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3960 when creating a resource patient where patientmetasource is provided with a hash the hash value is overwritten (#3965) 

* Adding failing test.

* What was done:
-Meta source id is not replaced if provided.
-Added change log.

* Fixed code

* More tests for meta source

* Overwriting meta source can be configured.

* Test naming convention uplift and renaming of overwrite flag along with setter/getter

* Fixed when the source did not return if there was no resourceID

* Test naming convention uplift and renaming of overwrite flag along with setter/getter

* WIP in getting search on _source to be returning the correct number of patients.

* Custom requestId now stored on its own column

* Simplified getRequestId method in BaseHapiFhirDao

* Simplified getRequestId method in BaseHapiFhirDao

* An unused variable has been removed

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
This commit is contained in:
MykolaMedynskyiSCDR 2022-09-19 10:17:09 -04:00 committed by GitHub
parent c3339f38c3
commit 14253dd0e3
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7 changed files with 276 additions and 17 deletions
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5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/3960-when-creating-a-resource-patient-where-patientmetasource-is-provided-with-a-hash-the-hash-value-is-overwritten.yaml Normal file
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@ -0,0 +1,5 @@
---
type: fix
issue: 3960
jira: SMILE-4679
title: "Previously, when a client would provide a requestId within the source uri of a Meta.source, the provided requestId would get discarded and replaced by an id generated by the system. This has been corrected. And now it depends on configuration."

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
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@ -20,7 +20,6 @@ import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceProvenanceDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
import ca.uhn.fhir.jpa.dao.expunge.ExpungeService;
@ -205,8 +204,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
@Autowired
protected IForcedIdDao myForcedIdDao;
@Autowired
protected IResourceProvenanceDao myResourceProvenanceDao;
@Autowired
protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
@Autowired
protected ITermReadSvc myTerminologySvc;
@ -1207,7 +1204,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
+ defaultString(provenanceRequestId);
MetaUtil.setSource(myContext, retVal, sourceString);
}
// 7. Add partition information
@ -1626,7 +1622,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
// Save resource source
String source = null;
String requestId = theRequest != null ? theRequest.getRequestId() : null;
if (theResource != null) {
if (myContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.R4)) {
IBaseMetaType meta = theResource.getMeta();
@ -1644,6 +1640,9 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
}
}
String requestId = getRequestId(theRequest, source);
source = cleanProvenanceSourceUri(source);
boolean haveSource = isNotBlank(source) && myConfig.getStoreMetaSourceInformation().isStoreSourceUri();
boolean haveRequestId = isNotBlank(requestId) && myConfig.getStoreMetaSourceInformation().isStoreRequestId();
if (haveSource || haveRequestId) {
@ -1661,6 +1660,13 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
}
}
private String getRequestId(RequestDetails theRequest, String theSource) {
if (myConfig.isPreserveRequestIdInResourceBody()) {
return StringUtils.substringAfter(theSource, "#");
}
return theRequest != null ? theRequest.getRequestId() : null;
}
private void validateIncomingResourceTypeMatchesExisting(IBaseResource theResource, BaseHasResource entity) {
String resourceType = myContext.getResourceType(theResource);
if (!resourceType.equals(entity.getResourceType())) {

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceProvenanceDao.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceHistoryProvenanceDao.java
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@ -1,18 +1,11 @@
package ca.uhn.fhir.jpa.dao.data;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryProvenanceEntity;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Modifying;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
import java.util.Date;
import java.util.List;
import java.util.Map;
/*
* #%L
* HAPI FHIR JPA Server
@ -33,7 +26,7 @@ import java.util.Map;
* #L%
*/
public interface IResourceProvenanceDao extends JpaRepository<ResourceHistoryProvenanceEntity, Long>, IHapiFhirJpaRepository {
public interface IResourceHistoryProvenanceDao extends JpaRepository<ResourceHistoryProvenanceEntity, Long>, IHapiFhirJpaRepository {
@Modifying
@Query("DELETE FROM ResourceHistoryProvenanceEntity t WHERE t.myId = :pid")

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ResourceExpungeService.java
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@ -41,7 +41,7 @@ import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamStringDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamTokenDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
import ca.uhn.fhir.jpa.dao.data.IResourceLinkDao;
import ca.uhn.fhir.jpa.dao.data.IResourceProvenanceDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryProvenanceDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
import ca.uhn.fhir.jpa.dao.data.ISearchParamPresentDao;
@ -116,7 +116,7 @@ public class ResourceExpungeService implements IResourceExpungeService {
@Autowired
private DaoRegistry myDaoRegistry;
@Autowired
private IResourceProvenanceDao myResourceHistoryProvenanceTableDao;
private IResourceHistoryProvenanceDao myResourceHistoryProvenanceTableDao;
@Autowired
private ISearchParamPresentDao mySearchParamPresentDao;
@Autowired

