Merge remote-tracking branch 'remotes/origin/master' into ks-flyway
This commit is contained in:
Ken Stevens
commit
047fefce5e
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@ -20,15 +20,7 @@ package ca.uhn.fhir.jpa.dao;
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* #L%
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*/
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import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
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import ca.uhn.fhir.context.BaseRuntimeDeclaredChildDefinition;
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import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
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import ca.uhn.fhir.context.ConfigurationException;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
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import ca.uhn.fhir.context.RuntimeChildResourceDefinition;
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import ca.uhn.fhir.context.RuntimeResourceDefinition;
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import ca.uhn.fhir.context.RuntimeSearchParam;
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import ca.uhn.fhir.context.*;
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import ca.uhn.fhir.interceptor.api.HookParams;
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import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
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import ca.uhn.fhir.interceptor.api.Pointcut;
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@ -51,18 +43,8 @@ import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
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import ca.uhn.fhir.jpa.searchparam.util.SourceParam;
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import ca.uhn.fhir.jpa.term.VersionIndependentConcept;
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import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
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import ca.uhn.fhir.jpa.util.BaseIterator;
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import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
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import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
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import ca.uhn.fhir.jpa.util.ScrollableResultsIterator;
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import ca.uhn.fhir.jpa.util.SqlQueryList;
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import ca.uhn.fhir.model.api.IPrimitiveDatatype;
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import ca.uhn.fhir.model.api.IQueryParameterAnd;
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import ca.uhn.fhir.model.api.IQueryParameterOr;
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import ca.uhn.fhir.model.api.IQueryParameterType;
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import ca.uhn.fhir.model.api.IResource;
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import ca.uhn.fhir.model.api.Include;
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import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
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import ca.uhn.fhir.jpa.util.*;
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import ca.uhn.fhir.model.api.*;
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import ca.uhn.fhir.model.base.composite.BaseCodingDt;
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import ca.uhn.fhir.model.base.composite.BaseIdentifierDt;
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import ca.uhn.fhir.model.base.composite.BaseQuantityDt;
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@ -70,11 +52,7 @@ import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.model.primitive.InstantDt;
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import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
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import ca.uhn.fhir.parser.DataFormatException;
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import ca.uhn.fhir.rest.api.Constants;
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import ca.uhn.fhir.rest.api.QualifiedParamList;
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import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
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import ca.uhn.fhir.rest.api.SortOrderEnum;
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import ca.uhn.fhir.rest.api.SortSpec;
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import ca.uhn.fhir.rest.api.*;
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import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
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import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.fhir.rest.param.*;
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@ -85,6 +63,7 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
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import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
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import ca.uhn.fhir.util.StopWatch;
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import ca.uhn.fhir.util.UrlUtil;
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import com.google.common.annotations.VisibleForTesting;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Maps;
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import com.google.common.collect.Sets;
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@ -119,11 +98,7 @@ import java.util.Map.Entry;
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import java.util.stream.Collectors;
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import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
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import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
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import static org.apache.commons.lang3.StringUtils.defaultString;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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import static org.apache.commons.lang3.StringUtils.trim;
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import static org.apache.commons.lang3.StringUtils.*;
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/**
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* The SearchBuilder is responsible for actually forming the SQL query that handles
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@ -2595,6 +2570,8 @@ public class SearchBuilder implements ISearchBuilder {
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nextRoundMatches = pidsToInclude;
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} while (includes.size() > 0 && nextRoundMatches.size() > 0 && addedSomeThisRound);
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allAdded.removeAll(original);
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ourLog.info("Loaded {} {} in {} rounds and {} ms for search {}", allAdded.size(), theReverseMode ? "_revincludes" : "_includes", roundCounts, w.getMillisAndRestart(), theSearchIdOrDescription);
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// Interceptor call: STORAGE_PREACCESS_RESOURCES
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@ -3109,19 +3086,26 @@ public class SearchBuilder implements ISearchBuilder {
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}
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@VisibleForTesting
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void setParamsForUnitTest(SearchParameterMap theParams) {
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myParams = theParams;
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}
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SearchParameterMap getParams() {
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return myParams;
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}
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public class IncludesIterator extends BaseIterator<ResourcePersistentId> implements Iterator<ResourcePersistentId> {
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private final RequestDetails myRequest;
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private Iterator<ResourcePersistentId> myCurrentIterator;
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private int myCurrentOffset;
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private ArrayList<ResourcePersistentId> myCurrentPids;
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private Set<ResourcePersistentId> myCurrentPids;
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private ResourcePersistentId myNext;
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private int myPageSize = myDaoConfig.getEverythingIncludesFetchPageSize();
