Fix '_include' to work for canonical urls (#3440)
* Added test to verify BUG: #2843 (_include doesn't return canonically referred resource) * Fix '_include' query search by native query to support canonical url references * Fixed code review comments
This commit is contained in:
Jaison Baskaran
GitHub
parent
20e092ba6d
commit
ecf782d59e
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@ -20,12 +20,12 @@ package ca.uhn.fhir.jpa.search.builder;
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* #L%
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*/
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import ca.uhn.fhir.i18n.Msg;
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import ca.uhn.fhir.context.ComboSearchParamType;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.FhirVersionEnum;
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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.i18n.Msg;
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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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@ -96,6 +96,7 @@ import com.google.common.annotations.VisibleForTesting;
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import com.google.common.collect.Lists;
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import com.healthmarketscience.sqlbuilder.Condition;
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import org.apache.commons.lang3.Validate;
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import org.apache.commons.lang3.math.NumberUtils;
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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.slf4j.Logger;
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@ -109,6 +110,9 @@ import javax.annotation.Nonnull;
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import javax.persistence.EntityManager;
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import javax.persistence.PersistenceContext;
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import javax.persistence.PersistenceContextType;
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import javax.persistence.Query;
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import javax.persistence.SqlResultSetMapping;
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import javax.persistence.Tuple;
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import javax.persistence.TypedQuery;
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import javax.persistence.criteria.CriteriaBuilder;
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import javax.persistence.criteria.CriteriaQuery;
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@ -148,6 +152,11 @@ public class SearchBuilder implements ISearchBuilder {
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public static final int MAXIMUM_PAGE_SIZE_FOR_TESTING = 50;
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private static final Logger ourLog = LoggerFactory.getLogger(SearchBuilder.class);
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private static final ResourcePersistentId NO_MORE = new ResourcePersistentId(-1L);
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private static final String MY_TARGET_RESOURCE_PID = "myTargetResourcePid";
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private static final String MY_SOURCE_RESOURCE_PID = "mySourceResourcePid";
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private static final String MY_TARGET_RESOURCE_VERSION = "myTargetResourceVersion";
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public static final String RESOURCE_ID_ALIAS = "resource_id";
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public static final String RESOURCE_VERSION_ALIAS = "resource_version";
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public static boolean myUseMaxPageSize50ForTest = false;
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private final String myResourceName;
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private final Class<? extends IBaseResource> myResourceType;
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@ -888,11 +897,11 @@ public class SearchBuilder implements ISearchBuilder {
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if (theIncludes == null || theIncludes.isEmpty()) {
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return new HashSet<>();
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}
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String searchPidFieldName = theReverseMode ? "myTargetResourcePid" : "mySourceResourcePid";
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String findPidFieldName = theReverseMode ? "mySourceResourcePid" : "myTargetResourcePid";
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String searchPidFieldName = theReverseMode ? MY_TARGET_RESOURCE_PID : MY_SOURCE_RESOURCE_PID;
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String findPidFieldName = theReverseMode ? MY_SOURCE_RESOURCE_PID : MY_TARGET_RESOURCE_PID;
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String findVersionFieldName = null;
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if (!theReverseMode && myModelConfig.isRespectVersionsForSearchIncludes()) {
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findVersionFieldName = "myTargetResourceVersion";
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findVersionFieldName = MY_TARGET_RESOURCE_VERSION;
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}
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List<ResourcePersistentId> nextRoundMatches = new ArrayList<>(theMatches);
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@ -1011,25 +1020,55 @@ public class SearchBuilder implements ISearchBuilder {
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String targetResourceType = defaultString(nextInclude.getParamTargetType(), null);
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for (String nextPath : paths) {
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String sql;
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boolean haveTargetTypesDefinedByParam = param.hasTargets();
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String fieldsToLoad = "r." + findPidFieldName;
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String findPidFieldSqlColumn = findPidFieldName.equals(MY_SOURCE_RESOURCE_PID) ? "src_resource_id" : "target_resource_id";
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String fieldsToLoad = "r." + findPidFieldSqlColumn + " AS " + RESOURCE_ID_ALIAS;
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if (findVersionFieldName != null) {
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fieldsToLoad += ", r." + findVersionFieldName;
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fieldsToLoad += ", r.target_resource_version AS " + RESOURCE_VERSION_ALIAS;
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}
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if (targetResourceType != null) {