4
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4FilterTest.java
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@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.IResourceProvenanceDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryProvenanceDao;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.rest.api.Constants;
@ -38,7 +38,7 @@ public class FhirResourceDaoR4FilterTest extends BaseJpaR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoR4FilterTest.class);
@Autowired
private IResourceProvenanceDao myResourceProvenanceDao;
private IResourceHistoryProvenanceDao myResourceProvenanceDao;
@AfterEach
public void after() {

229
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
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@ -2,9 +2,11 @@ package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryProvenanceDao;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryProvenanceEntity;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.model.util.UcumServiceUtil;
@ -245,6 +247,8 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myClient.unregisterInterceptor(myCapturingInterceptor);
myDaoConfig.setUpdateWithHistoryRewriteEnabled(false);
myDaoConfig.setPreserveRequestIdInResourceBody(false);
}
@BeforeEach
@ -7092,6 +7096,231 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
}
}
@Test
public void createResource_withPreserveRequestIdEnabled_requestIdIsPreserved(){
myDaoConfig.setPreserveRequestIdInResourceBody(true);
String expectedMetaSource = "mySource#345676";
String patientId = "1234a";
Patient patient = new Patient();
patient.getMeta().setSource(expectedMetaSource);
patient.setId(patientId);
patient.addName().addGiven("Phil").setFamily("Sick");
MethodOutcome outcome = myClient.update().resource(patient).execute();
IIdType iIdType = outcome.getId();
Patient returnedPatient = myClient.read().resource(Patient.class).withId(iIdType).execute();
String returnedPatientMetaSource = returnedPatient.getMeta().getSource();
assertEquals(expectedMetaSource, returnedPatientMetaSource);
}
@Test
public void createResource_withPreserveRequestIdEnabledAndRequestIdLengthGT16_requestIdIsPreserved(){
myDaoConfig.setPreserveRequestIdInResourceBody(true);
String metaSource = "mySource#123456789012345678901234567890";
String expectedMetaSource = "mySource#1234567890123456";
String patientId = "1234a";
Patient patient = new Patient();
patient.getMeta().setSource(metaSource);
patient.setId(patientId);
patient.addName().addGiven("Phil").setFamily("Sick");
MethodOutcome outcome = myClient.update().resource(patient).execute();
IIdType iIdType = outcome.getId();
Patient returnedPatient = myClient.read().resource(Patient.class).withId(iIdType).execute();
String returnedPatientMetaSource = returnedPatient.getMeta().getSource();
assertEquals(expectedMetaSource, returnedPatientMetaSource);
}
@Test
public void createResource_withPreserveRequestIdDisabled_RequestIdIsOverwritten(){
String sourceURL = "mySource";
String requestId = "#345676";
String patientId = "1234a";
Patient patient = new Patient();
patient.getMeta().setSource(sourceURL + requestId);
patient.setId(patientId);
patient.addName().addGiven("Phil").setFamily("Sick");
MethodOutcome outcome = myClient.update().resource(patient).execute();
IIdType iIdType = outcome.getId();
Patient returnedPatient = myClient.read().resource(Patient.class).withId(iIdType).execute();
String returnedPatientMetaSource = returnedPatient.getMeta().getSource();
assertTrue(returnedPatientMetaSource.startsWith(sourceURL));
assertFalse(returnedPatientMetaSource.endsWith(requestId));
}
@Test
public void searchResource_bySourceAndRequestIdWithPreserveRequestIdEnabled_isSuccess(){
myDaoConfig.setPreserveRequestIdInResourceBody(true);
String sourceUri = "mySource";
String requestId = "345676";
String expectedSourceUrl = sourceUri + "#" + requestId;
Patient patient = new Patient();
patient.getMeta().setSource(expectedSourceUrl);
myClient
.create()
.resource(patient)
.execute();
Bundle results = myClient
.search()
.byUrl(ourServerBase + "/Patient?_source=" + sourceUri + "%23" + requestId)
.returnBundle(Bundle.class)
.execute();
Patient returnedPatient = (Patient) results.getEntry().get(0).getResource();
String returnedPatientMetaSource = returnedPatient.getMeta().getSource();
assertEquals(1, results.getEntry().size());
assertEquals(expectedSourceUrl, returnedPatientMetaSource);
}
@Test
public void searchResource_bySourceAndRequestIdWithPreserveRequestIdDisabled_fails(){
