Work on everything fixes for #674
This commit is contained in:
James Agnew
parent
e6cb973f5f
commit
b3b9273ca7
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@ -44,6 +44,7 @@ import org.hl7.fhir.instance.model.api.*;
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import com.google.common.collect.*;
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import ca.uhn.fhir.context.*;
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import ca.uhn.fhir.jpa.dao.SearchBuilder.IncludesIterator;
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import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
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import ca.uhn.fhir.jpa.entity.*;
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@ -71,6 +72,7 @@ import ca.uhn.fhir.util.UrlUtil;
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*/
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public class SearchBuilder implements ISearchBuilder {
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private static Long NO_MORE = Long.valueOf(-1);
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchBuilder.class);
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private List<Long> myAlsoIncludePids;
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private CriteriaBuilder myBuilder;
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@ -90,7 +92,6 @@ public class SearchBuilder implements ISearchBuilder {
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private ISearchParamRegistry mySearchParamRegistry;
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private String mySearchUuid;
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private IHapiTerminologySvc myTerminologySvc;
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/**
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* Constructor
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*/
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@ -1048,7 +1049,7 @@ public class SearchBuilder implements ISearchBuilder {
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if (!isBlank(unitsValue)) {
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code = theBuilder.equal(theFrom.get("myUnits"), unitsValue);
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}
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cmpValue = ObjectUtils.defaultIfNull(cmpValue, ParamPrefixEnum.EQUAL);
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final Expression<BigDecimal> path = theFrom.get("myValue");
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String invalidMessageName = "invalidQuantityPrefix";
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@ -1357,11 +1358,11 @@ public class SearchBuilder implements ISearchBuilder {
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* Now perform the search
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*/
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final TypedQuery<Long> query = myEntityManager.createQuery(outerQuery);
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if (theMaximumResults != null) {
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query.setMaxResults(theMaximumResults);
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}
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return query;
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}
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@ -1629,12 +1630,6 @@ public class SearchBuilder implements ISearchBuilder {
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List<ResourceLink> results = q.getResultList();
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for (ResourceLink resourceLink : results) {
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if (theReverseMode) {
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// if (theEverythingModeEnum.isEncounter()) {
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// if (resourceLink.getSourcePath().equals("Encounter.subject") ||
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// resourceLink.getSourcePath().equals("Encounter.patient")) {
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// nextRoundOmit.add(resourceLink.getSourceResourcePid());
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// }
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// }
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pidsToInclude.add(resourceLink.getSourceResourcePid());
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} else {
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pidsToInclude.add(resourceLink.getTargetResourcePid());
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@ -1745,10 +1740,10 @@ public class SearchBuilder implements ISearchBuilder {
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}
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private void searchForIdsWithAndOr(String theResourceName, String theParamName, List<List<? extends IQueryParameterType>> theAndOrParams) {
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for (int andListIdx = 0; andListIdx < theAndOrParams.size(); andListIdx++) {
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List<? extends IQueryParameterType> nextOrList = theAndOrParams.get(andListIdx);
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for (int orListIdx = 0; orListIdx < nextOrList.size(); orListIdx++) {
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IQueryParameterType nextOr = nextOrList.get(orListIdx);
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boolean hasNoValue = false;
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@ -1760,14 +1755,14 @@ public class SearchBuilder implements ISearchBuilder {
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hasNoValue = true;
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}
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}
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if (hasNoValue) {
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ourLog.debug("Ignoring empty parameter: {}", theParamName);
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nextOrList.remove(orListIdx);
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orListIdx--;
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}
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}
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if (nextOrList.isEmpty()) {
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theAndOrParams.remove(andListIdx);
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andListIdx--;
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@ -1777,7 +1772,7 @@ public class SearchBuilder implements ISearchBuilder {
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if (theAndOrParams.isEmpty()) {
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return;
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}
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if (theParamName.equals(BaseResource.SP_RES_ID)) {
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addPredicateResourceId(theAndOrParams);
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@ -1973,6 +1968,34 @@ public class SearchBuilder implements ISearchBuilder {
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return thePredicates.toArray(new Predicate[thePredicates.size()]);
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}
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public class IncludesIterator implements Iterator<Long>{
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private Long myNext;
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@Override
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public boolean hasNext() {
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fetchNext();
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return myNext != NO_MORE;
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}
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@Override
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public Long next() {
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fetchNext();
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Long retVal = myNext;
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myNext = null;
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return retVal;
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}
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private void fetchNext() {
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if (myNext == null) {
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}
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}
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}
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private enum JoinEnum {
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DATE, NUMBER, QUANTITY, REFERENCE, STRING, TOKEN, URI
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@ -2007,16 +2030,24 @@ public class SearchBuilder implements ISearchBuilder {
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}
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private final class QueryIterator implements Iterator<Long> {
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private boolean myFirst = true;
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private IncludesIterator myIncludesIterator;
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private Long myNext;
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private final Set<Long> myPidSet = new HashSet<Long>();
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private Iterator<Long> myPreResultsIterator;
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private Iterator<Long> myResultsIterator;
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private SortSpec mySort;
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private boolean myStillNeedToFetchIncludes;
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private StopWatch myStopwatch = null;
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private QueryIterator() {
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mySort = myParams.getSort();
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// Includes are processed inline for $everything query
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if (myParams.getEverythingMode() != null) {
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myStillNeedToFetchIncludes = true;
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}
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}
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private void fetchNext() {
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@ -2061,7 +2092,24 @@ public class SearchBuilder implements ISearchBuilder {
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}
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if (myNext == null) {
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myNext = NO_MORE;
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if (myStillNeedToFetchIncludes) {
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myIncludesIterator = new IncludesIterator();
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myStillNeedToFetchIncludes = false;
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}
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if (myIncludesIterator != null) {
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while (myIncludesIterator.hasNext()) {
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Long next = myIncludesIterator.next();
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if (next != null && myPidSet.add(next)) {
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myNext = next;
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break;
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}
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}
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if (myNext == null) {
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myNext = NO_MORE;
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}
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} else {
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myNext = NO_MORE;
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}
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}
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} // if we need to fetch the next result
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@ -2070,9 +2118,11 @@ public class SearchBuilder implements ISearchBuilder {
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ourLog.info("Initial query result returned in {}ms for query {}", myStopwatch.getMillis(), mySearchUuid);
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myFirst = false;
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}
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if (myNext == NO_MORE) {
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ourLog.info("Query found {} matches in {}ms for query {}", myPidSet.size(), myStopwatch.getMillis(), mySearchUuid);
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}
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}
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@Override
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@ -241,8 +241,8 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
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Set<Long> includedPids = new HashSet<Long>();
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if (mySearchEntity.getSearchType() == SearchTypeEnum.SEARCH) {
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includedPids.addAll(sb.loadReverseIncludes(myDao, myContext, myEntityManager, pidsSubList, mySearchEntity.toRevIncludesList(), true, mySearchEntity.getLastUpdated()));
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includedPids.addAll(sb.loadReverseIncludes(myDao, myContext, myEntityManager, pidsSubList, mySearchEntity.toIncludesList(), false, mySearchEntity.getLastUpdated()));
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}
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includedPids.addAll(sb.loadReverseIncludes(myDao, myContext, myEntityManager, pidsSubList, mySearchEntity.toIncludesList(), false, mySearchEntity.getLastUpdated()));
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// Execute the query and make sure we return distinct results
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List<IBaseResource> resources = new ArrayList<IBaseResource>();
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@ -0,0 +1,195 @@
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package ca.uhn.fhir.jpa.provider.dstu3;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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import static org.hamcrest.Matchers.contains;
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import static org.hamcrest.Matchers.containsInAnyOrder;
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import static org.hamcrest.Matchers.containsInRelativeOrder;
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import static org.hamcrest.Matchers.containsString;
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import static org.hamcrest.Matchers.empty;
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import static org.hamcrest.Matchers.greaterThan;
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import static org.hamcrest.Matchers.hasItem;
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import static org.hamcrest.Matchers.hasItems;
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import static org.hamcrest.Matchers.hasSize;
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import static org.hamcrest.Matchers.lessThan;
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import static org.hamcrest.Matchers.lessThanOrEqualTo;
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import static org.hamcrest.Matchers.not;
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import static org.hamcrest.Matchers.startsWith;
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import static org.hamcrest.Matchers.stringContainsInOrder;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertFalse;
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import static org.junit.Assert.assertNotEquals;
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import static org.junit.Assert.assertNotNull;
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import static org.junit.Assert.assertThat;
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import static org.junit.Assert.assertTrue;
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import static org.junit.Assert.fail;
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import java.io.*;
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import java.net.*;
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import java.nio.charset.StandardCharsets;
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import java.util.*;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.Validate;
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import org.apache.http.NameValuePair;
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import org.apache.http.client.ClientProtocolException;
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import org.apache.http.client.entity.UrlEncodedFormEntity;
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import org.apache.http.client.methods.*;
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import org.apache.http.entity.*;
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import org.apache.http.message.BasicNameValuePair;
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import org.hl7.fhir.dstu3.model.*;
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import org.hl7.fhir.dstu3.model.Bundle.*;
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import org.hl7.fhir.dstu3.model.Encounter.EncounterLocationComponent;
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import org.hl7.fhir.dstu3.model.Encounter.EncounterStatus;
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import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
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import org.hl7.fhir.dstu3.model.Narrative.NarrativeStatus;
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import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
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import org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemType;
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import org.hl7.fhir.dstu3.model.Subscription.SubscriptionChannelType;
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import org.hl7.fhir.dstu3.model.Subscription.SubscriptionStatus;
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import org.hl7.fhir.instance.model.Encounter.EncounterState;
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import org.hl7.fhir.instance.model.api.*;
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import org.junit.*;
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import org.springframework.transaction.TransactionStatus;
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import org.springframework.transaction.support.TransactionCallback;
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import com.google.common.base.Charsets;