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sql = "SELECT " + fieldsToLoad + " FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchPidFieldName + " IN (:target_pids) AND r.myTargetResourceType = :target_resource_type";
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} else if (haveTargetTypesDefinedByParam) {
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sql = "SELECT " + fieldsToLoad + " FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchPidFieldName + " IN (:target_pids) AND r.myTargetResourceType in (:target_resource_types)";
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} else {
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sql = "SELECT " + fieldsToLoad + " FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchPidFieldName + " IN (:target_pids)";
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// Query for includes lookup has consider 2 cases
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// Case 1: Where target_resource_id is available in hfj_res_link table for local references
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// Case 2: Where target_resource_id is null in hfj_res_link table and referred by a canonical url in target_resource_url
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// Case 1:
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String searchPidFieldSqlColumn = searchPidFieldName.equals(MY_TARGET_RESOURCE_PID) ? "target_resource_id" : "src_resource_id";
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StringBuilder resourceIdBasedQuery = new StringBuilder("SELECT " + fieldsToLoad +
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" FROM hfj_res_link r " +
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" WHERE r.src_path = :src_path AND " +
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" r.target_resource_id IS NOT NULL AND " +
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" r." + searchPidFieldSqlColumn + " IN (:target_pids) ");
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if(targetResourceType != null) {
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resourceIdBasedQuery.append(" AND r.target_resource_type = :target_resource_type ");
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} else if(haveTargetTypesDefinedByParam) {
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resourceIdBasedQuery.append(" AND r.target_resource_type in (:target_resource_types) ");
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}
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// Case 2:
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String fieldsToLoadFromSpidxUriTable = "rUri.res_id";
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// to match the fields loaded in union
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if(fieldsToLoad.split(",").length > 1) {
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for (int i = 0; i < fieldsToLoad.split(",").length - 1; i++) {
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fieldsToLoadFromSpidxUriTable += ", NULL";
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}
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}
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//@formatter:off
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StringBuilder resourceUrlBasedQuery = new StringBuilder("SELECT " + fieldsToLoadFromSpidxUriTable +
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" FROM hfj_res_link r " +
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" JOIN hfj_spidx_uri rUri ON ( " +
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" r.target_resource_url = rUri.sp_uri AND " +
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" rUri.sp_name = 'url' " +
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" ) " +
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" WHERE r.src_path = :src_path AND " +
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" r.target_resource_id IS NULL AND " +
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" r." + searchPidFieldSqlColumn + " IN (:target_pids) ");
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//@formatter:on
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String sql = resourceIdBasedQuery + " UNION " + resourceUrlBasedQuery;
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List<Collection<ResourcePersistentId>> partitions = partition(nextRoundMatches, getMaximumPageSize());
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for (Collection<ResourcePersistentId> nextPartition : partitions) {
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TypedQuery<?> q = theEntityManager.createQuery(sql, Object[].class);
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Query q = theEntityManager.createNativeQuery(sql, Tuple.class);
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q.setParameter("src_path", nextPath);
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q.setParameter("target_pids", ResourcePersistentId.toLongList(nextPartition));
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if (targetResourceType != null) {
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@ -1037,21 +1076,18 @@ public class SearchBuilder implements ISearchBuilder {
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} else if (haveTargetTypesDefinedByParam) {
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q.setParameter("target_resource_types", param.getTargets());
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}
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List<?> results = q.getResultList();
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List<Tuple> results = q.getResultList();
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if (theMaxCount != null) {
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q.setMaxResults(theMaxCount);
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}
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for (Object resourceLink : results) {
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if (resourceLink != null) {
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ResourcePersistentId persistentId;
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if (findVersionFieldName != null) {
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persistentId = new ResourcePersistentId(((Object[]) resourceLink)[0]);
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persistentId.setVersion((Long) ((Object[]) resourceLink)[1]);
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} else {
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persistentId = new ResourcePersistentId(resourceLink);
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for (Tuple result : results) {
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if (result != null) {
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Long resourceId = NumberUtils.createLong(String.valueOf(result.get(RESOURCE_ID_ALIAS)));
