Merge branch 'master' into 2948
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VK-SMILECDR
GitHub
commit
39f18e1897
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@ -1,4 +0,0 @@
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---
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type: fix
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issue: 2837
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title: "The :not modifier does not currently work for observations with multiple codes for the search. This is fixed."
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@ -989,11 +989,8 @@ public class QueryStack {
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SearchFilterParser.CompareOperation theOperation, RequestPartitionId theRequestPartitionId) {
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List<IQueryParameterType> tokens = new ArrayList<>();
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boolean paramInverted = false;
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TokenParamModifier modifier = null;
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for (IQueryParameterType nextOr : theList) {
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if (nextOr instanceof TokenParam) {
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if (!((TokenParam) nextOr).isEmpty()) {
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TokenParam id = (TokenParam) nextOr;
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@ -1014,18 +1011,15 @@ public class QueryStack {
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return createPredicateString(theSourceJoinColumn, theResourceName, theSpnamePrefix, theSearchParam, theList, null, theRequestPartitionId);
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}
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modifier = id.getModifier();
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// for :not modifier, create a token and remove the :not modifier
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if (modifier != null && modifier == TokenParamModifier.NOT) {
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tokens.add(new TokenParam(((TokenParam) nextOr).getSystem(), ((TokenParam) nextOr).getValue()));
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paramInverted = true;
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} else {
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tokens.add(nextOr);
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}
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tokens.add(nextOr);
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}
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} else {
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tokens.add(nextOr);
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}
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}
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if (tokens.isEmpty()) {
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@ -1033,31 +1027,14 @@ public class QueryStack {
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}
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String paramName = getParamNameWithPrefix(theSpnamePrefix, theSearchParam.getName());
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Condition predicate;
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BaseJoiningPredicateBuilder join;
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if (paramInverted) {
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SearchQueryBuilder sqlBuilder = mySqlBuilder.newChildSqlBuilder();
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TokenPredicateBuilder tokenSelector = sqlBuilder.addTokenPredicateBuilder(null);
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sqlBuilder.addPredicate(tokenSelector.createPredicateToken(tokens, theResourceName, theSpnamePrefix, theSearchParam, theRequestPartitionId));
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SelectQuery sql = sqlBuilder.getSelect();
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Expression subSelect = new Subquery(sql);
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TokenPredicateBuilder join = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.TOKEN, theSourceJoinColumn, paramName, () -> mySqlBuilder.addTokenPredicateBuilder(theSourceJoinColumn)).getResult();
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join = mySqlBuilder.getOrCreateFirstPredicateBuilder();
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predicate = new InCondition(join.getResourceIdColumn(), subSelect).setNegate(true);
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} else {
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TokenPredicateBuilder tokenJoin = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.TOKEN, theSourceJoinColumn, paramName, () -> mySqlBuilder.addTokenPredicateBuilder(theSourceJoinColumn)).getResult();
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if (theList.get(0).getMissing() != null) {
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return tokenJoin.createPredicateParamMissingForNonReference(theResourceName, paramName, theList.get(0).getMissing(), theRequestPartitionId);
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}
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predicate = tokenJoin.createPredicateToken(tokens, theResourceName, theSpnamePrefix, theSearchParam, theOperation, theRequestPartitionId);
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join = tokenJoin;
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if (theList.get(0).getMissing() != null) {
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return join.createPredicateParamMissingForNonReference(theResourceName, paramName, theList.get(0).getMissing(), theRequestPartitionId);
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}
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Condition predicate = join.createPredicateToken(tokens, theResourceName, theSpnamePrefix, theSearchParam, theOperation, theRequestPartitionId);
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return join.combineWithRequestPartitionIdPredicate(theRequestPartitionId, predicate);
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}
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@ -1,248 +0,0 @@
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package ca.uhn.fhir.jpa.provider.r4;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import java.io.IOException;
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import java.nio.charset.StandardCharsets;
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import java.util.ArrayList;
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import java.util.List;
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import org.apache.commons.io.IOUtils;
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import org.apache.http.client.methods.CloseableHttpResponse;
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import org.apache.http.client.methods.HttpGet;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.Bundle;
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import org.hl7.fhir.r4.model.CodeableConcept;
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import org.hl7.fhir.r4.model.DateTimeType;
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import org.hl7.fhir.r4.model.Observation;
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import org.hl7.fhir.r4.model.Observation.ObservationStatus;
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import org.hl7.fhir.r4.model.Patient;
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import org.hl7.fhir.r4.model.Quantity;
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import org.junit.jupiter.api.AfterEach;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Test;
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import ca.uhn.fhir.jpa.api.config.DaoConfig;
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import ca.uhn.fhir.parser.StrictErrorHandler;
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import ca.uhn.fhir.rest.client.interceptor.CapturingInterceptor;
