient(Patient thePatient, boolean theMdmManaged, boolean isRedirect) {
return createPatientWithUpdate(
thePatient, theMdmManaged, isRedirect, false
);
}
protected Patient createPatientWithUpdate(
Patient thePatient,
boolean theMdmManaged,
boolean isRedirect,
boolean theUseUpdateBool
) {
if (theMdmManaged) {
MdmResourceUtil.setMdmManaged(thePatient);
if (isRedirect) {
@ -192,9 +203,15 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test {
}
}
DaoMethodOutcome outcome = myPatientDao.create(thePatient);
Patient patient = (Patient) outcome.getResource();
patient.setId(outcome.getId());
Patient patient;
if (theUseUpdateBool) {
DaoMethodOutcome outcome = myPatientDao.update(thePatient);
patient = (Patient) outcome.getResource();
} else {
DaoMethodOutcome outcome = myPatientDao.create(thePatient);
patient = (Patient) outcome.getResource();
patient.setId(outcome.getId());
}
return patient;
}
@ -209,8 +226,25 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test {
return patient;
}
public Patient createPatientOnPartition(
Patient thePatient,
boolean theMdmManaged,
boolean isRedirect,
RequestPartitionId theRequestPartitionId
) {
return createPatientOnPartition(
thePatient, theMdmManaged, isRedirect, theRequestPartitionId, false
);
}
@Nonnull
protected Patient createPatientOnPartition(Patient thePatient, boolean theMdmManaged, boolean isRedirect, RequestPartitionId theRequestPartitionId) {
protected Patient createPatientOnPartition(
Patient thePatient,
boolean theMdmManaged,
boolean isRedirect,
RequestPartitionId theRequestPartitionId,
boolean theDoUpdate
) {
if (theMdmManaged) {
MdmResourceUtil.setMdmManaged(thePatient);
if (isRedirect) {
@ -222,9 +256,17 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test {
SystemRequestDetails systemRequestDetails = new SystemRequestDetails();
systemRequestDetails.setRequestPartitionId(theRequestPartitionId);
DaoMethodOutcome outcome = myPatientDao.create(thePatient, systemRequestDetails);
Patient patient = (Patient) outcome.getResource();
patient.setId(outcome.getId());
Patient patient;
if (theDoUpdate) {
DaoMethodOutcome outcome = myPatientDao.update(thePatient, systemRequestDetails);
patient = (Patient) outcome.getResource();
patient.setId(outcome.getId());
} else {
DaoMethodOutcome outcome = myPatientDao.create(thePatient, systemRequestDetails);
patient = (Patient) outcome.getResource();
patient.setId(outcome.getId());
}
patient.setUserData(Constants.RESOURCE_PARTITION_ID, theRequestPartitionId);
return patient;
}

82
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmResourceDaoSvcTest.java
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@ -2,28 +2,42 @@ package ca.uhn.fhir.jpa.mdm.svc;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.entity.PartitionEntity;
import ca.uhn.fhir.jpa.interceptor.PatientIdPartitionInterceptor;
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamExtractor;
import ca.uhn.fhir.mdm.util.MdmResourceUtil;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.rest.param.StringOrListParam;
import ca.uhn.fhir.rest.param.StringParam;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.is;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
public class MdmResourceDaoSvcTest extends BaseMdmR4Test {
private static final String TEST_EID = "TEST_EID";
@Autowired
MdmResourceDaoSvc myResourceDaoSvc;
@Autowired
private ISearchParamExtractor mySearchParamExtractor;
@Override
@AfterEach
@ -77,6 +91,74 @@ public class MdmResourceDaoSvcTest extends BaseMdmR4Test {
assertThat(foundSourcePatient.get().getIdElement().toUnqualifiedVersionless().getValue(), is(goodSourcePatient.getIdElement().toUnqualifiedVersionless().getValue()));
}
@Test
public void testSearchForMultiplePatientsByIdInPartitionedEnvironment() {
// setup
int resourceCount = 3;
String[] idPrefaces = new String[] {
"RED", "BLUE", "GREEN"
};
SearchParameterMap map;
IBundleProvider result;
myPartitionSettings.setPartitioningEnabled(true);
myPartitionSettings.setUnnamedPartitionMode(true);
myPartitionSettings.setIncludePartitionInSearchHashes(false);
PatientIdPartitionInterceptor interceptor = new PatientIdPartitionInterceptor(myFhirContext, mySearchParamExtractor, myPartitionSettings);
myInterceptorRegistry.registerInterceptor(interceptor);
try {
StringOrListParam patientIds = new StringOrListParam();
for (int i = 0; i < resourceCount; i++) {
String idPreface = idPrefaces[i];
Patient patient = new Patient();
patient.setId("Patient/" + idPreface + i);
// patients must be created with a forced id for PatientId partitioning
Patient patientOnPartition = createPatientWithUpdate(patient,
true, false, true);
patientIds.add(new StringParam("Patient/" +
patientOnPartition.getIdElement().getIdPart()
));
}
// test
map = SearchParameterMap.newSynchronous();
map.add("_id", patientIds);
result = myPatientDao.search(map, new SystemRequestDetails());
// verify
assertNotNull(result);
assertFalse(result.isEmpty());
List<IBaseResource> resources = result.getAllResources();
assertEquals(resourceCount, resources.size());
int count = 0;
for (IBaseResource resource : resources) {
String id = idPrefaces[count++];
assertTrue(resource instanceof Patient);
Patient patient = (Patient) resource;
assertTrue(patient.getId().contains(id));
}
// ensure single id works too
StringParam firstId = patientIds.getValuesAsQueryTokens().get(0);
map = SearchParameterMap.newSynchronous();
map.add("_id", firstId);
result = myPatientDao.search(map, new SystemRequestDetails());
// verify 2
assertNotNull(result);
resources = result.getAllResources();
assertEquals(1, resources.size());
assertTrue(result.getAllResources().get(0) instanceof Patient);
Patient patient = (Patient) result.getAllResources().get(0);
assertTrue(patient.getId().contains(firstId.getValue()));
} finally {
myInterceptorRegistry.unregisterInterceptor(interceptor);
}
}
@Test
public void testSearchGoldenResourceOnDifferentPartitions() {
myPartitionSettings.setPartitioningEnabled(true);