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Long resourceVersion = null;
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if (findVersionFieldName != null && result.get(RESOURCE_VERSION_ALIAS) != null) {
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resourceVersion = NumberUtils.createLong(String.valueOf(result.get(RESOURCE_VERSION_ALIAS)));
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}
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assert persistentId.getId() instanceof Long;
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pidsToInclude.add(persistentId);
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pidsToInclude.add(new ResourcePersistentId(resourceId, resourceVersion));
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}
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}
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}
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@ -14,20 +14,28 @@ import org.apache.http.client.methods.HttpPost;
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import org.apache.http.entity.ContentType;
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import org.apache.http.entity.StringEntity;
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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.Coding;
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import org.hl7.fhir.r4.model.DateType;
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import org.hl7.fhir.r4.model.DecimalType;
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import org.hl7.fhir.r4.model.Enumerations;
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import org.hl7.fhir.r4.model.IdType;
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import org.hl7.fhir.r4.model.Identifier;
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import org.hl7.fhir.r4.model.Patient;
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import org.hl7.fhir.r4.model.Questionnaire;
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import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemType;
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import org.hl7.fhir.r4.model.QuestionnaireResponse;
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import org.hl7.fhir.r4.model.QuestionnaireResponse.QuestionnaireResponseStatus;
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import org.hl7.fhir.r4.model.StringType;
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import org.junit.jupiter.api.AfterAll;
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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 java.nio.charset.StandardCharsets;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.List;
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import java.util.stream.Collectors;
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import static org.hamcrest.MatcherAssert.assertThat;
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import static org.hamcrest.Matchers.containsString;
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@ -71,12 +79,12 @@ public class ResourceProviderQuestionnaireResponseR4Test extends BaseResourcePro
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public void testCreateWithNonLocalReferenceWorksWithIncludes() {
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String baseUrl = "https://hapi.fhir.org/baseR4/";
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myModelConfig.setTreatBaseUrlsAsLocal(Collections.singleton(baseUrl));
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Questionnaire questionnaire = new Questionnaire();
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questionnaire.setUrl(baseUrl + "Questionnaire/my-questionnaire");
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questionnaire.setId("my-questionnaire");
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QuestionnaireResponse questionnaireResponse = new QuestionnaireResponse();
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questionnaireResponse.setQuestionnaire(baseUrl + "Questionnaire/my-questionnaire");
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questionnaireResponse.setQuestionnaire(questionnaire.getUrl());
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questionnaireResponse.setId("my-questionnaire-response");
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myQuestionnaireDao.update(questionnaire);
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@ -100,7 +108,7 @@ public class ResourceProviderQuestionnaireResponseR4Test extends BaseResourcePro
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Questionnaire q1 = new Questionnaire();
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q1.addItem().setLinkId("link1").setType(QuestionnaireItemType.STRING);
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IIdType qId = myQuestionnaireDao.create(q1, mySrd).getId().toUnqualifiedVersionless();
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QuestionnaireResponse qr1 = new QuestionnaireResponse();
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qr1.setQuestionnaire(qId.getValue());
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qr1.setStatus(QuestionnaireResponseStatus.COMPLETED);
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@ -112,49 +120,99 @@ public class ResourceProviderQuestionnaireResponseR4Test extends BaseResourcePro
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assertThat(myFhirContext.newJsonParser().encodeResourceToString(e.getOperationOutcome()), containsString("Answer value must be of type string"));
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}
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}
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/**
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* Test added to verify <a href="https://github.com/hapifhir/hapi-fhir/issues/2843">https://github.com/hapifhir/hapi-fhir/issues/2843</a>
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*/
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@Test
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public void testSearch_withIncludeQuestionnaire_shouldReturnWithCanonicalReferencedQuestionnaire() {
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String questionnaireCanonicalUrl = "https://hapi.fhir.org/baseR4/Questionnaire/xl-54127-6-hapi";
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Questionnaire questionnaire = new Questionnaire();
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questionnaire.setId("xl-54127-6-hapi");
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questionnaire.setUrl(questionnaireCanonicalUrl);
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questionnaire.addIdentifier(new Identifier().setSystem("http://loinc.org").setValue("54127-6"));
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questionnaire.setName("US Surgeon General family health portrait");
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questionnaire.setTitle(questionnaire.getName());
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questionnaire.setStatus(Enumerations.PublicationStatus.DRAFT);
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questionnaire.addSubjectType("Patient").addSubjectType("Person");
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questionnaire.addCode(new Coding("http://loinc.org", "54127-6", questionnaire.getName()));
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questionnaire.addItem().setLinkId("/54126-8")
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.setType(QuestionnaireItemType.GROUP)
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.setRequired(false)
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.setText("My health history")
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.addCode(new Coding("http://loinc.org", "54126-8", "My health history"));
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IIdType qIdType = myQuestionnaireDao.create(questionnaire, mySrd).getId().toUnqualifiedVersionless();
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QuestionnaireResponse questionnaireResponse = new QuestionnaireResponse();
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questionnaireResponse.setId("xl-54127-6-hapi-response");
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questionnaireResponse.setQuestionnaire(questionnaireCanonicalUrl);
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questionnaireResponse.setStatus(QuestionnaireResponseStatus.COMPLETED);
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questionnaireResponse.addItem().setLinkId("/54126-8")
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.setText("My health history")
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.addItem().setLinkId("/54126-8/54125-0").setText("Name").addAnswer().setValue(new StringType("TAMBRA AGARWAL"))
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.addItem().setLinkId("/54126-8/21112-8").setText("Birth Date").addAnswer().setValue(new DateType("1994-01-01"));
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IIdType qrIdType = myQuestionnaireResponseDao.create(questionnaireResponse, mySrd).getId().toUnqualifiedVersionless();
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// Search
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Bundle results = myClient.search()
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.byUrl("QuestionnaireResponse?_id=" + qrIdType.toUnqualifiedVersionless() + "&_include=QuestionnaireResponse:questionnaire")
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.returnBundle(Bundle.class)
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.execute();
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assertThat(results.getEntry().size(), is(equalTo(2)));
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List<String> expectedIds = new ArrayList<>();
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expectedIds.add(qrIdType.getValue());
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expectedIds.add(qIdType.getValue());
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List<String> actualIds = results.getEntry().stream()
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.map(Bundle.BundleEntryComponent::getResource)
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.map(resource -> resource.getIdElement().toUnqualifiedVersionless().toString())
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.collect(Collectors.toList());
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assertEquals(expectedIds, actualIds);
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}
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@Test
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public void testSaveQuestionnaire() throws Exception {
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String input = "<QuestionnaireResponse xmlns=\"http://hl7.org/fhir\">\n" +
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" <status value=\"completed\"/>\n" +
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" <authored value=\"2016-05-03T13:05:20-04:00\"/>\n" +
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" <item>\n" +
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" <linkId value=\"breast-feeding-intention\"/>\n" +
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" <text value=\"Breast Feeding Intention:\"/>\n" +
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" <answer>\n" +
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" <valueCoding>\n" +
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" <system value=\"http://example.org/codesystem-breastfeeding-intention\"/>\n" +
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" <code value=\"true\"/>\n" +
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" <display value=\"Mother wants to provide formula exclusively\"/>\n" +
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" </valueCoding>\n" +
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" </answer>\n" +
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" </item>\n" +
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" <item>\n" +
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" <linkId value=\"breast-feeding-education\"/>\n" +
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" <text value=\"Answer if not exclusive BM:\"/>\n" +
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" <answer>\n" +
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" <valueCoding>\n" +
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" <system value=\"http://example.org/codesystem-breastfeeding-education\"/>\n" +
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" <code value=\"true\"/>\n" +
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" <display value=\"Mother not given comprehensive education per protocol\"/>\n" +
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" </valueCoding>\n" +
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" </answer>\n" +
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" </item>\n" +
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" <item>\n" +
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" <linkId value=\"breast-feeding-exclusion\"/>\n" +
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" <text value=\"Exclusion Criteria:\"/>\n" +
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" <answer>\n" +
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" <valueCoding>\n" +
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" <system value=\"http://example.org/codesystem-breastfeeding-exclusion\"/>\n" +
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" <code value=\"true\"/>\n" +
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" <display\n" +
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" value=\"Maternal use of drugs of abuse, antimetabolites, chemotherapeutic agents, or radioisotopes\"\n" +
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" />\n" +
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" </valueCoding>\n" +
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" </answer>\n" +
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" </item>\n" +
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"</QuestionnaireResponse>";
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String input = "<QuestionnaireResponse xmlns=\"http://hl7.org/fhir\">\n" +
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" <status value=\"completed\"/>\n" +
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" <authored value=\"2016-05-03T13:05:20-04:00\"/>\n" +
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" <item>\n" +
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" <linkId value=\"breast-feeding-intention\"/>\n" +
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" <text value=\"Breast Feeding Intention:\"/>\n" +
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" <answer>\n" +
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" <valueCoding>\n" +
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" <system value=\"http://example.org/codesystem-breastfeeding-intention\"/>\n" +
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" <code value=\"true\"/>\n" +
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" <display value=\"Mother wants to provide formula exclusively\"/>\n" +
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" </valueCoding>\n" +
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" </answer>\n" +
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" </item>\n" +
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" <item>\n" +
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" <linkId value=\"breast-feeding-education\"/>\n" +
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" <text value=\"Answer if not exclusive BM:\"/>\n" +
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" <answer>\n" +
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" <valueCoding>\n" +
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" <system value=\"http://example.org/codesystem-breastfeeding-education\"/>\n" +
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" <code value=\"true\"/>\n" +
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" <display value=\"Mother not given comprehensive education per protocol\"/>\n" +
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" </valueCoding>\n" +
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" </answer>\n" +
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" </item>\n" +
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" <item>\n" +
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" <linkId value=\"breast-feeding-exclusion\"/>\n" +
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" <text value=\"Exclusion Criteria:\"/>\n" +
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" <answer>\n" +
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" <valueCoding>\n" +
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" <system value=\"http://example.org/codesystem-breastfeeding-exclusion\"/>\n" +
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" <code value=\"true\"/>\n" +
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" <display\n" +
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" value=\"Maternal use of drugs of abuse, antimetabolites, chemotherapeutic agents, or radioisotopes\"\n" +
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" />\n" +
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" </valueCoding>\n" +
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" </answer>\n" +
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" </item>\n" +
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"</QuestionnaireResponse>";
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HttpPost post = new HttpPost(ourServerBase + "/QuestionnaireResponse");
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post.setEntity(new StringEntity(input, ContentType.create(ca.uhn.fhir.rest.api.Constants.CT_FHIR_XML, "UTF-8")));
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CloseableHttpResponse response = ourHttpClient.execute(post);
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@ -179,9 +237,8 @@ public class ResourceProviderQuestionnaireResponseR4Test extends BaseResourcePro
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} finally {
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IOUtils.closeQuietly(response);
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}
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}
|
||||
|
||||
@Test
|
||||
|
|
@ -196,16 +253,16 @@ public class ResourceProviderQuestionnaireResponseR4Test extends BaseResourcePro
|
|||
} finally {
|
||||
IOUtils.closeQuietly(response);
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* From a Skype message from Brian Postlethwaite
|
||||
*/
|
||||
@Test
|
||||
public void testValidateQuestionnaireResponseWithNoIdForCreate() throws Exception {
|
||||
|
||||
|
||||
String input = "{\"resourceType\":\"Parameters\",\"parameter\":[{\"name\":\"mode\",\"valueString\":\"create\"},{\"name\":\"resource\",\"resource\":{\"resourceType\":\"QuestionnaireResponse\",\"questionnaire\":\"http://fhirtest.uhn.ca/baseDstu2/Questionnaire/MedsCheckEligibility\",\"text\":{\"status\":\"generated\",\"div\":\"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">!-- populated from the rendered HTML below --></div>\"},\"status\":\"completed\",\"authored\":\"2017-02-10T00:02:58.098Z\"}}]}";
|
||||
HttpPost post = new HttpPost(ourServerBase + "/QuestionnaireResponse/$validate?_pretty=true");
|
||||
post.setEntity(new StringEntity(input, ContentType.APPLICATION_JSON));
|
||||
|
|
@ -217,15 +274,15 @@ public class ResourceProviderQuestionnaireResponseR4Test extends BaseResourcePro
|
|||
} finally {
|
||||
IOUtils.closeQuietly(response);
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* From a Skype message from Brian Postlethwaite
|
||||
*/
|
||||
@Test
|
||||
public void testValidateQuestionnaireResponseWithNoIdForUpdate() throws Exception {
|
||||
|
||||
|
||||
String input = "{\"resourceType\":\"Parameters\",\"parameter\":[{\"name\":\"mode\",\"valueString\":\"update\"},{\"name\":\"resource\",\"resource\":{\"resourceType\":\"QuestionnaireResponse\",\"questionnaire\":\"http://fhirtest.uhn.ca/baseDstu2/Questionnaire/MedsCheckEligibility\",\"text\":{\"status\":\"generated\",\"div\":\"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">!-- populated from the rendered HTML below --></div>\"},\"status\":\"completed\",\"authored\":\"2017-02-10T00:02:58.098Z\"}}]}";
|
||||
HttpPost post = new HttpPost(ourServerBase + "/QuestionnaireResponse/$validate?_pretty=true");
|
||||
post.setEntity(new StringEntity(input, ContentType.APPLICATION_JSON));
|
||||
|
|
@ -238,9 +295,8 @@ public class ResourceProviderQuestionnaireResponseR4Test extends BaseResourcePro
|
|||
} finally {
|
||||
IOUtils.closeQuietly(response);
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue