This shockingly works
This commit is contained in:
Tadgh
parent
a15ded7140
commit
419a5829ea
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@ -58,7 +58,7 @@ public interface IMdmLinkDao extends JpaRepository<MdmLink, Long> {
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Long getSourcePid();
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}
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@Query("SELECT ml.myGoldenResourcePid, ml.mySourcePid " +
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@Query("SELECT ml.myGoldenResourcePid as goldenPid, ml.mySourcePid as sourcePid " +
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"FROM MdmLink ml " +
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"INNER JOIN MdmLink ml2 " +
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"on ml.myGoldenResourcePid=ml2.myGoldenResourcePid " +
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@ -20,35 +20,22 @@ package ca.uhn.fhir.jpa.interceptor;
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* #L%
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*/
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.RuntimeSearchParam;
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import ca.uhn.fhir.interceptor.api.Hook;
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import ca.uhn.fhir.interceptor.api.Interceptor;
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import ca.uhn.fhir.interceptor.api.Pointcut;
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import ca.uhn.fhir.jpa.dao.index.IdHelperService;
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import ca.uhn.fhir.jpa.dao.mdm.MdmLinkExpandSvc;
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import ca.uhn.fhir.jpa.search.helper.SearchParamHelper;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.mdm.log.Logs;
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import ca.uhn.fhir.model.api.IQueryParameterAnd;
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import ca.uhn.fhir.model.api.IQueryParameterType;
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import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.rest.api.EncodingEnum;
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import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.fhir.rest.param.ReferenceParam;
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import ca.uhn.fhir.rest.param.StringParam;
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import ca.uhn.fhir.util.ClasspathUtil;
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import org.apache.commons.lang3.Validate;
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import org.hl7.fhir.instance.model.api.IBaseConformance;
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import org.slf4j.Logger;
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import org.springframework.beans.factory.annotation.Autowired;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.stream.Collectors;
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import static org.slf4j.LoggerFactory.getLogger;
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@ -62,24 +49,35 @@ public class MdmSearchExpandingInterceptorInterceptor {
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@Autowired
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private MdmLinkExpandSvc myMdmLinkExpandSvc;
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@Autowired
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private FhirContext myFhirContext;
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@Autowired
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private IdHelperService myIdHelperService;
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@Hook(Pointcut.STORAGE_PRESEARCH_REGISTERED)
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public void hook(RequestDetails theRequestDetails, SearchParameterMap theSearchParameterMap) {
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System.out.println("zoop");
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theSearchParameterMap.values().stream()
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.flatMap(Collection::stream)
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.flatMap(Collection::stream)
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.filter(param -> param instanceof ReferenceParam)
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.map(untypedParam -> (ReferenceParam)untypedParam)
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.filter(ReferenceParam::isMdmExpand)
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.forEach(mdmReferenceParam -> {
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Set<String> strings = myMdmLinkExpandSvc.expandMdmBySourceResourceId(new IdDt(mdmReferenceParam.getValue()));
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System.out.println(String.join(",", strings));
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//TODO in AM, start here with a test that actually has an expansion to expand against.
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});
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public void hook(SearchParameterMap theSearchParameterMap) {
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for (List<List<IQueryParameterType>> andList : theSearchParameterMap.values()) {
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for (List<IQueryParameterType> orList : andList) {
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expandAnyReferenceParameters(orList);
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}
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}
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}
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/**
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* If a Parameter is a reference parameter, and it has been set to expand MDM, perform the expansion.
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*/
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private void expandAnyReferenceParameters(List<IQueryParameterType> orList) {
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List<IQueryParameterType> toRemove = new ArrayList<>();
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List<IQueryParameterType> toAdd = new ArrayList<>();
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for (IQueryParameterType iQueryParameterType : orList) {
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if (iQueryParameterType instanceof ReferenceParam) {
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ReferenceParam refParam = (ReferenceParam) iQueryParameterType;
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if (refParam.isMdmExpand()) {
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Set<String> strings = myMdmLinkExpandSvc.expandMdmBySourceResourceId(new IdDt(refParam.getValue()));
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if (!strings.isEmpty()) {
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toRemove.add(refParam);
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strings.stream().map(resourceId -> new ReferenceParam(refParam.getResourceType() + "/" + resourceId)).forEach(toAdd::add);
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}
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}
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}
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}
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orList.removeAll(toRemove);
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orList.addAll(toAdd);
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}
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}
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@ -0,0 +1,348 @@
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package ca.uhn.fhir.jpa.mdm.interceptor;
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import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
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import ca.uhn.fhir.jpa.dao.index.IdHelperService;
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import ca.uhn.fhir.jpa.entity.MdmLink;
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import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
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import ca.uhn.fhir.jpa.mdm.helper.MdmHelperConfig;
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import ca.uhn.fhir.jpa.mdm.helper.MdmHelperR4;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.mdm.model.CanonicalEID;
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import ca.uhn.fhir.mdm.rules.config.MdmSettings;
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import ca.uhn.fhir.model.dstu2.resource.Observation;
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import ca.uhn.fhir.rest.api.server.IBundleProvider;
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import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
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import ca.uhn.fhir.rest.param.ReferenceOrListParam;
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import ca.uhn.fhir.rest.param.ReferenceParam;
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import ca.uhn.fhir.rest.param.StringParam;
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import ca.uhn.fhir.rest.param.TokenParam;
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import ca.uhn.fhir.rest.server.TransactionLogMessages;
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import ca.uhn.fhir.rest.server.exceptions.ForbiddenOperationException;
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import org.hl7.fhir.instance.model.api.IAnyResource;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.Enumerations;
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import org.hl7.fhir.r4.model.Medication;
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import org.hl7.fhir.r4.model.Organization;
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import org.hl7.fhir.r4.model.Patient;
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import org.hl7.fhir.r4.model.SearchParameter;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.extension.RegisterExtension;
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import org.slf4j.Logger;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.test.annotation.DirtiesContext;
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import org.springframework.test.context.ContextConfiguration;
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import java.util.Date;
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import java.util.List;
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import static ca.uhn.fhir.mdm.api.MdmConstants.CODE_GOLDEN_RECORD;
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import static ca.uhn.fhir.mdm.api.MdmConstants.CODE_GOLDEN_RECORD_REDIRECTED;
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import static ca.uhn.fhir.mdm.api.MdmConstants.CODE_HAPI_MDM_MANAGED;
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import static ca.uhn.fhir.mdm.api.MdmConstants.SYSTEM_GOLDEN_RECORD_STATUS;
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import static ca.uhn.fhir.mdm.api.MdmConstants.SYSTEM_MDM_MANAGED;
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import static org.hamcrest.CoreMatchers.equalTo;
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import static org.hamcrest.CoreMatchers.is;
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import static org.hamcrest.CoreMatchers.notNullValue;
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import static org.hamcrest.CoreMatchers.startsWith;
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import static org.hamcrest.MatcherAssert.assertThat;
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import static org.hamcrest.Matchers.hasSize;
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import static org.hamcrest.Matchers.nullValue;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertNotNull;
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import static org.junit.jupiter.api.Assertions.fail;
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import static org.slf4j.LoggerFactory.getLogger;
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@DirtiesContext(classMode = DirtiesContext.ClassMode.AFTER_CLASS)
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@ContextConfiguration(classes = {MdmHelperConfig.class})
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public class MdmSearchExpandingInterceptorIT extends BaseMdmR4Test {
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private static final Logger ourLog = getLogger(MdmSearchExpandingInterceptorIT.class);
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@RegisterExtension
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@Autowired
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public MdmHelperR4 myMdmHelper;
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@Autowired
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private IdHelperService myIdHelperService;
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@Test
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public void testCreatePractitioner() throws InterruptedException {
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MdmHelperR4.OutcomeAndLogMessageWrapper withLatch = myMdmHelper.createWithLatch(addExternalEID(buildJanePatient(), "123"));
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IIdType id = withLatch.getDaoMethodOutcome().getId();
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myMdmHelper.createWithLatch(addExternalEID(buildJanePatient(), "123"));
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myMdmHelper.createWithLatch(addExternalEID(buildJanePatient(), "123"));
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myMdmHelper.createWithLatch(addExternalEID(buildJanePatient(), "123"));
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assertLinkCount(4);
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SearchParameterMap searchParameterMap = new SearchParameterMap();
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searchParameterMap.setLoadSynchronous(true);
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ReferenceOrListParam referenceOrListParam = new ReferenceOrListParam();
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referenceOrListParam.addOr(new ReferenceParam(id.toVersionless()).setMdmExpand(true));
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referenceOrListParam.addOr(new ReferenceParam(id.toVersionless()));
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referenceOrListParam.addOr(new ReferenceParam(id.toVersionless()));
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searchParameterMap.add(Observation.SP_SUBJECT, referenceOrListParam);
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searchParameterMap.add(Observation.SP_CATEGORY, new TokenParam("test-1", "test-2"));
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searchParameterMap.add(Observation.SP_ENCOUNTER, new ReferenceParam("Encounter/abc"));