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IncludesIterator(Set<ResourcePersistentId> thePidSet, RequestDetails theRequest) {
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myCurrentPids = new ArrayList<>(thePidSet);
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myCurrentPids = new HashSet<>(thePidSet);
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myCurrentIterator = EMPTY_LONG_LIST.iterator();
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myCurrentOffset = 0;
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myRequest = theRequest;
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}
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@ -3133,21 +3117,13 @@ public class SearchBuilder implements ISearchBuilder {
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break;
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}
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int start = myCurrentOffset;
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int end = myCurrentOffset + myPageSize;
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if (end > myCurrentPids.size()) {
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end = myCurrentPids.size();
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}
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if (end - start <= 0) {
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Set<Include> includes = Collections.singleton(new Include("*", true));
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Set<ResourcePersistentId> newPids = loadIncludes(myContext, myEntityManager, myCurrentPids, includes, false, getParams().getLastUpdated(), mySearchUuid, myRequest);
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if (newPids.isEmpty()) {
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myNext = NO_MORE;
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break;
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}
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myCurrentOffset = end;
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Collection<ResourcePersistentId> pidsToScan = myCurrentPids.subList(start, end);
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Set<Include> includes = Collections.singleton(new Include("*", true));
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Set<ResourcePersistentId> newPids = loadIncludes(myContext, myEntityManager, pidsToScan, includes, false, myParams.getLastUpdated(), mySearchUuid, myRequest);
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myCurrentIterator = newPids.iterator();
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}
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}
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@ -3484,4 +3460,8 @@ public class SearchBuilder implements ISearchBuilder {
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return thePredicates.toArray(new Predicate[0]);
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}
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@VisibleForTesting
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void setEntityManagerForUnitTest(EntityManager theEntityManager) {
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myEntityManager = theEntityManager;
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}
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}
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@ -1,25 +1,34 @@
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package ca.uhn.fhir.jpa.dao;
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import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
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import ca.uhn.fhir.jpa.model.entity.ResourceLink;
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import ca.uhn.fhir.jpa.model.entity.ResourceTable;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.rest.param.ParamPrefixEnum;
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import org.junit.Test;
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import org.junit.runner.RunWith;
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import org.mockito.junit.MockitoJUnitRunner;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import javax.persistence.EntityManager;
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import javax.persistence.TypedQuery;
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import java.math.BigDecimal;
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import java.math.MathContext;
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import java.util.ArrayList;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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import static org.hamcrest.Matchers.startsWith;
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import static org.junit.Assert.*;
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import static org.mockito.ArgumentMatchers.any;
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import static org.mockito.Mockito.mock;
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import static org.mockito.Mockito.when;
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import java.math.BigDecimal;
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import java.math.MathContext;
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import org.junit.AfterClass;
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import org.junit.Test;
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import ca.uhn.fhir.rest.param.ParamPrefixEnum;
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import ca.uhn.fhir.util.TestUtil;
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@RunWith(MockitoJUnitRunner.class)
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public class SearchBuilderTest {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchBuilderTest.class);
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@AfterClass
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public static void afterClassClearContext() {
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TestUtil.clearAllStaticFieldsForUnitTest();
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}
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private static final Logger ourLog = LoggerFactory.getLogger(SearchBuilderTest.class);
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@Test
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public void testCalculateMultiplierEqualNoDecimal() {
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@ -97,5 +106,32 @@ public class SearchBuilderTest {
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assertThat(out.toPlainString(), startsWith("20.000"));
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}
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@Test
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public void testIncludeIterator() {
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BaseHapiFhirDao<?> mockDao = mock(BaseHapiFhirDao.class);
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when(mockDao.getConfig()).thenReturn(new DaoConfig());
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SearchBuilder searchBuilder = new SearchBuilder(mockDao);
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searchBuilder.setParamsForUnitTest(new SearchParameterMap());
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EntityManager mockEntityManager = mock(EntityManager.class);
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searchBuilder.setEntityManagerForUnitTest(mockEntityManager);
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Set<ResourcePersistentId> pidSet = new HashSet<>();
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pidSet.add(new ResourcePersistentId(1L));
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pidSet.add(new ResourcePersistentId(2L));
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TypedQuery mockQuery = mock(TypedQuery.class);
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when(mockEntityManager.createQuery(any(), any())).thenReturn(mockQuery);
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List<ResourceLink> resultList = new ArrayList<>();
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ResourceLink link = new ResourceLink();
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ResourceTable target = new ResourceTable();
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target.setId(1L);
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link.setTargetResource(target);
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resultList.add(link);
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when(mockQuery.getResultList()).thenReturn(resultList);
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SearchBuilder.IncludesIterator includesIterator = searchBuilder.new IncludesIterator(pidSet, null);
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// hasNext() should return false if the pid added was already on our list going in.
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assertFalse(includesIterator.hasNext());
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}
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}
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@ -1,11 +1,10 @@
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package ca.uhn.fhir.jpa.provider.dstu3;
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import static org.hamcrest.Matchers.*;
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import static org.junit.Assert.*;
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import java.io.IOException;
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import java.util.*;
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import ca.uhn.fhir.jpa.dao.DaoConfig;
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import ca.uhn.fhir.parser.StrictErrorHandler;
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import ca.uhn.fhir.rest.api.EncodingEnum;
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import ca.uhn.fhir.util.TestUtil;
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import com.google.common.base.Charsets;
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import org.apache.commons.io.IOUtils;
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import org.apache.http.client.ClientProtocolException;
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import org.apache.http.client.methods.CloseableHttpResponse;
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@ -14,25 +13,31 @@ import org.hl7.fhir.dstu3.model.*;
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import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
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import org.hl7.fhir.dstu3.model.Encounter.EncounterStatus;
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import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
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import org.junit.*;
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import org.junit.After;
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import org.junit.AfterClass;
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import org.junit.Before;
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import org.junit.Test;
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import com.google.common.base.Charsets;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Set;
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import java.util.TreeSet;
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import ca.uhn.fhir.jpa.dao.DaoConfig;
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import ca.uhn.fhir.parser.StrictErrorHandler;
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import ca.uhn.fhir.rest.api.EncodingEnum;
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import ca.uhn.fhir.util.TestUtil;
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import static org.hamcrest.Matchers.*;
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import static org.junit.Assert.*;
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public class PatientEverythingDstu3Test extends BaseResourceProviderDstu3Test {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(PatientEverythingDstu3Test.class);
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private String orgId;
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private String patId;
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private String myOrgId;
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private String myPatientId;
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private String encId1;
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private String encId2;
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private ArrayList<String> myObsIds;
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private String myWrongPatId;
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private String myWrongEnc1;
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private Organization myOrg;
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private Patient myPatient;
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@Before
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public void beforeDisableResultReuse() {
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@ -55,41 +60,43 @@ public class PatientEverythingDstu3Test extends BaseResourceProviderDstu3Test {
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myDaoConfig.setAllowMultipleDelete(true);
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Organization org = new Organization();
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org.setName("an org");
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orgId = ourClient.create().resource(org).execute().getId().toUnqualifiedVersionless().getValue();
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ourLog.info("OrgId: {}", orgId);
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myOrg = new Organization();
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myOrg.setName("an org");
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myOrgId = ourClient.create().resource(myOrg).execute().getId().toUnqualifiedVersionless().getValue();
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myOrg.setId(myOrgId);
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ourLog.info("OrgId: {}", myOrgId);
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Patient patient = new Patient();
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patient.getManagingOrganization().setReference(orgId);
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patId = ourClient.create().resource(patient).execute().getId().toUnqualifiedVersionless().getValue();
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myPatient = new Patient();
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myPatient.getManagingOrganization().setReference(myOrgId);
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myPatientId = ourClient.create().resource(myPatient).execute().getId().toUnqualifiedVersionless().getValue();
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myPatient.setId(myPatientId);
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Patient patient2 = new Patient();
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patient2.getManagingOrganization().setReference(orgId);
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patient2.getManagingOrganization().setReference(myOrgId);
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myWrongPatId = ourClient.create().resource(patient2).execute().getId().toUnqualifiedVersionless().getValue();
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Encounter enc1 = new Encounter();
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enc1.setStatus(EncounterStatus.CANCELLED);
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enc1.getSubject().setReference(patId);
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enc1.getServiceProvider().setReference(orgId);
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enc1.getSubject().setReference(myPatientId);
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enc1.getServiceProvider().setReference(myOrgId);
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encId1 = ourClient.create().resource(enc1).execute().getId().toUnqualifiedVersionless().getValue();
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Encounter enc2 = new Encounter();
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enc2.setStatus(EncounterStatus.ARRIVED);
|
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enc2.getSubject().setReference(patId);
|
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enc2.getServiceProvider().setReference(orgId);
|
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enc2.getSubject().setReference(myPatientId);
|
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enc2.getServiceProvider().setReference(myOrgId);
|
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encId2 = ourClient.create().resource(enc2).execute().getId().toUnqualifiedVersionless().getValue();
|
||||
|
||||
Encounter wrongEnc1 = new Encounter();
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wrongEnc1.setStatus(EncounterStatus.ARRIVED);
|
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wrongEnc1.getSubject().setReference(myWrongPatId);
|
||||
wrongEnc1.getServiceProvider().setReference(orgId);
|
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wrongEnc1.getServiceProvider().setReference(myOrgId);
|
||||
myWrongEnc1 = ourClient.create().resource(wrongEnc1).execute().getId().toUnqualifiedVersionless().getValue();
|
||||
|
||||
myObsIds = new ArrayList<String>();
|
||||
for (int i = 0; i < 20; i++) {
|
||||
Observation obs = new Observation();
|
||||
obs.getSubject().setReference(patId);
|
||||
obs.getSubject().setReference(myPatientId);
|
||||
obs.setStatus(ObservationStatus.FINAL);
|
||||
String obsId = ourClient.create().resource(obs).execute().getId().toUnqualifiedVersionless().getValue();
|
||||
myObsIds.add(obsId);
|
||||
|
|
@ -103,7 +110,7 @@ public class PatientEverythingDstu3Test extends BaseResourceProviderDstu3Test {
|
|||
@Test
|
||||
public void testEverythingReturnsCorrectResources() throws Exception {
|
||||
|
||||
Bundle bundle = fetchBundle(ourServerBase + "/" + patId + "/$everything?_format=json&_count=100", EncodingEnum.JSON);
|
||||
Bundle bundle = fetchBundle(ourServerBase + "/" + myPatientId + "/$everything?_format=json&_count=100", EncodingEnum.JSON);
|
||||
|
||||
assertNull(bundle.getLink("next"));
|
||||
|