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public class ResourceProviderSearchModifierR4Test extends BaseResourceProviderR4Test {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderSearchModifierR4Test.class);
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private CapturingInterceptor myCapturingInterceptor = new CapturingInterceptor();
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@Override
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@AfterEach
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public void after() throws Exception {
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super.after();
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myDaoConfig.setAllowMultipleDelete(new DaoConfig().isAllowMultipleDelete());
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myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
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myDaoConfig.setReuseCachedSearchResultsForMillis(new DaoConfig().getReuseCachedSearchResultsForMillis());
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myDaoConfig.setCountSearchResultsUpTo(new DaoConfig().getCountSearchResultsUpTo());
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myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
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myDaoConfig.setAllowContainsSearches(new DaoConfig().isAllowContainsSearches());
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myDaoConfig.setIndexMissingFields(new DaoConfig().getIndexMissingFields());
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myClient.unregisterInterceptor(myCapturingInterceptor);
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}
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@BeforeEach
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@Override
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public void before() throws Exception {
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super.before();
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myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
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myDaoConfig.setAllowMultipleDelete(true);
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myClient.registerInterceptor(myCapturingInterceptor);
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myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
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}
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@BeforeEach
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public void beforeDisableResultReuse() {
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myDaoConfig.setReuseCachedSearchResultsForMillis(null);
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}
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@Test
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public void testSearch_SingleCode_not_modifier() throws Exception {
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List<IIdType> obsList = createObs(10, false);
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String uri = ourServerBase + "/Observation?code:not=2345-3";
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List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
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assertEquals(9, ids.size());
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assertEquals(obsList.get(0).toString(), ids.get(0));
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assertEquals(obsList.get(1).toString(), ids.get(1));
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assertEquals(obsList.get(2).toString(), ids.get(2));
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assertEquals(obsList.get(4).toString(), ids.get(3));
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assertEquals(obsList.get(5).toString(), ids.get(4));
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assertEquals(obsList.get(6).toString(), ids.get(5));
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assertEquals(obsList.get(7).toString(), ids.get(6));
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assertEquals(obsList.get(8).toString(), ids.get(7));
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assertEquals(obsList.get(9).toString(), ids.get(8));
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}
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@Test
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public void testSearch_SingleCode_multiple_not_modifier() throws Exception {
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List<IIdType> obsList = createObs(10, false);
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String uri = ourServerBase + "/Observation?code:not=2345-3&code:not=2345-7&code:not=2345-9";
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List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
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assertEquals(7, ids.size());
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assertEquals(obsList.get(0).toString(), ids.get(0));
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assertEquals(obsList.get(1).toString(), ids.get(1));
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assertEquals(obsList.get(2).toString(), ids.get(2));
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assertEquals(obsList.get(4).toString(), ids.get(3));
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assertEquals(obsList.get(5).toString(), ids.get(4));
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assertEquals(obsList.get(6).toString(), ids.get(5));
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assertEquals(obsList.get(8).toString(), ids.get(6));
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}
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@Test
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public void testSearch_SingleCode_mix_modifier() throws Exception {
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List<IIdType> obsList = createObs(10, false);
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// Observation?code:not=2345-3&code:not=2345-7&code:not=2345-9
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// slower than Observation?code:not=2345-3&code=2345-7&code:not=2345-9
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String uri = ourServerBase + "/Observation?code:not=2345-3&code=2345-7&code:not=2345-9";
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List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
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assertEquals(1, ids.size());
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assertEquals(obsList.get(7).toString(), ids.get(0));
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}
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@Test
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public void testSearch_SingleCode_or_not_modifier() throws Exception {
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List<IIdType> obsList = createObs(10, false);
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String uri = ourServerBase + "/Observation?code:not=2345-3,2345-7,2345-9";
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List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
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assertEquals(7, ids.size());
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assertEquals(obsList.get(0).toString(), ids.get(0));
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assertEquals(obsList.get(1).toString(), ids.get(1));
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assertEquals(obsList.get(2).toString(), ids.get(2));
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assertEquals(obsList.get(4).toString(), ids.get(3));
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assertEquals(obsList.get(5).toString(), ids.get(4));
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assertEquals(obsList.get(6).toString(), ids.get(5));
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assertEquals(obsList.get(8).toString(), ids.get(6));
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}
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@Test
