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This commit is contained in:
Tadgh 2021-03-23 18:11:39 -04:00
parent 659a877100
commit e6cfb77c79
7 changed files with 32 additions and 12 deletions
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7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
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@ -59,6 +59,7 @@ import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.graphql.JpaStorageServices;
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
import ca.uhn.fhir.jpa.interceptor.JpaConsentContextServices;
import ca.uhn.fhir.jpa.interceptor.MdmSearchExpandingInterceptorInterceptor;
import ca.uhn.fhir.jpa.interceptor.OverridePathBasedReferentialIntegrityForDeletesInterceptor;
import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingRuleBuilder;
import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
@ -457,6 +458,12 @@ public abstract class BaseConfig {
return new RequestTenantPartitionInterceptor();
}
@Bean
@Lazy
public MdmSearchExpandingInterceptorInterceptor mdmSearchExpandingInterceptorInterceptor() {
return new MdmSearchExpandingInterceptorInterceptor();
}
@Bean
@Lazy
public TerminologyUploaderProvider terminologyUploaderProvider() {

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/mdm/MdmLinkExpandSvc.java
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@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.dao.mdm;
import ca.uhn.fhir.jpa.dao.data.IMdmLinkDao;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -39,7 +40,7 @@ import java.util.Set;
@Service
public class MdmLinkExpandSvc {
private static final Logger ourLog = LoggerFactory.getLogger(MdmLinkExpandSvc.class);
private static final Logger ourLog = Logs.getMdmTroubleshootingLog();
@Autowired
private IMdmLinkDao myMdmLinkDao;
@ -54,6 +55,7 @@ public class MdmLinkExpandSvc {
* @return A set of strings representing the FHIR IDs of the expanded resources.
*/
public Set<String> expandMdmBySourceResource(IBaseResource theResource) {
ourLog.debug("About to MDM-expand source resource {}", theResource);
return expandMdmBySourceResourceId(theResource.getIdElement());
}
@ -65,6 +67,7 @@ public class MdmLinkExpandSvc {
* @return A set of strings representing the FHIR ids of the expanded resources.
*/
public Set<String> expandMdmBySourceResourceId(IIdType theId) {
ourLog.debug("About to expand source resource with resource id {}", theId);
Long pidOrThrowException = myIdHelperService.getPidOrThrowException(theId);
return expandMdmBySourceResourcePid(pidOrThrowException);
}
@ -77,11 +80,12 @@ public class MdmLinkExpandSvc {
* @return A set of strings representing the FHIR ids of the expanded resources.
*/
public Set<String> expandMdmBySourceResourcePid(Long theSourceResourcePid) {
ourLog.debug("About to expand source resource with PID {}", theSourceResourcePid);
List<List<Long>> goldenPidSourcePidTuples = myMdmLinkDao.expandPidsBySourcePidAndMatchResult(theSourceResourcePid, MdmMatchResultEnum.MATCH);
Set<Long> flattenedPids = new HashSet<>();
goldenPidSourcePidTuples.forEach(flattenedPids::addAll);
Set<String> resourceIds = myIdHelperService.translatePidsToFhirResourceIds(flattenedPids);
ourLog.debug("Pid {} has been expanded to [{}]", theSourceResourcePid, String.join(",", resourceIds));
return resourceIds;
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/MdmSearchExpandingInterceptorInterceptor.java
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@ -29,6 +29,7 @@ import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.dao.mdm.MdmLinkExpandSvc;
import ca.uhn.fhir.jpa.search.helper.SearchParamHelper;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.model.api.IQueryParameterAnd;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.primitive.IdDt;
@ -56,7 +57,7 @@ import static org.slf4j.LoggerFactory.getLogger;
*/
@Interceptor
public class MdmSearchExpandingInterceptorInterceptor {
private static final Logger ourLog = getLogger(MdmSearchExpandingInterceptorInterceptor.class);
private static final Logger ourLog = Logs.getMdmTroubleshootingLog();
@Autowired
private MdmLinkExpandSvc myMdmLinkExpandSvc;
@ -67,7 +68,6 @@ public class MdmSearchExpandingInterceptorInterceptor {
@Autowired
private IdHelperService myIdHelperService;
@Hook(Pointcut.STORAGE_PRECHECK_FOR_CACHED_SEARCH)
public boolean hook(RequestDetails theRequestDetails, SearchParameterMap theSearchParameterMap) {
Map<String, String[]> parameters =theRequestDetails.getParameters();
@ -75,11 +75,11 @@ public class MdmSearchExpandingInterceptorInterceptor {
if (parameters.containsKey("_mdm")) {
shouldExpandMdm = parameters.get("_mdm").length == 1 && parameters.get("_mdm")[0].equalsIgnoreCase("true");
}
if (shouldExpandMdm) {
ourLog.debug("Detected that incoming request has _mdm=true. The request was: {}", theRequestDetails.getRequestPath());
String resourceName = theRequestDetails.getResourceName();
Collection<RuntimeSearchParam> patientSearchParams = mySearchParamHelper.getPatientSearchParamsForResourceType(resourceName);
ourLog.debug("Resource type {} has patient search parameters [{}]", resourceName, patientSearchParams.stream().map(RuntimeSearchParam::getName).collect(Collectors.joining(", ")));
for (RuntimeSearchParam patientSearchParam: patientSearchParams) {
if (!theSearchParameterMap.containsKey(patientSearchParam.getName())) {
continue;

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
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@ -129,6 +129,7 @@ import org.hl7.fhir.r4.model.DocumentReference;
import org.hl7.fhir.r4.model.Encounter;
import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
import org.hl7.fhir.r4.model.EpisodeOfCare;
import org.hl7.fhir.r4.model.ExplanationOfBenefit;
import org.hl7.fhir.r4.model.Group;
import org.hl7.fhir.r4.model.Immunization;
import org.hl7.fhir.r4.model.ImmunizationRecommendation;
@ -378,6 +379,9 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
@Qualifier("myPatientDaoR4")
protected IFhirResourceDaoPatient<Patient> myPatientDao;
@Autowired
@Qualifier("myExplanationOfBenefitDaoR4")
protected IFhirResourceDao<ExplanationOfBenefit> myExplanationOfBenefitDao;
@Autowired
protected IResourceTableDao myResourceTableDao;
@Autowired
protected IResourceHistoryTableDao myResourceHistoryTableDao;

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchCustomSearchParamTest.java
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@ -38,6 +38,7 @@ import org.hl7.fhir.r4.model.DiagnosticReport;
import org.hl7.fhir.r4.model.Encounter;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
import org.hl7.fhir.r4.model.ExplanationOfBenefit;
import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.Group;
import org.hl7.fhir.r4.model.IntegerType;
@ -193,10 +194,8 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
search = myPatientDao.search(SearchParameterMap.newSynchronous("future-appointment-count", new NumberParam("lt0")));
assertEquals(0, search.size());
}
/**
* Draft search parameters should be ok even if they aren't completely valid
*/

9
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderCustomSearchParamR4Test.java
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@ -13,8 +13,11 @@ import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.gclient.DateClientParam;
import ca.uhn.fhir.rest.gclient.ReferenceClientParam;
import ca.uhn.fhir.rest.gclient.StringClientParam;
import ca.uhn.fhir.rest.gclient.TokenClientParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.BundleUtil;
import org.apache.commons.io.IOUtils;
@ -31,6 +34,7 @@ import org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestResource
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
import org.hl7.fhir.r4.model.ExplanationOfBenefit;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Observation.ObservationStatus;
import org.hl7.fhir.r4.model.Patient;
@ -54,6 +58,8 @@ import java.util.stream.Collectors;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.is;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull;
@ -328,9 +334,9 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
List<String> foundResources = toUnqualifiedVersionlessIdValues(bundle);
assertThat(foundResources, contains(p1id.getValue()));
}
@SuppressWarnings("unused")
@Test
public void testSearchQualifiedWithCustomReferenceParam() {
@ -416,6 +422,7 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
}
/**
* See #1300
*/

5
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmStorageInterceptor.java
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@ -36,6 +36,8 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.ForbiddenOperationException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.Patient;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
@ -57,13 +59,10 @@ public class MdmStorageInterceptor implements IMdmStorageInterceptor {
private EIDHelper myEIDHelper;
@Autowired
private IMdmSettings myMdmSettings;
@Autowired
private GoldenResourceHelper myGoldenResourceHelper;
@Hook(Pointcut.STORAGE_PRESTORAGE_RESOURCE_CREATED)
public void blockManualResourceManipulationOnCreate(IBaseResource theBaseResource, RequestDetails theRequestDetails, ServletRequestDetails theServletRequestDetails) {
//If running in single EID mode, forbid multiple eids.
if (myMdmSettings.isPreventMultipleEids()) {
forbidIfHasMultipleEids(theBaseResource);