||||
|
|
@ -114,15 +121,51 @@ public class PatientEverythingDstu3Test extends BaseResourceProviderDstu3Test {
|
|||
|
||||
ourLog.info("Found IDs: {}", actual);
|
||||
|
||||
assertThat(actual, hasItem(patId));
|
||||
assertThat(actual, hasItem(myPatientId));
|
||||
assertThat(actual, hasItem(encId1));
|
||||
assertThat(actual, hasItem(encId2));
|
||||
assertThat(actual, hasItem(orgId));
|
||||
assertThat(actual, hasItem(myOrgId));
|
||||
assertThat(actual, hasItems(myObsIds.toArray(new String[0])));
|
||||
assertThat(actual, not(hasItem(myWrongPatId)));
|
||||
assertThat(actual, not(hasItem(myWrongEnc1)));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testEverythingHandlesCircularReferences() throws Exception {
|
||||
Patient linkedPatient1 = new Patient();
|
||||
linkedPatient1.addLink().setOther(new Reference(myPatientId));
|
||||
String linkedPatient1Id = ourClient.create().resource(linkedPatient1).execute().getId().toUnqualifiedVersionless().getValue();
|
||||
|
||||
Patient linkedPatient2 = new Patient();
|
||||
linkedPatient2.addLink().setOther(new Reference(linkedPatient1Id));
|
||||
String linkedPatient2Id = ourClient.create().resource(linkedPatient2).execute().getId().toUnqualifiedVersionless().getValue();
|
||||
|
||||
myPatient.addLink().setOther(new Reference(linkedPatient2Id));
|
||||
ourClient.update().resource(myPatient).execute();
|
||||
|
||||
Bundle bundle = fetchBundle(ourServerBase + "/" + myPatientId + "/$everything?_format=json&_count=100", EncodingEnum.JSON);
|
||||
|
||||
assertNull(bundle.getLink("next"));
|
||||
|
||||
Set<String> actual = new TreeSet<String>();
|
||||
for (BundleEntryComponent nextEntry : bundle.getEntry()) {
|
||||
actual.add(nextEntry.getResource().getIdElement().toUnqualifiedVersionless().getValue());
|
||||
}
|
||||
|
||||
ourLog.info("Found IDs: {}", actual);
|
||||
|
||||
assertThat(actual, hasItem(myPatientId));
|
||||
assertThat(actual, hasItem(linkedPatient1Id));
|
||||
assertThat(actual, hasItem(linkedPatient2Id));
|
||||
assertThat(actual, hasItem(encId1));
|
||||
assertThat(actual, hasItem(encId2));
|
||||
assertThat(actual, hasItem(myOrgId));
|
||||
assertThat(actual, hasItems(myObsIds.toArray(new String[0])));
|
||||
assertThat(actual, not(hasItem(myWrongPatId)));
|
||||
assertThat(actual, not(hasItem(myWrongEnc1)));
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* See #674
|
||||
*/
|
||||
|
|
@ -130,7 +173,7 @@ public class PatientEverythingDstu3Test extends BaseResourceProviderDstu3Test {
|
|||
public void testEverythingReturnsCorrectResourcesSmallPage() throws Exception {
|
||||
myDaoConfig.setEverythingIncludesFetchPageSize(1);
|
||||
|
||||
Bundle bundle = fetchBundle(ourServerBase + "/" + patId + "/$everything?_format=json&_count=100", EncodingEnum.JSON);
|
||||
Bundle bundle = fetchBundle(ourServerBase + "/" + myPatientId + "/$everything?_format=json&_count=100", EncodingEnum.JSON);
|
||||
|
||||
assertNull(bundle.getLink("next"));
|
||||
|
||||
|
|
@ -141,10 +184,10 @@ public class PatientEverythingDstu3Test extends BaseResourceProviderDstu3Test {
|
|||
|
||||
ourLog.info("Found IDs: {}", actual);
|
||||
|
||||
assertThat(actual, hasItem(patId));
|
||||
assertThat(actual, hasItem(myPatientId));
|
||||
assertThat(actual, hasItem(encId1));
|
||||
assertThat(actual, hasItem(encId2));
|
||||
assertThat(actual, hasItem(orgId));
|
||||
assertThat(actual, hasItem(myOrgId));
|
||||
assertThat(actual, hasItems(myObsIds.toArray(new String[0])));
|
||||
assertThat(actual, not(hasItem(myWrongPatId)));
|
||||
assertThat(actual, not(hasItem(myWrongEnc1)));
|
||||
|
|
@ -156,7 +199,7 @@ public class PatientEverythingDstu3Test extends BaseResourceProviderDstu3Test {
|
|||
@Test
|
||||
public void testEverythingPagesWithCorrectEncodingJson() throws Exception {
|
||||
|
||||
Bundle bundle = fetchBundle(ourServerBase + "/" + patId + "/$everything?_format=json&_count=1", EncodingEnum.JSON);
|
||||
Bundle bundle = fetchBundle(ourServerBase + "/" + myPatientId + "/$everything?_format=json&_count=1", EncodingEnum.JSON);
|
||||
|
||||
assertNotNull(bundle.getLink("next").getUrl());
|
||||
assertThat(bundle.getLink("next").getUrl(), containsString("_format=json"));
|
||||
|
|
@ -173,7 +216,7 @@ public class PatientEverythingDstu3Test extends BaseResourceProviderDstu3Test {
|
|||
@Test
|
||||
public void testEverythingPagesWithCorrectEncodingXml() throws Exception {
|
||||
|
||||
Bundle bundle = fetchBundle(ourServerBase + "/" + patId + "/$everything?_format=xml&_count=1", EncodingEnum.XML);
|
||||
Bundle bundle = fetchBundle(ourServerBase + "/" + myPatientId + "/$everything?_format=xml&_count=1", EncodingEnum.XML);
|
||||
|
||||
assertNotNull(bundle.getLink("next").getUrl());
|
||||
ourLog.info("Next link: {}", bundle.getLink("next").getUrl());
|
||||
|
|
|
|||
Loading…
Reference in New Issue