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import com.google.common.collect.Lists;
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import ca.uhn.fhir.jpa.dao.DaoConfig;
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import ca.uhn.fhir.jpa.entity.Search;
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import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
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import ca.uhn.fhir.model.primitive.InstantDt;
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import ca.uhn.fhir.model.primitive.UriDt;
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import ca.uhn.fhir.parser.IParser;
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import ca.uhn.fhir.parser.StrictErrorHandler;
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import ca.uhn.fhir.rest.api.MethodOutcome;
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import ca.uhn.fhir.rest.api.SummaryEnum;
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import ca.uhn.fhir.rest.client.IGenericClient;
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import ca.uhn.fhir.rest.gclient.StringClientParam;
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import ca.uhn.fhir.rest.param.*;
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import ca.uhn.fhir.rest.server.Constants;
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import ca.uhn.fhir.rest.server.EncodingEnum;
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import ca.uhn.fhir.rest.server.exceptions.*;
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import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
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import ca.uhn.fhir.util.TestUtil;
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import ca.uhn.fhir.util.UrlUtil;
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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 encId1;
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private String encId2;
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private ArrayList<String> myObsIds;
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@Before
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public void beforeDisableResultReuse() {
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myDaoConfig.setReuseCachedSearchResultsForMillis(null);
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}
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@Override
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@After
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public void after() throws Exception {
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super.after();
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myDaoConfig.setReuseCachedSearchResultsForMillis(new DaoConfig().getReuseCachedSearchResultsForMillis());
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}
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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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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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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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Patient patient2 = new Patient();
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patient2.getManagingOrganization().setReference(orgId);
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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.getServiceProvider().setReference(orgId);
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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.getServiceProvider().setReference(orgId);
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encId2 = ourClient.create().resource(enc2).execute().getId().toUnqualifiedVersionless().getValue();
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myObsIds = new ArrayList<String>();
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for (int i = 0; i < 20; i++) {
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Observation obs = new Observation();
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obs.getSubject().setReference(patId);
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obs.setStatus(ObservationStatus.FINAL);
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String obsId = ourClient.create().resource(obs).execute().getId().toUnqualifiedVersionless().getValue();
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myObsIds.add(obsId);
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}
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}
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/**
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* See #674
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*/
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@Test
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public void testEverythingPagesWithCorrectEncodingJson() throws Exception {
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Bundle bundle = fetchBundle(ourServerBase + "/" + patId + "/$everything?_format=json&_count=1", EncodingEnum.JSON);
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assertNotNull(bundle.getLink("next").getUrl());
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assertThat(bundle.getLink("next").getUrl(), containsString("_format=json"));
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bundle = fetchBundle(bundle.getLink("next").getUrl(), EncodingEnum.JSON);
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assertNotNull(bundle.getLink("next").getUrl());
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assertThat(bundle.getLink("next").getUrl(), containsString("_format=json"));
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bundle = fetchBundle(bundle.getLink("next").getUrl(), EncodingEnum.JSON);
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}
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/**
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* See #674
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*/
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@Test
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public void testEverythingPagesWithCorrectEncodingXml() throws Exception {
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Bundle bundle = fetchBundle(ourServerBase + "/" + patId + "/$everything?_format=xml&_count=1", EncodingEnum.XML);
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assertNotNull(bundle.getLink("next").getUrl());
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ourLog.info("Next link: {}", bundle.getLink("next").getUrl());
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assertThat(bundle.getLink("next").getUrl(), containsString("_format=xml"));
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bundle = fetchBundle(bundle.getLink("next").getUrl(), EncodingEnum.XML);
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assertNotNull(bundle.getLink("next").getUrl());
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ourLog.info("Next link: {}", bundle.getLink("next").getUrl());
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assertThat(bundle.getLink("next").getUrl(), containsString("_format=xml"));
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bundle = fetchBundle(bundle.getLink("next").getUrl(), EncodingEnum.XML);
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}
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private Bundle fetchBundle(String theUrl, EncodingEnum theEncoding) throws IOException, ClientProtocolException {
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Bundle bundle;
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HttpGet get = new HttpGet(theUrl);
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CloseableHttpResponse resp = ourHttpClient.execute(get);
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try {
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assertEquals(theEncoding.getResourceContentTypeNonLegacy(), resp.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue().replaceAll(";.*", ""));
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bundle = theEncoding.newParser(myFhirCtx).parseResource(Bundle.class, IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8));
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} finally {
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IOUtils.closeQuietly(resp);
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}
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return bundle;
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}
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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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}
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@ -47,6 +47,7 @@ import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
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import org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemType;
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import org.hl7.fhir.dstu3.model.Subscription.SubscriptionChannelType;
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import org.hl7.fhir.dstu3.model.Subscription.SubscriptionStatus;
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import org.hl7.fhir.instance.model.Encounter.EncounterState;
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import org.hl7.fhir.instance.model.api.*;
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import org.junit.*;
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import org.springframework.transaction.TransactionStatus;
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