String sourceURI = "mySource";
String requestId = "345676";
Patient patient = new Patient();
patient.getMeta().setSource(sourceURI + "#" + requestId);
myClient
.create()
.resource(patient)
.execute();
Bundle results = myClient
.search()
.byUrl(ourServerBase + "/Patient?_source=" + sourceURI + "%23" + requestId)
.returnBundle(Bundle.class)
.execute();
assertEquals(0, results.getEntry().size());
}
@Test
public void searchResource_bySourceWithPreserveRequestIdDisabled_isSuccess() {
String sourceUri = "http://acme.org";
String requestId = "my-fragment";
Patient p1 = new Patient();
p1.getMeta().setSource(sourceUri + "#" + requestId);
myClient
.create()
.resource(p1)
.execute();
Bundle results = myClient
.search()
.byUrl(ourServerBase + "/Patient?_source=" + sourceUri)
.returnBundle(Bundle.class)
.execute();
Patient returnedPatient = (Patient) results.getEntry().get(0).getResource();
String returnedPatientMetaSource = returnedPatient.getMeta().getSource();
assertEquals(1, results.getEntry().size());
assertTrue(returnedPatientMetaSource.startsWith(sourceUri));
assertFalse(returnedPatientMetaSource.endsWith(requestId));
}
@Test
public void searchResource_bySourceWithPreserveRequestIdEnabled_isSuccess() {
myDaoConfig.setPreserveRequestIdInResourceBody(true);
String sourceUri = "http://acme.org";
String requestId = "my-fragment";
String expectedSourceUrl = sourceUri + "#" + requestId;
Patient p1 = new Patient();
p1.getMeta().setSource(expectedSourceUrl);
myClient
.create()
.resource(p1)
.execute();
Bundle results = myClient
.search()
.byUrl(ourServerBase + "/Patient?_source=" + sourceUri)
.returnBundle(Bundle.class)
.execute();
Patient returnedPatient = (Patient) results.getEntry().get(0).getResource();
String returnedPatientMetaSource = returnedPatient.getMeta().getSource();
assertEquals(1, results.getEntry().size());
assertEquals(expectedSourceUrl, returnedPatientMetaSource);
}
@Test
public void searchResource_byRequestIdWithPreserveRequestIdEnabled_isSuccess() {
myDaoConfig.setPreserveRequestIdInResourceBody(true);
String sourceUri = "http://acme.org";
String requestId = "my-fragment";
String expectedSourceUrl = sourceUri + "#" + requestId;
Patient patient = new Patient();
patient.getMeta().setSource(expectedSourceUrl);
myClient
.create()
.resource(patient)
.execute();
Bundle results = myClient
.search()
.byUrl(ourServerBase + "/Patient?_source=%23" + requestId)
.returnBundle(Bundle.class)
.execute();
assertEquals(1, results.getEntry().size());
Patient returnedPatient = (Patient) results.getEntry().get(0).getResource();
String returnedPatientMetaSource = returnedPatient.getMeta().getSource();
assertEquals(expectedSourceUrl, returnedPatientMetaSource);
}
@Test
public void searchResource_bySourceAndWrongRequestIdWithPreserveRequestIdEnabled_fails() {
myDaoConfig.setPreserveRequestIdInResourceBody(true);
Patient patient = new Patient();
patient.getMeta().setSource("urn:source:0#my-fragment123");
myClient
.create()
.resource(patient)
.execute();
Bundle results = myClient
.search()
.byUrl(ourServerBase + "/Patient?_source=%23my-fragment000")
.returnBundle(Bundle.class)
.execute();
assertEquals(0, results.getEntry().size());
}
@Nonnull
private IIdType createNewPatientWithHistory() {
String TEST_SYSTEM_NAME = "testHistoryRewrite";

26
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java
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@ -319,6 +319,11 @@ public class DaoConfig {
*/
private boolean myUpdateWithHistoryRewriteEnabled = false;
/**
* Since 6.2.0
*/
private boolean myPreserveRequestIdInResourceBody = false;
/**
* Constructor
*/
@ -2911,6 +2916,27 @@ public class DaoConfig {
myUpdateWithHistoryRewriteEnabled = theUpdateWithHistoryRewriteEnabled;
}
/**
* This setting indicate whether a providedResource.meta.source requestID (source#requestID)
* should be preserved or overwritten.
*
* @since 6.2.0
*/
public boolean isPreserveRequestIdInResourceBody() {
return myPreserveRequestIdInResourceBody;
}
/**
* This setting indicate whether a providedResource.meta.source requestID (source#requestID)
* should be preserved or overwritten.
* Default is false. This means that a client provided requestId will be overwritten.
*
* @since 6.2.0
*/
public void setPreserveRequestIdInResourceBody(boolean thePreserveRequestIdInResourceBody) {
myPreserveRequestIdInResourceBody = thePreserveRequestIdInResourceBody;
}
public enum StoreMetaSourceInformationEnum {
NONE(false, false),