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myObservationDao.search(searchParameterMap);
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}
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@Test
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public void testSearchExpandingInterceptorWorks() {
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SearchParameterMap subject = new SearchParameterMap("subject", new ReferenceParam("Patient/123").setMdmExpand(true)).setLoadSynchronous(true);
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myObservationDao.search(subject);
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}
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@Test
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public void testDeleteGoldenResourceDeletesLinks() throws InterruptedException {
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myMdmHelper.createWithLatch(buildPaulPatient());
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assertLinkCount(1);
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Patient sourcePatient = getOnlyGoldenPatient();
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myPatientDao.delete(sourcePatient.getIdElement());
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assertLinkCount(0);
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}
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@Test
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public void testCreatePatientWithMdmTagForbidden() throws InterruptedException {
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//Creating a golden resource with the MDM-MANAGED tag should fail
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Patient patient = new Patient();
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patient.getMeta().addTag(SYSTEM_MDM_MANAGED, CODE_HAPI_MDM_MANAGED, "User is managed by MDM");
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try {
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myMdmHelper.doCreateResource(patient, true);
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fail();
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} catch (ForbiddenOperationException e) {
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assertThat(e.getMessage(), startsWith("Cannot create or modify Resources that are managed by MDM."));
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}
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}
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@Test
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public void testCreatePatientWithGoldenRecordTagForbidden() throws InterruptedException {
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Patient patient = new Patient();
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patient.getMeta().addTag(SYSTEM_GOLDEN_RECORD_STATUS, CODE_GOLDEN_RECORD, "Golden Record");
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try {
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myMdmHelper.doCreateResource(patient, true);
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fail();
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} catch (ForbiddenOperationException e) {
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assertThat(e.getMessage(), startsWith("Cannot create or modify Resources that are managed by MDM."));
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}
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}
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@Test
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public void testCreateMedicationWithGoldenRecordRedirectTagForbidden() throws InterruptedException {
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Medication medication = new Medication();
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medication.getMeta().addTag(SYSTEM_GOLDEN_RECORD_STATUS, CODE_GOLDEN_RECORD_REDIRECTED, "Golden Record");
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try {
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myMdmHelper.doCreateResource(medication, true);
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fail();
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} catch (ForbiddenOperationException e) {
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assertThat(e.getMessage(), startsWith("Cannot create or modify Resources that are managed by MDM."));
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}
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}
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@Test
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public void testCreatingGoldenResourceWithInsufficentMDMAttributesIsNotMDMProcessed() throws InterruptedException {
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myMdmHelper.doCreateResource(new Patient(), true);
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assertLinkCount(0);
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}
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@Test
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public void testCreatingPatientWithOneOrMoreMatchingAttributesIsMDMProcessed() throws InterruptedException {
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myMdmHelper.createWithLatch(buildPaulPatient());
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assertLinkCount(1);
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}
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@Test
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public void testCreateOrganizationWithMdmTagForbidden() throws InterruptedException {
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//Creating a organization with the MDM-MANAGED tag should fail
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Organization organization = new Organization();
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organization.getMeta().addTag(SYSTEM_MDM_MANAGED, CODE_HAPI_MDM_MANAGED, "User is managed by MDM");
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try {
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myMdmHelper.doCreateResource(organization, true);
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fail();
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} catch (ForbiddenOperationException e) {
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assertThat(e.getMessage(), startsWith("Cannot create or modify Resources that are managed by MDM."));
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}
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}
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@Test
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public void testUpdateOrganizationWithMdmTagForbidden() throws InterruptedException {
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//Creating a organization with the MDM-MANAGED tag should fail
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Organization organization = new Organization();
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myMdmHelper.doCreateResource(organization, true);
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organization.getMeta().addTag(SYSTEM_MDM_MANAGED, CODE_HAPI_MDM_MANAGED, "User is managed by MDM");
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try {
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myMdmHelper.doUpdateResource(organization, true);
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fail();
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} catch (ForbiddenOperationException e) {
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assertEquals("The HAPI-MDM tag on a resource may not be changed once created.", e.getMessage());
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}
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}
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@Test
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public void testGoldenResourceRecordsManagedByMdmAllShareSameTag() throws InterruptedException {
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myMdmHelper.createWithLatch(buildJanePatient());
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myMdmHelper.createWithLatch(buildPaulPatient());
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//TODO GGG MDM: this test is out of date, since we now are using golden record Patients
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IBundleProvider search = myPatientDao.search(buildGoldenResourceSearchParameterMap());
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List<IBaseResource> resources = search.getResources(0, search.size());
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for (IBaseResource r : resources) {
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assertThat(r.getMeta().getTag(SYSTEM_MDM_MANAGED, CODE_HAPI_MDM_MANAGED), is(notNullValue()));
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}
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}
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@Test
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public void testNonMdmManagedGoldenResourceCannotHaveMdmManagedTagAddedToThem() {
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// GoldenResource created manually.
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Patient patient = new Patient();
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DaoMethodOutcome daoMethodOutcome = myMdmHelper.doCreateResource(patient, true);
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assertNotNull(daoMethodOutcome.getId());
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//Updating that patient to set them as MDM managed is not allowed.
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patient.getMeta().addTag(SYSTEM_MDM_MANAGED, CODE_HAPI_MDM_MANAGED, "User is managed by MDM");
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try {
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myMdmHelper.doUpdateResource(patient, true);
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fail();
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} catch (ForbiddenOperationException e) {
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assertEquals("The HAPI-MDM tag on a resource may not be changed once created.", e.getMessage());
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}
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}
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@Test
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public void testMdmManagedGoldenResourceCannotBeModifiedByGoldenResourceUpdateRequest() throws InterruptedException {
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// When MDM is enabled, only the MDM system is allowed to modify GoldenResource links of GoldenResources with the MDM-MANAGED tag.
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Patient patient = new Patient();
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IIdType patientId = myMdmHelper.createWithLatch(buildPaulPatient()).getDaoMethodOutcome().getId().toUnqualifiedVersionless();
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patient.setId(patientId);
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// Updating a Golden Resource Patient who was created via MDM should fail.
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MdmLink mdmLink = myMdmLinkDaoSvc.getMatchedLinkForSourcePid(myIdHelperService.getPidOrNull(patient)).get();
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Long sourcePatientPid = mdmLink.getGoldenResourcePid();
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Patient goldenResourcePatient = (Patient) myPatientDao.readByPid(new ResourcePersistentId(sourcePatientPid));
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goldenResourcePatient.setGender(Enumerations.AdministrativeGender.MALE);
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try {
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myMdmHelper.doUpdateResource(goldenResourcePatient, true);
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fail();
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} catch (ForbiddenOperationException e) {
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assertThat(e.getMessage(), startsWith("Cannot create or modify Resources that are managed by MDM."));
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}
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}
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@Test
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public void testMdmPointcutReceivesTransactionLogMessages() throws InterruptedException {
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MdmHelperR4.OutcomeAndLogMessageWrapper wrapper = myMdmHelper.createWithLatch(buildJanePatient());
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TransactionLogMessages mdmTransactionLogMessages = wrapper.getLogMessages();
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//There is no TransactionGuid here as there is no TransactionLog in this context.