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public void testSearch_MultiCode_not_modifier() throws Exception {
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List<IIdType> obsList = createObs(10, true);
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String uri = ourServerBase + "/Observation?code:not=2345-3";
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List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
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assertEquals(8, ids.size());
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assertEquals(obsList.get(0).toString(), ids.get(0));
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assertEquals(obsList.get(1).toString(), ids.get(1));
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assertEquals(obsList.get(4).toString(), ids.get(2));
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assertEquals(obsList.get(5).toString(), ids.get(3));
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assertEquals(obsList.get(6).toString(), ids.get(4));
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assertEquals(obsList.get(7).toString(), ids.get(5));
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assertEquals(obsList.get(8).toString(), ids.get(6));
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assertEquals(obsList.get(9).toString(), ids.get(7));
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}
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@Test
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public void testSearch_MultiCode_multiple_not_modifier() throws Exception {
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List<IIdType> obsList = createObs(10, true);
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String uri = ourServerBase + "/Observation?code:not=2345-3&code:not=2345-4";
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List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
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assertEquals(7, ids.size());
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assertEquals(obsList.get(0).toString(), ids.get(0));
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assertEquals(obsList.get(1).toString(), ids.get(1));
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assertEquals(obsList.get(5).toString(), ids.get(2));
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assertEquals(obsList.get(6).toString(), ids.get(3));
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assertEquals(obsList.get(7).toString(), ids.get(4));
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assertEquals(obsList.get(8).toString(), ids.get(5));
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assertEquals(obsList.get(9).toString(), ids.get(6));
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}
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@Test
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public void testSearch_MultiCode_mix_modifier() throws Exception {
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List<IIdType> obsList = createObs(10, true);
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String uri = ourServerBase + "/Observation?code:not=2345-3&code=2345-7&code:not=2345-9";
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List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
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assertEquals(2, ids.size());
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assertEquals(obsList.get(6).toString(), ids.get(0));
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assertEquals(obsList.get(7).toString(), ids.get(1));
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}
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@Test
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public void testSearch_MultiCode_or_not_modifier() throws Exception {
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List<IIdType> obsList = createObs(10, true);
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String uri = ourServerBase + "/Observation?code:not=2345-3,2345-7,2345-9";
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List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
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assertEquals(4, ids.size());
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assertEquals(obsList.get(0).toString(), ids.get(0));
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assertEquals(obsList.get(1).toString(), ids.get(1));
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assertEquals(obsList.get(4).toString(), ids.get(2));
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assertEquals(obsList.get(5).toString(), ids.get(3));
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}
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private List<String> searchAndReturnUnqualifiedVersionlessIdValues(String uri) throws IOException {
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List<String> ids;
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HttpGet get = new HttpGet(uri);
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try (CloseableHttpResponse response = ourHttpClient.execute(get)) {
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String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
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ourLog.info("Response was: {}", resp);
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Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, resp);
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ourLog.info("Bundle: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
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ids = toUnqualifiedVersionlessIdValues(bundle);
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}
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return ids;
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}
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private List<IIdType> createObs(int obsNum, boolean isMultiple) {
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Patient patient = new Patient();
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patient.addIdentifier().setSystem("urn:system").setValue("001");
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patient.addName().setFamily("Tester").addGiven("Joe");
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IIdType pid = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
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List<IIdType> obsIds = new ArrayList<>();
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IIdType obsId = null;
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for (int i=0; i<obsNum; i++) {
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Observation obs = new Observation();
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obs.setStatus(ObservationStatus.FINAL);
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obs.getSubject().setReferenceElement(pid);
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obs.setEffective(new DateTimeType("2001-02-01"));
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CodeableConcept cc = obs.getCode();
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cc.addCoding().setCode("2345-"+i).setSystem("http://loinc.org");
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obs.setValue(new Quantity().setValue(200));
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if (isMultiple) {
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cc = obs.getCode();
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cc.addCoding().setCode("2345-"+(i+1)).setSystem("http://loinc.org");
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obs.setValue(new Quantity().setValue(300));
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}
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obsId = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
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obsIds.add(obsId);
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}
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return obsIds;
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}
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}
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