2
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/candidate/MdmPartitionedGoldenResourceFindingTest.java
View File

@ -28,6 +28,7 @@ public class MdmPartitionedGoldenResourceFindingTest extends BaseMdmR4Test {
public void testNoMatchOnResourcesInDifferentPartition(){
myMdmSettings.setSearchAllPartitionForMatch(false);
myPartitionSettings.setPartitioningEnabled(true);
myPartitionSettings.setUnnamedPartitionMode(false);
myPartitionLookupSvc.createPartition(new PartitionEntity().setId(1).setName(PARTITION_1), null);
myPartitionLookupSvc.createPartition(new PartitionEntity().setId(2).setName(PARTITION_2), null);
@ -51,6 +52,7 @@ public class MdmPartitionedGoldenResourceFindingTest extends BaseMdmR4Test {
public void testMatchOnResourcesInDifferentPartitionIfSearchAllPartition(){
myMdmSettings.setSearchAllPartitionForMatch(true);
myPartitionSettings.setPartitioningEnabled(true);
myPartitionSettings.setUnnamedPartitionMode(false);
myPartitionLookupSvc.createPartition(new PartitionEntity().setId(1).setName(PARTITION_1), null);
myPartitionLookupSvc.createPartition(new PartitionEntity().setId(2).setName(PARTITION_2), null);

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

@ -279,7 +279,7 @@ public class PatientIdPartitionInterceptorTest extends BaseJpaR4SystemTest {
.add("subject", new TokenParam("http://foo", "2"))
, mySrd);
} catch (MethodNotAllowedException e) {
assertEquals(Msg.code(1325) + "Multiple values for parameter subject is not supported in patient compartment mode", e.getMessage());
assertEquals(Msg.code(1324) + "Multiple values for parameter subject is not supported in patient compartment mode", e.getMessage());
}
// Multiple ORs

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

@ -117,6 +117,7 @@ public class JpaPackageCacheTest extends BaseJpaR4Test {
public void testSaveAndDeletePackageUnnamedPartitionsEnabled() throws IOException {
myPartitionSettings.setPartitioningEnabled(true);
myPartitionSettings.setDefaultPartitionId(0);
boolean isUnnamed = myPartitionSettings.isUnnamedPartitionMode();
myPartitionSettings.setUnnamedPartitionMode(true);
PatientIdPartitionInterceptor patientIdPartitionInterceptor = new PatientIdPartitionInterceptor(myFhirContext, mySearchParamExtractor, myPartitionSettings);
myInterceptorService.registerInterceptor(patientIdPartitionInterceptor);
@ -145,6 +146,7 @@ public class JpaPackageCacheTest extends BaseJpaR4Test {
List<String> deleteOutcomeMsgs = deleteOutcomeJson.getMessage();
assertEquals("Deleting package hl7.fhir.uv.shorthand#0.12.0", deleteOutcomeMsgs.get(0));
} finally {
myPartitionSettings.setUnnamedPartitionMode(isUnnamed);
myInterceptorService.unregisterInterceptor(patientIdPartitionInterceptor);
myInterceptorService.unregisterInterceptor(myRequestTenantPartitionInterceptor);
}

78
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/interceptor/PatientIdPartitionInterceptor.java
View File

@ -43,6 +43,7 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.IdType;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
@ -150,23 +151,25 @@ public class PatientIdPartitionInterceptor {
}
break;
case SEARCH_TYPE:
SearchParameterMap params = (SearchParameterMap) theReadDetails.getSearchParams();
String idPart = null;
SearchParameterMap params = theReadDetails.getSearchParams();
if ("Patient".equals(theReadDetails.getResourceType())) {
idPart = getSingleResourceIdValueOrNull(params, "_id", "Patient");
List<String> idParts = getResourceIdList(params, "_id", "Patient", false);
if (idParts.size() == 1) {
return provideCompartmentMemberInstanceResponse(theRequestDetails, idParts.get(0));
} else {
return RequestPartitionId.allPartitions();
}
} else {
for (RuntimeSearchParam nextCompartmentSp : compartmentSps) {
idPart = getSingleResourceIdValueOrNull(params, nextCompartmentSp.getName(), "Patient");
if (idPart != null) {
break;
List<String> idParts = getResourceIdList(params, nextCompartmentSp.getName(), "Patient", true);
if (!idParts.isEmpty()) {
return provideCompartmentMemberInstanceResponse(theRequestDetails, idParts.get(0));
}
}
}
if (isNotBlank(idPart)) {
return provideCompartmentMemberInstanceResponse(theRequestDetails, idPart);
}
break;
default:
@ -191,39 +194,40 @@ public class PatientIdPartitionInterceptor {
.collect(Collectors.toList());
}
private String getSingleResourceIdValueOrNull(
SearchParameterMap theParams, String theParamName, String theResourceType) {
String idPart = null;
private List<String> getResourceIdList(
SearchParameterMap theParams, String theParamName, String theResourceType, boolean theExpectOnlyOneBool) {
List<String> idParts = new ArrayList<>();
List<List<IQueryParameterType>> idParamAndList = theParams.get(theParamName);
if (idParamAndList != null && idParamAndList.size() == 1) {
List<IQueryParameterType> idParamOrList = idParamAndList.get(0);
if (idParamOrList.size() == 1) {
IQueryParameterType idParam = idParamOrList.get(0);
if (isNotBlank(idParam.getQueryParameterQualifier())) {
throw new MethodNotAllowedException(Msg.code(1322) + "The parameter " + theParamName
+ idParam.getQueryParameterQualifier() + " is not supported in patient compartment mode");
}
if (idParam instanceof ReferenceParam) {
String chain = ((ReferenceParam) idParam).getChain();
if (chain != null) {
throw new MethodNotAllowedException(Msg.code(1323) + "The parameter " + theParamName + "."
+ chain + " is not supported in patient compartment mode");
if (idParamAndList != null) {
for (List<IQueryParameterType> idParamOrList : idParamAndList) {
for (IQueryParameterType idParam : idParamOrList) {
if (isNotBlank(idParam.getQueryParameterQualifier())) {
throw new MethodNotAllowedException(
Msg.code(1322) + "The parameter " + theParamName + idParam.getQueryParameterQualifier()
+ " is not supported in patient compartment mode");
}
if (idParam instanceof ReferenceParam) {
String chain = ((ReferenceParam) idParam).getChain();
if (chain != null) {
throw new MethodNotAllowedException(Msg.code(1323) + "The parameter " + theParamName + "."
+ chain + " is not supported in patient compartment mode");
}
}
IdType id = new IdType(idParam.getValueAsQueryToken(myFhirContext));
if (!id.hasResourceType() || id.getResourceType().equals(theResourceType)) {
idParts.add(id.getIdPart());
}
}
IdType id = new IdType(idParam.getValueAsQueryToken(myFhirContext));
if (!id.hasResourceType() || id.getResourceType().equals(theResourceType)) {
idPart = id.getIdPart();
}
} else if (idParamOrList.size() > 1) {
throw new MethodNotAllowedException(Msg.code(1324) + "Multiple values for parameter " + theParamName
+ " is not supported in patient compartment mode");
}
} else if (idParamAndList != null && idParamAndList.size() > 1) {
throw new MethodNotAllowedException(Msg.code(1325) + "Multiple values for parameter " + theParamName
}
if (theExpectOnlyOneBool && idParts.size() > 1) {
throw new MethodNotAllowedException(Msg.code(1324) + "Multiple values for parameter " + theParamName
+ " is not supported in patient compartment mode");
}
return idPart;
return idParts;
}
/**