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assertThat(mdmTransactionLogMessages.getTransactionGuid(), is(nullValue()));
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List<String> messages = mdmTransactionLogMessages.getValues();
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assertThat(messages.isEmpty(), is(false));
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}
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@Test
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public void testWhenASingularPatientUpdatesExternalEidThatGoldenResourceEidIsUpdated() throws InterruptedException {
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Patient jane = addExternalEID(buildJanePatient(), "some_eid");
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MdmHelperR4.OutcomeAndLogMessageWrapper latch = myMdmHelper.createWithLatch(jane);
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jane.setId(latch.getDaoMethodOutcome().getId());
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clearExternalEIDs(jane);
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jane = addExternalEID(jane, "some_new_eid");
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MdmHelperR4.OutcomeAndLogMessageWrapper outcomeWrapper = myMdmHelper.updateWithLatch(jane);
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IAnyResource patient = getGoldenResourceFromTargetResource(jane);
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List<CanonicalEID> externalEids = myEIDHelper.getExternalEid(patient);
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assertThat(externalEids, hasSize(1));
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assertThat("some_new_eid", is(equalTo(externalEids.get(0).getValue())));
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}
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@Test
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public void testWhenEidUpdatesAreDisabledForbidsUpdatesToEidsOnTargets() throws InterruptedException {
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setPreventEidUpdates(true);
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Patient jane = addExternalEID(buildJanePatient(), "some_eid");
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MdmHelperR4.OutcomeAndLogMessageWrapper latch = myMdmHelper.createWithLatch(jane);
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jane.setId(latch.getDaoMethodOutcome().getId());
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clearExternalEIDs(jane);
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jane = addExternalEID(jane, "some_new_eid");
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try {
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myMdmHelper.doUpdateResource(jane, true);
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fail();
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} catch (ForbiddenOperationException e) {
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assertThat(e.getMessage(), is(equalTo("While running with EID updates disabled, EIDs may not be updated on source resources")));
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}
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setPreventEidUpdates(false);
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}
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@Test
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public void testWhenMultipleEidsAreDisabledThatTheInterceptorRejectsCreatesWithThem() {
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setPreventMultipleEids(true);
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Patient patient = buildJanePatient();
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addExternalEID(patient, "123");
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addExternalEID(patient, "456");
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try {
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myMdmHelper.doCreateResource(patient, true);
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fail();
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} catch (ForbiddenOperationException e) {
|
||||
assertThat(e.getMessage(), is(equalTo("While running with multiple EIDs disabled, source resources may have at most one EID.")));
|
||||
}
|
||||
|
||||
setPreventMultipleEids(false);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testInterceptorHandlesNonMdmResources() {
|
||||
setPreventEidUpdates(true);
|
||||
|
||||
//Create some arbitrary resource.
|
||||
SearchParameter fooSp = new SearchParameter();
|
||||
fooSp.setCode("foo");
|
||||
fooSp.addBase("Bundle");
|
||||
fooSp.setType(Enumerations.SearchParamType.REFERENCE);
|
||||
fooSp.setTitle("FOO SP");
|
||||
fooSp.setExpression("Bundle.entry[0].resource.as(Composition).encounter");
|
||||
fooSp.setXpathUsage(SearchParameter.XPathUsageType.NORMAL);
|
||||
fooSp.setStatus(Enumerations.PublicationStatus.ACTIVE);
|
||||
|
||||
myMdmHelper.doCreateResource(fooSp, true);
|
||||
fooSp.setXpathUsage(SearchParameter.XPathUsageType.PHONETIC);
|
||||
myMdmHelper.doUpdateResource(fooSp, true);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testPatientsWithNoEIDCanBeUpdated() throws InterruptedException {
|
||||
setPreventEidUpdates(true);
|
||||
Patient p = buildPaulPatient();
|
||||
MdmHelperR4.OutcomeAndLogMessageWrapper wrapper = myMdmHelper.createWithLatch(p);
|
||||
|
||||
p.setId(wrapper.getDaoMethodOutcome().getId());
|
||||
p.setBirthDate(new Date());
|
||||
myMdmHelper.updateWithLatch(p);
|
||||
setPreventEidUpdates(false);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testPatientsCanHaveEIDAddedInStrictMode() throws InterruptedException {
|
||||
setPreventEidUpdates(true);
|
||||
Patient p = buildPaulPatient();
|
||||
MdmHelperR4.OutcomeAndLogMessageWrapper messageWrapper = myMdmHelper.createWithLatch(p);
|
||||
p.setId(messageWrapper.getDaoMethodOutcome().getId());
|
||||
addExternalEID(p, "external eid");
|
||||
myMdmHelper.updateWithLatch(p);
|
||||
setPreventEidUpdates(false);
|
||||
}
|
||||
|
||||
private void setPreventEidUpdates(boolean thePrevent) {
|
||||
((MdmSettings) myMdmSettings).setPreventEidUpdates(thePrevent);
|
||||
}
|
||||
|
||||
private void setPreventMultipleEids(boolean thePrevent) {
|
||||
((MdmSettings) myMdmSettings).setPreventMultipleEids(thePrevent);
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue