5198 fixing searching everything op (#5201)
* fixing searches * fixing paging in master * cleanup * Fixing the tests * fixing tests * fixing test * cleanup * fixing * removing unneeded class * adding a changelog and cleaning some final details * code styles * cleaning up imports * review notes * formatting --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
This commit is contained in:
TipzCM
GitHub
parent
a10856e091
commit
fdfda37f73
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@ -0,0 +1,7 @@
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---
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type: fix
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issue: 5198
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title: "Resolved an issue with type-everything search operations (eg, /Patient/$everything),
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where not all page results were being returned if _count was specified to be
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the same value as the maximum page size to fetch.
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"
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@ -55,6 +55,7 @@ import ca.uhn.fhir.jpa.model.search.SearchBuilderLoadIncludesParameters;
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import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
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import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
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import ca.uhn.fhir.jpa.search.SearchConstants;
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import ca.uhn.fhir.jpa.search.builder.models.ResolvedSearchQueryExecutor;
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import ca.uhn.fhir.jpa.search.builder.sql.GeneratedSql;
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import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
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import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryExecutor;
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@ -116,7 +117,6 @@ import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.Set;
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import java.util.stream.Collectors;
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import javax.annotation.Nonnull;
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@ -178,7 +178,6 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
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@PersistenceContext(type = PersistenceContextType.TRANSACTION)
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protected EntityManager myEntityManager;
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private List<JpaPid> myAlsoIncludePids;
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private CriteriaBuilder myCriteriaBuilder;
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private SearchParameterMap myParams;
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private String mySearchUuid;
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@ -449,9 +448,8 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
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}
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} else {
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// do everything in the database.
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Optional<SearchQueryExecutor> query = createChunkedQuery(
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theParams, sort, theOffset, theMaximumResults, theCountOnlyFlag, theRequest, null);
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query.ifPresent(queries::add);
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createChunkedQuery(
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theParams, sort, theOffset, theMaximumResults, theCountOnlyFlag, theRequest, null, queries);
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}
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return queries;
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@ -541,9 +539,7 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
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if (thePids.size() < getMaximumPageSize()) {
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normalizeIdListForLastNInClause(thePids);
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}
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Optional<SearchQueryExecutor> query =
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createChunkedQuery(theParams, sort, theOffset, thePids.size(), theCount, theRequest, thePids);
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query.ifPresent(t -> theQueries.add(t));
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createChunkedQuery(theParams, sort, theOffset, thePids.size(), theCount, theRequest, thePids, theQueries);
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}
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/**
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@ -551,7 +547,8 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
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*
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* @param theTargetPids
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*/
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private void extractTargetPidsFromIdParams(HashSet<Long> theTargetPids) {
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private void extractTargetPidsFromIdParams(
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HashSet<Long> theTargetPids, List<ISearchQueryExecutor> theSearchQueryExecutors) {
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// get all the IQueryParameterType objects
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// for _id -> these should all be StringParam values
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HashSet<String> ids = new HashSet<>();
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@ -575,25 +572,26 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
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// this will throw if an id is not found
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Map<String, JpaPid> idToPid = myIdHelperService.resolveResourcePersistentIds(
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myRequestPartitionId, myResourceName, new ArrayList<>(ids));
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if (myAlsoIncludePids == null) {
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myAlsoIncludePids = new ArrayList<>();
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}
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// add the pids to targetPids
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for (JpaPid pid : idToPid.values()) {
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myAlsoIncludePids.add(pid);
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theTargetPids.add(pid.getId());
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}
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// add the target pids to our executors as the first
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// results iterator to go through
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theSearchQueryExecutors.add(new ResolvedSearchQueryExecutor(new ArrayList<>(theTargetPids)));
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}
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private Optional<SearchQueryExecutor> createChunkedQuery(
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private void createChunkedQuery(
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SearchParameterMap theParams,
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SortSpec sort,
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Integer theOffset,
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Integer theMaximumResults,
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boolean theCountOnlyFlag,
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RequestDetails theRequest,
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List<Long> thePidList) {
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List<Long> thePidList,
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List<ISearchQueryExecutor> theSearchQueryExecutors) {
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String sqlBuilderResourceName = myParams.getEverythingMode() == null ? myResourceName : null;
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SearchQueryBuilder sqlBuilder = new SearchQueryBuilder(
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myContext,
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@ -627,7 +625,9 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
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if (myParams.getEverythingMode() != null) {
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HashSet<Long> targetPids = new HashSet<>();
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if (myParams.get(IAnyResource.SP_RES_ID) != null) {
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extractTargetPidsFromIdParams(targetPids);
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// will add an initial search executor for
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// _id params
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extractTargetPidsFromIdParams(targetPids, theSearchQueryExecutors);
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} else {
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// For Everything queries, we make the query root by the ResourceLink table, since this query
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// is basically a reverse-include search. For type/Everything (as opposed to instance/Everything)
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@ -645,11 +645,11 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
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GeneratedSql allTargetsSql = fetchPidsSqlBuilder.generate(theOffset, myMaxResultsToFetch);
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String sql = allTargetsSql.getSql();
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Object[] args = allTargetsSql.getBindVariables().toArray(new Object[0]);
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List<Long> output = jdbcTemplate.query(sql, args, new SingleColumnRowMapper<>(Long.class));
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if (myAlsoIncludePids == null) {
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myAlsoIncludePids = new ArrayList<>(output.size());
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}
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myAlsoIncludePids.addAll(JpaPid.fromLongList(output));
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// we add a search executor to fetch unlinked patients first
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theSearchQueryExecutors.add(new ResolvedSearchQueryExecutor(output));
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}
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List<String> typeSourceResources = new ArrayList<>();
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@ -747,12 +747,11 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
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* Now perform the search
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*/
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GeneratedSql generatedSql = sqlBuilder.generate(theOffset, myMaxResultsToFetch);
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if (generatedSql.isMatchNothing()) {
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return Optional.empty();
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if (!generatedSql.isMatchNothing()) {
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SearchQueryExecutor executor =
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mySqlBuilderFactory.newSearchQueryExecutor(generatedSql, myMaxResultsToFetch);
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theSearchQueryExecutors.add(executor);
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}
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SearchQueryExecutor executor = mySqlBuilderFactory.newSearchQueryExecutor(generatedSql, myMaxResultsToFetch);
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return Optional.of(executor);
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}
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private Collection<String> extractTypeSourceResourcesFromParams() {
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@ -1925,11 +1924,35 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
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private final Integer myOffset;
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private boolean myFirst = true;
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private IncludesIterator myIncludesIterator;
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/**
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* The next JpaPid value of the next result in this query.
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* Will not be null if fetched using getNext()
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*/
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private JpaPid myNext;
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/**
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* The current query result iterator running sql and supplying PIDs
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* @see #myQueryList
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*/
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private ISearchQueryExecutor myResultsIterator;
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private boolean myFetchIncludesForEverythingOperation;
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/**
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* The count of resources skipped because they were seen in earlier results
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*/
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private int mySkipCount = 0;
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/**
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* The count of resources that are new in this search
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* (ie, not cached in previous searches)
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*/
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private int myNonSkipCount = 0;
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/**
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* The list of queries to use to find all results.
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* Normal JPA queries will normally have a single entry.
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* Queries that involve Hibernate Search/Elastisearch may have
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* multiple queries because of chunking.
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* The $everything operation also jams some extra results in.
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*/
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private List<ISearchQueryExecutor> myQueryList = new ArrayList<>();
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private QueryIterator(SearchRuntimeDetails theSearchRuntimeDetails, RequestDetails theRequest) {
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@ -1967,30 +1990,25 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
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}
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}
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// assigns the results iterator
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/*
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* assigns the results iterator
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* and populates the myQueryList.
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*/
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initializeIteratorQuery(myOffset, myMaxResultsToFetch);
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if (myAlsoIncludePids == null) {
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myAlsoIncludePids = new ArrayList<>();
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}
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}
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if (myNext == null) {
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for (Iterator<JpaPid> myPreResultsIterator = myAlsoIncludePids.iterator();
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myPreResultsIterator.hasNext(); ) {
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JpaPid next = myPreResultsIterator.next();
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if (next != null)
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if (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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// no next means we need a new query (if one is available)
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while (myResultsIterator.hasNext() || !myQueryList.isEmpty()) {
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// Update iterator with next chunk if necessary.
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if (!myResultsIterator.hasNext()) {
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retrieveNextIteratorQuery();
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// if our new results iterator is also empty
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// we're done here
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if (!myResultsIterator.hasNext()) {
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break;
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}
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}
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Long nextLong = myResultsIterator.next();
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@ -2017,26 +2035,10 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
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}
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if (!myResultsIterator.hasNext()) {
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if (myMaxResultsToFetch != null
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&& (mySkipCount + myNonSkipCount == myMaxResultsToFetch)) {
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if (myMaxResultsToFetch != null && (mySkipCount + myNonSkipCount == myMaxResultsToFetch)) {
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if (mySkipCount > 0 && myNonSkipCount == 0) {
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StorageProcessingMessage message = new StorageProcessingMessage();
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String msg = "Pass completed with no matching results seeking rows "
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+ myPidSet.size() + "-" + mySkipCount
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+ ". This indicates an inefficient query! Retrying with new max count of "
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+ myMaxResultsToFetch;
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ourLog.warn(msg);
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message.setMessage(msg);
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HookParams params = new HookParams()
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.add(RequestDetails.class, myRequest)
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.addIfMatchesType(ServletRequestDetails.class, myRequest)
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.add(StorageProcessingMessage.class, message);
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CompositeInterceptorBroadcaster.doCallHooks(
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myInterceptorBroadcaster,
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myRequest,
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Pointcut.JPA_PERFTRACE_WARNING,
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params);
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sendProcessingMsgAndFirePerformanceHook();
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myMaxResultsToFetch += 1000;
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initializeIteratorQuery(myOffset, myMaxResultsToFetch);
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@ -2069,7 +2071,6 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
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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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mySearchRuntimeDetails.setFoundMatchesCount(myPidSet.size());
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@ -2100,6 +2101,22 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
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}
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}
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private void sendProcessingMsgAndFirePerformanceHook() {
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StorageProcessingMessage message = new StorageProcessingMessage();
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String msg = "Pass completed with no matching results seeking rows "
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+ myPidSet.size() + "-" + mySkipCount
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+ ". This indicates an inefficient query! Retrying with new max count of "
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+ myMaxResultsToFetch;
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ourLog.warn(msg);
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message.setMessage(msg);
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HookParams params = new HookParams()
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.add(RequestDetails.class, myRequest)
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.addIfMatchesType(ServletRequestDetails.class, myRequest)
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.add(StorageProcessingMessage.class, message);
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CompositeInterceptorBroadcaster.doCallHooks(
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myInterceptorBroadcaster, myRequest, Pointcut.JPA_PERFTRACE_WARNING, params);
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}
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private void initializeIteratorQuery(Integer theOffset, Integer theMaxResultsToFetch) {
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if (myQueryList.isEmpty()) {
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// Capture times for Lucene/Elasticsearch queries as well
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@ -20,6 +20,7 @@
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package ca.uhn.fhir.jpa.search.builder;
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import ca.uhn.fhir.jpa.model.dao.JpaPid;
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import ca.uhn.fhir.jpa.search.builder.models.ResolvedSearchQueryExecutor;
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import org.apache.commons.lang3.Validate;
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import java.util.Iterator;
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@ -57,41 +58,6 @@ public class SearchQueryExecutors {
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return new ResolvedSearchQueryExecutor(rawPids);
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}
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/**
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* Adapt bare Iterator to our internal query interface.
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*/
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static class ResolvedSearchQueryExecutor implements ISearchQueryExecutor {
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private final Iterator<Long> myIterator;
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ResolvedSearchQueryExecutor(Iterable<Long> theIterable) {
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this(theIterable.iterator());
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}
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ResolvedSearchQueryExecutor(Iterator<Long> theIterator) {
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myIterator = theIterator;
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}
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@Nonnull
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public static ResolvedSearchQueryExecutor from(List<Long> rawPids) {
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return new ResolvedSearchQueryExecutor(rawPids);
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}
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@Override
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public boolean hasNext() {
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return myIterator.hasNext();
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}
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@Override
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public Long next() {
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return myIterator.next();
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}
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@Override
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public void close() {
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// empty
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}
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}
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public static ISearchQueryExecutor from(Iterator<JpaPid> theIterator) {
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return new JpaPidQueryAdaptor(theIterator);
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}
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@ -0,0 +1,39 @@
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package ca.uhn.fhir.jpa.search.builder.models;
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import ca.uhn.fhir.jpa.search.builder.ISearchQueryExecutor;
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import java.util.Iterator;
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import java.util.List;
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import javax.annotation.Nonnull;
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public class ResolvedSearchQueryExecutor implements ISearchQueryExecutor {
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private final Iterator<Long> myIterator;
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public ResolvedSearchQueryExecutor(Iterable<Long> theIterable) {
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this(theIterable.iterator());
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}
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public ResolvedSearchQueryExecutor(Iterator<Long> theIterator) {
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myIterator = theIterator;
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}
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@Nonnull
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public static ResolvedSearchQueryExecutor from(List<Long> rawPids) {
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return new ResolvedSearchQueryExecutor(rawPids);
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}
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@Override
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public boolean hasNext() {
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return myIterator.hasNext();
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}
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@Override
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public Long next() {
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return myIterator.next();
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}
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@Override
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public void close() {
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// empty
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}
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}
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@ -122,9 +122,11 @@ public class SearchTask implements Callable<Void> {
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private boolean myAdditionalPrefetchThresholdsRemaining;
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private List<JpaPid> myPreviouslyAddedResourcePids;
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private Integer myMaxResultsToFetch;
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/**
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* Constructor
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*/
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@SuppressWarnings({"unchecked", "rawtypes"})
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public SearchTask(
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SearchTaskParameters theCreationParams,
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HapiTransactionService theManagedTxManager,
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@ -198,6 +200,7 @@ public class SearchTask implements Callable<Void> {
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myCountSavedTotal = myPreviouslyAddedResourcePids.size();
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}
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@SuppressWarnings("rawtypes")
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private ISearchBuilder newSearchBuilder() {
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Class<? extends IBaseResource> resourceTypeClass =
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myContext.getResourceDefinition(myResourceType).getImplementingClass();
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@ -281,6 +284,7 @@ public class SearchTask implements Callable<Void> {
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.execute(() -> doSaveSearch());
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}
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@SuppressWarnings("rawtypes")
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private void saveUnsynced(final IResultIterator theResultIter) {
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myTxService
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.withRequest(myRequest)
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@ -296,7 +300,7 @@ public class SearchTask implements Callable<Void> {
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// Interceptor call: STORAGE_PREACCESS_RESOURCES
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// This can be used to remove results from the search result details before
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// the user has a chance to know that they were in the results
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if (mySearchRuntimeDetails.getRequestDetails() != null && unsyncedPids.isEmpty() == false) {
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if (mySearchRuntimeDetails.getRequestDetails() != null && !unsyncedPids.isEmpty()) {
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JpaPreResourceAccessDetails accessDetails =
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new JpaPreResourceAccessDetails(unsyncedPids, () -> newSearchBuilder());
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HookParams params = new HookParams()
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@ -332,10 +336,8 @@ public class SearchTask implements Callable<Void> {
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mySyncedPids.addAll(unsyncedPids);
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unsyncedPids.clear();
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if (theResultIter.hasNext() == false) {
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if (!theResultIter.hasNext()) {
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int skippedCount = theResultIter.getSkippedCount();
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int nonSkippedCount = theResultIter.getNonSkippedCount();
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int totalFetched = skippedCount + myCountSavedThisPass + myCountBlockedThisPass;
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ourLog.trace(
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"MaxToFetch[{}] SkippedCount[{}] CountSavedThisPass[{}] CountSavedThisTotal[{}] AdditionalPrefetchRemaining[{}]",
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myMaxResultsToFetch,
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@ -344,16 +346,18 @@ public class SearchTask implements Callable<Void> {
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myCountSavedTotal,
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myAdditionalPrefetchThresholdsRemaining);
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if (nonSkippedCount == 0
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|| (myMaxResultsToFetch != null && totalFetched < myMaxResultsToFetch)) {
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if (isFinished(theResultIter)) {
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// finished
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ourLog.trace("Setting search status to FINISHED");
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mySearch.setStatus(SearchStatusEnum.FINISHED);
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mySearch.setTotalCount(myCountSavedTotal - countBlocked);
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} else if (myAdditionalPrefetchThresholdsRemaining) {
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// pass complete
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ourLog.trace("Setting search status to PASSCMPLET");
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mySearch.setStatus(SearchStatusEnum.PASSCMPLET);
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mySearch.setSearchParameterMap(myParams);
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} else {
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// also finished
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ourLog.trace("Setting search status to FINISHED");
|
||||
mySearch.setStatus(SearchStatusEnum.FINISHED);
|
||||
mySearch.setTotalCount(myCountSavedTotal - countBlocked);
|
||||
|
|
@ -382,8 +386,34 @@ public class SearchTask implements Callable<Void> {
|
|||
ourLog.trace("saveUnsynced() - post-commit");
|
||||
}
|
||||
|
||||
@SuppressWarnings("rawtypes")
|
||||
private boolean isFinished(final IResultIterator theResultIter) {
|
||||
int skippedCount = theResultIter.getSkippedCount();
|
||||
int nonSkippedCount = theResultIter.getNonSkippedCount();
|
||||
int totalFetched = skippedCount + myCountSavedThisPass + myCountBlockedThisPass;
|
||||
|
||||
if (myMaxResultsToFetch != null && totalFetched < myMaxResultsToFetch) {
|
||||
// total fetched < max results to fetch -> we've exhausted the search
|
||||
return true;
|
||||
} else {
|
||||
if (nonSkippedCount == 0) {
|
||||
// no skipped resources in this query
|
||||
if (myParams.getCount() != null) {
|
||||
// count supplied
|
||||
// if the count is > what we've fetched -> we've exhausted the query
|
||||
return myParams.getCount() > totalFetched;
|
||||
} else {
|
||||
// legacy - we have no skipped resources - we are done
|
||||
return true;
|
||||
}
|
||||
}
|
||||
// skipped resources means we have more to fetch
|
||||
return false;
|
||||
}
|
||||
}
|
||||
|
||||
public boolean isNotAborted() {
|
||||
return myAbortRequested == false;
|
||||
return !myAbortRequested;
|
||||
}
|
||||
|
||||
public void markComplete() {
|
||||
|
|
@ -517,6 +547,7 @@ public class SearchTask implements Callable<Void> {
|
|||
* This method actually creates the database query to perform the
|
||||
* search, and starts it.
|
||||
*/
|
||||
@SuppressWarnings({"rawtypes", "unchecked"})
|
||||
private void doSearch() {
|
||||
/*
|
||||
* If the user has explicitly requested a _count, perform a
|
||||
|
|
@ -531,32 +562,7 @@ public class SearchTask implements Callable<Void> {
|
|||
: SearchParameterMapCalculator.isWantCount(myStorageSettings.getDefaultTotalMode());
|
||||
|
||||
if (myParamWantOnlyCount || myParamOrDefaultWantCount) {
|
||||
ourLog.trace("Performing count");
|
||||
ISearchBuilder sb = newSearchBuilder();
|
||||
|
||||
/*
|
||||
* createCountQuery
|
||||
* NB: (see createQuery below)
|
||||
* Because FulltextSearchSvcImpl will (internally)
|
||||
* mutate the myParams (searchmap),
|
||||
* (specifically removing the _content and _text filters)
|
||||
* we will have to clone those parameters here so that
|
||||
* the "correct" params are used in createQuery below
|
||||
*/
|
||||
Long count = sb.createCountQuery(myParams.clone(), mySearch.getUuid(), myRequest, myRequestPartitionId);
|
||||
|
||||
ourLog.trace("Got count {}", count);
|
||||
|
||||
myTxService
|
||||
.withRequest(myRequest)
|
||||
.withRequestPartitionId(myRequestPartitionId)
|
||||
.execute(() -> {
|
||||
mySearch.setTotalCount(count.intValue());
|
||||
if (myParamWantOnlyCount) {
|
||||
mySearch.setStatus(SearchStatusEnum.FINISHED);
|
||||
}
|
||||
doSaveSearch();
|
||||
});
|
||||
doCountOnlyQuery(myParamWantOnlyCount);
|
||||
if (myParamWantOnlyCount) {
|
||||
return;
|
||||
}
|
||||
|
|
@ -573,12 +579,16 @@ public class SearchTask implements Callable<Void> {
|
|||
*/
|
||||
int currentlyLoaded = defaultIfNull(mySearch.getNumFound(), 0);
|
||||
int minWanted = 0;
|
||||
|
||||
// if no count is provided,
|
||||
// we only use the values in SearchPreFetchThresholds
|
||||
// but if there is a count...
|
||||
if (myParams.getCount() != null) {
|
||||
minWanted = myParams.getCount() + 1; // Always fetch one past this page, so we know if there is a next page.
|
||||
minWanted = Math.min(minWanted, myPagingProvider.getMaximumPageSize());
|
||||
minWanted = Math.min(myParams.getCount(), myPagingProvider.getMaximumPageSize());
|
||||
minWanted += currentlyLoaded;
|
||||
}
|
||||
|
||||
// iterate through the search thresholds
|
||||
for (Iterator<Integer> iter =
|
||||
myStorageSettings.getSearchPreFetchThresholds().iterator();
|
||||
iter.hasNext(); ) {
|
||||
|
|
@ -590,8 +600,11 @@ public class SearchTask implements Callable<Void> {
|
|||
if (next == -1) {
|
||||
sb.setMaxResultsToFetch(null);
|
||||
} else {
|
||||
// we want at least 1 more than our requested amount
|
||||
// so we know that there are other results
|
||||
// (in case we get the exact amount back)
|
||||
myMaxResultsToFetch = Math.max(next, minWanted);
|
||||
sb.setMaxResultsToFetch(myMaxResultsToFetch);
|
||||
sb.setMaxResultsToFetch(myMaxResultsToFetch + 1);
|
||||
}
|
||||
|
||||
if (iter.hasNext()) {
|
||||
|
|
@ -633,6 +646,7 @@ public class SearchTask implements Callable<Void> {
|
|||
*/
|
||||
try (IResultIterator<JpaPid> resultIterator =
|
||||
sb.createQuery(myParams, mySearchRuntimeDetails, myRequest, myRequestPartitionId)) {
|
||||
// resultIterator is SearchBuilder.QueryIterator
|
||||
assert (resultIterator != null);
|
||||
|
||||
/*
|
||||
|
|
@ -678,4 +692,38 @@ public class SearchTask implements Callable<Void> {
|
|||
throw new InternalErrorException(Msg.code(1166) + e);
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Does the query but only for the count.
|
||||
* @param theParamWantOnlyCount - if count query is wanted only
|
||||
*/
|
||||
private void doCountOnlyQuery(boolean theParamWantOnlyCount) {
|
||||
ourLog.trace("Performing count");
|
||||
@SuppressWarnings("rawtypes")
|
||||
ISearchBuilder sb = newSearchBuilder();
|
||||
|
||||
/*
|
||||
* createCountQuery
|
||||
* NB: (see createQuery below)
|
||||
* Because FulltextSearchSvcImpl will (internally)
|
||||
* mutate the myParams (searchmap),
|
||||
* (specifically removing the _content and _text filters)
|
||||
* we will have to clone those parameters here so that
|
||||
* the "correct" params are used in createQuery below
|
||||
*/
|
||||
Long count = sb.createCountQuery(myParams.clone(), mySearch.getUuid(), myRequest, myRequestPartitionId);
|
||||
|
||||
ourLog.trace("Got count {}", count);
|
||||
|
||||
myTxService
|
||||
.withRequest(myRequest)
|
||||
.withRequestPartitionId(myRequestPartitionId)
|
||||
.execute(() -> {
|
||||
mySearch.setTotalCount(count.intValue());
|
||||
if (theParamWantOnlyCount) {
|
||||
mySearch.setStatus(SearchStatusEnum.FINISHED);
|
||||
}
|
||||
doSaveSearch();
|
||||
});
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -93,7 +93,7 @@ public class ConsentEventsDaoR4Test extends BaseJpaR4SystemTest {
|
|||
List<String> returnedIdValues = toUnqualifiedVersionlessIdValues(resources);
|
||||
assertEquals(myObservationIds.subList(0, 10), returnedIdValues);
|
||||
assertEquals(1, hitCount.get());
|
||||
assertEquals(myObservationIds.subList(0, 20), interceptedResourceIds);
|
||||
assertEquals(myObservationIds.subList(0, 21), interceptedResourceIds);
|
||||
|
||||
// Fetch the next 30 (do cross a fetch boundary)
|
||||
outcome = myPagingProvider.retrieveResultList(mySrd, outcome.getUuid());
|
||||
|
|
@ -125,7 +125,7 @@ public class ConsentEventsDaoR4Test extends BaseJpaR4SystemTest {
|
|||
List<String> returnedIdValues = toUnqualifiedVersionlessIdValues(resources);
|
||||
assertEquals(myObservationIdsEvenOnly.subList(0, 10), returnedIdValues);
|
||||
assertEquals(1, hitCount.get());
|
||||
assertEquals(myObservationIds.subList(0, 20), interceptedResourceIds, "Wrong response from " + outcome.getClass());
|
||||
assertEquals(myObservationIds.subList(0, 21), interceptedResourceIds, "Wrong response from " + outcome.getClass());
|
||||
|
||||
// Fetch the next 30 (do cross a fetch boundary)
|
||||
String searchId = outcome.getUuid();
|
||||
|
|
|
|||
|
|
@ -26,12 +26,12 @@ import org.springframework.beans.factory.annotation.Autowired;
|
|||
|
||||
import java.util.Comparator;
|
||||
import java.util.List;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import static org.hamcrest.MatcherAssert.assertThat;
|
||||
import static org.hamcrest.Matchers.contains;
|
||||
import static org.hamcrest.Matchers.containsInAnyOrder;
|
||||
import static org.hamcrest.Matchers.containsString;
|
||||
import static org.hamcrest.Matchers.in;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
|
|
@ -178,7 +178,9 @@ public class FhirResourceDaoR4ComboNonUniqueParamTest extends BaseComboParamsR4T
|
|||
IIdType id1 = createPatient1();
|
||||
assertNotNull(id1);
|
||||
|
||||
assertEquals(0, myCaptureQueriesListener.countSelectQueries());
|
||||
assertEquals(0, myCaptureQueriesListener.countSelectQueries(),
|
||||
String.join(",", "\n" + myCaptureQueriesListener.getSelectQueries().stream().map(q -> q.getThreadName()).collect(Collectors.toList()))
|
||||
);
|
||||
assertEquals(12, myCaptureQueriesListener.countInsertQueries());
|
||||
assertEquals(0, myCaptureQueriesListener.countUpdateQueries());
|
||||
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
|
||||
|
|
|
|||
|
|
@ -421,7 +421,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
|
|||
|
||||
runInTransaction(() -> {
|
||||
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
|
||||
assertEquals(20, search.getNumFound());
|
||||
assertEquals(21, search.getNumFound());
|
||||
assertEquals(search.getNumFound(), mySearchResultDao.count());
|
||||
assertNull(search.getTotalCount());
|
||||
assertEquals(1, search.getVersion().intValue());
|
||||
|
|
@ -462,7 +462,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
|
|||
runInTransaction(() -> {
|
||||
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
|
||||
assertEquals(SearchStatusEnum.PASSCMPLET, search.getStatus());
|
||||
assertEquals(50, search.getNumFound());
|
||||
assertEquals(51, search.getNumFound());
|
||||
assertEquals(search.getNumFound(), mySearchResultDao.count());
|
||||
assertNull(search.getTotalCount());
|
||||
assertEquals(3, search.getVersion().intValue());
|
||||
|
|
@ -501,9 +501,9 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
|
|||
*/
|
||||
runInTransaction(() -> {
|
||||
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
|
||||
assertEquals(190, search.getNumFound());
|
||||
assertEquals(191, search.getNumFound());
|
||||
assertEquals(search.getNumFound(), mySearchResultDao.count());
|
||||
assertEquals(190, search.getTotalCount().intValue());
|
||||
assertEquals(191, search.getTotalCount().intValue());
|
||||
assertEquals(5, search.getVersion().intValue());
|
||||
assertEquals(SearchStatusEnum.FINISHED, search.getStatus());
|
||||
});
|
||||
|
|
@ -513,10 +513,10 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
|
|||
*/
|
||||
|
||||
ids = toUnqualifiedVersionlessIdValues(results, 180, 200, false);
|
||||
assertEquals(10, ids.size());
|
||||
assertEquals(11, ids.size());
|
||||
assertEquals("Patient/PT00180", ids.get(0));
|
||||
assertEquals("Patient/PT00189", ids.get(9));
|
||||
assertEquals(190, myDatabaseBackedPagingProvider.retrieveResultList(null, uuid).size().intValue());
|
||||
assertEquals(191, myDatabaseBackedPagingProvider.retrieveResultList(null, uuid).size().intValue());
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -554,7 +554,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
|
|||
});
|
||||
runInTransaction(() -> {
|
||||
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
|
||||
assertEquals(50, search.getNumFound());
|
||||
assertEquals(51, search.getNumFound());
|
||||
assertEquals(search.getNumFound(), mySearchResultDao.count());
|
||||
assertEquals(null, search.getTotalCount());
|
||||
assertEquals(SearchStatusEnum.PASSCMPLET, search.getStatus());
|
||||
|
|
@ -589,10 +589,10 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
|
|||
await().until(() -> runInTransaction(() -> {
|
||||
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
|
||||
return search.getNumFound();
|
||||
}), equalTo(20));
|
||||
}), equalTo(21));
|
||||
runInTransaction(() -> {
|
||||
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
|
||||
assertEquals(20, search.getNumFound());
|
||||
assertEquals(21, search.getNumFound());
|
||||
assertEquals(search.getNumFound(), mySearchResultDao.count());
|
||||
assertNull(search.getTotalCount());
|
||||
assertEquals(1, search.getVersion().intValue());
|
||||
|
|
@ -649,14 +649,14 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
|
|||
*/
|
||||
|
||||
waitForSize(
|
||||
20,
|
||||
21,
|
||||
10000,
|
||||
() -> runInTransaction(() -> mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException("")).getNumFound()),
|
||||
() -> "Wanted 20: " + runInTransaction(() -> mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException("")).toString()));
|
||||
|
||||
runInTransaction(() -> {
|
||||
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
|
||||
assertEquals(20, search.getNumFound());
|
||||
assertEquals(21, search.getNumFound());
|
||||
assertEquals(search.getNumFound(), mySearchResultDao.count());
|
||||
assertNull(search.getTotalCount());
|
||||
assertEquals(1, search.getVersion().intValue());
|
||||
|
|
@ -1172,12 +1172,12 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
|
|||
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
|
||||
assertEquals(4, myCaptureQueriesListener.countSelectQueries());
|
||||
// first prefetch is 50+1
|
||||
assertEquals(51, myCaptureQueriesListener.logInsertQueries());
|
||||
assertEquals(52, myCaptureQueriesListener.logInsertQueries());
|
||||
assertEquals(1, myCaptureQueriesListener.countUpdateQueries());
|
||||
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
|
||||
|
||||
assertEquals(4, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
|
||||
assertEquals(51, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
|
||||
assertEquals(52, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
|
||||
assertEquals(1, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
|
||||
assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,191 @@
|
|||
package ca.uhn.fhir.jpa.provider.r4;
|
||||
|
||||
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
|
||||
import ca.uhn.fhir.jpa.provider.BaseResourceProviderR4Test;
|
||||
import ca.uhn.fhir.parser.StrictErrorHandler;
|
||||
import ca.uhn.fhir.rest.api.Constants;
|
||||
import ca.uhn.fhir.rest.api.EncodingEnum;
|
||||
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
|
||||
import ca.uhn.fhir.rest.server.BasePagingProvider;
|
||||
import ca.uhn.fhir.rest.server.IPagingProvider;
|
||||
import ca.uhn.fhir.rest.server.RestfulServer;
|
||||
import ca.uhn.fhir.util.BundleUtil;
|
||||
import com.google.common.base.Charsets;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.http.client.methods.CloseableHttpResponse;
|
||||
import org.apache.http.client.methods.HttpGet;
|
||||
import org.hl7.fhir.r4.model.Bundle;
|
||||
import org.hl7.fhir.r4.model.Patient;
|
||||
import org.junit.jupiter.api.AfterEach;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.params.ParameterizedTest;
|
||||
import org.junit.jupiter.params.provider.ValueSource;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.Arrays;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Set;
|
||||
|
||||
import static org.hl7.fhir.instance.model.api.IBaseBundle.LINK_NEXT;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
|
||||
@SuppressWarnings("Duplicates")
|
||||
public class PatientEverythingPaginationR4Test extends BaseResourceProviderR4Test {
|
||||
|
||||
private int myOriginalServerDefaultPageSize;
|
||||
|
||||
@Autowired
|
||||
JpaStorageSettings myStorageSettings;
|
||||
|
||||
@BeforeEach
|
||||
public void beforeDisableResultReuse() {
|
||||
myStorageSettings.setReuseCachedSearchResultsForMillis(null);
|
||||
}
|
||||
|
||||
@Override
|
||||
@BeforeEach
|
||||
public void before() throws Exception {
|
||||
super.before();
|
||||
myFhirContext.setParserErrorHandler(new StrictErrorHandler());
|
||||
|
||||
myStorageSettings.setAllowMultipleDelete(true);
|
||||
|
||||
myOriginalServerDefaultPageSize = myServer.getDefaultPageSize();
|
||||
myServer.setDefaultPageSize(50);
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
@AfterEach
|
||||
public void after() throws Exception {
|
||||
super.after();
|
||||
|
||||
myStorageSettings.setReuseCachedSearchResultsForMillis(new JpaStorageSettings().getReuseCachedSearchResultsForMillis());
|
||||
myServer.setDefaultPageSize(myOriginalServerDefaultPageSize);
|
||||
}
|
||||
|
||||
/**
|
||||
* Built to reproduce <a href="https://gitlab.com/simpatico.ai/cdr/-/issues/4940">this issue</a>
|
||||
* Notice that the issue is not gateway related. Is a plain server issue.
|
||||
*/
|
||||
@Test
|
||||
public void testEverythingPaginatesThroughAllPatients_whenCountIsEqualToMaxPageSize() throws IOException {
|
||||
// setup
|
||||
int totalPatients = 54;
|
||||
createPatients(totalPatients);
|
||||
|
||||
String url = myServerBase + "/Patient/$everything?_format=json&_count=" + BasePagingProvider.DEFAULT_MAX_PAGE_SIZE;
|
||||
|
||||
// test
|
||||
Bundle bundle = fetchBundle(url);
|
||||
|
||||
// first page
|
||||
List<Patient> patientsFirstPage = BundleUtil.toListOfResourcesOfType(myFhirContext, bundle, Patient.class);
|
||||
assertEquals(50, patientsFirstPage.size());
|
||||
|
||||
String nextUrl = BundleUtil.getLinkUrlOfType(myFhirContext, bundle, LINK_NEXT);
|
||||
|
||||
// 2nd/last page
|
||||
assertNotNull(nextUrl);
|
||||
Bundle page2 = fetchBundle(nextUrl);
|
||||
assertNotNull(page2);
|
||||
List<Patient> patientsPage2 = BundleUtil.toListOfResourcesOfType(myFhirContext, page2, Patient.class);
|
||||
|
||||
assertEquals(4, patientsPage2.size());
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@ValueSource(booleans = {true, false})
|
||||
public void testEverythingTypeOperationPagination_withDifferentPrefetchThresholds_coverageTest(boolean theProvideCountBool) throws IOException {
|
||||
// setup
|
||||
List<Integer> previousPrefetchThreshold = myStorageSettings.getSearchPreFetchThresholds();
|
||||
// other tests may be resetting this
|
||||
// so we'll set it
|
||||
int pageSize = myPagingProvider.getDefaultPageSize();
|
||||
int serverPageSize = myServer.getDefaultPageSize();
|
||||
try {
|
||||
int defaultPageSize = theProvideCountBool ? 50 : 10;
|
||||
// set our prefetch thresholds to ensure we run out of them
|
||||
List<Integer> prefetchThreshold = Arrays.asList(10, 50, -1);
|
||||
myStorageSettings.setSearchPreFetchThresholds(prefetchThreshold);
|
||||
|
||||
// the number of patients to create
|
||||
int total = 154;
|
||||
String nextUrl;
|
||||
createPatients(total);
|
||||
Set<String> ids = new HashSet<>();
|
||||
|
||||
String url = myServerBase + "/Patient/$everything?_format=json";
|
||||
if (theProvideCountBool) {
|
||||
url += "&_count=" + BasePagingProvider.DEFAULT_MAX_PAGE_SIZE;
|
||||
}
|
||||
myPagingProvider.setDefaultPageSize(defaultPageSize);
|
||||
myServer.setDefaultPageSize(defaultPageSize);
|
||||
|
||||
// test
|
||||
Bundle bundle = fetchBundle(url);
|
||||
|
||||
// first page
|
||||
List<Patient> patientsPage = BundleUtil.toListOfResourcesOfType(myFhirContext, bundle, Patient.class);
|
||||
assertEquals(defaultPageSize, patientsPage.size());
|
||||
|
||||
for (Patient p : patientsPage) {
|
||||
assertTrue(ids.add(p.getId()));
|
||||
}
|
||||
nextUrl = BundleUtil.getLinkUrlOfType(myFhirContext, bundle, LINK_NEXT);
|
||||
assertNotNull(nextUrl);
|
||||
|
||||
// all future pages
|
||||
do {
|
||||
bundle = fetchBundle(nextUrl);
|
||||
assertNotNull(bundle);
|
||||
patientsPage = BundleUtil.toListOfResourcesOfType(myFhirContext, bundle, Patient.class);
|
||||
for (Patient p : patientsPage) {
|
||||
assertTrue(ids.add(p.getId()));
|
||||
}
|
||||
nextUrl = BundleUtil.getLinkUrlOfType(myFhirContext, bundle, LINK_NEXT);
|
||||
if (nextUrl != null) {
|
||||
assertEquals(defaultPageSize, patientsPage.size());
|
||||
} else {
|
||||
assertEquals(4, patientsPage.size());
|
||||
}
|
||||
} while (nextUrl != null);
|
||||
|
||||
// ensure we found everything
|
||||
assertEquals(total, ids.size());
|
||||
} finally {
|
||||
// set it back, just in case
|
||||
myStorageSettings.setSearchPreFetchThresholds(previousPrefetchThreshold);
|
||||
myPagingProvider.setDefaultPageSize(pageSize);
|
||||
myServer.setDefaultPageSize(serverPageSize);
|
||||
}
|
||||
}
|
||||
|
||||
private void createPatients(int theCount) {
|
||||
for (int i = 0; i < theCount; i++) {
|
||||
Patient patient = new Patient();
|
||||
patient.addName().setFamily("lastn").addGiven("name");
|
||||
myPatientDao.create(patient, new SystemRequestDetails()).getId().toUnqualifiedVersionless();
|
||||
}
|
||||
}
|
||||
|
||||
private Bundle fetchBundle(String theUrl) throws IOException {
|
||||
Bundle bundle;
|
||||
HttpGet get = new HttpGet(theUrl);
|
||||
CloseableHttpResponse resp = ourHttpClient.execute(get);
|
||||
try {
|
||||
assertEquals(EncodingEnum.JSON.getResourceContentTypeNonLegacy(), resp.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue().replaceAll(";.*", ""));
|
||||
bundle = EncodingEnum.JSON.newParser(myFhirContext).parseResource(Bundle.class, IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8));
|
||||
} finally {
|
||||
IOUtils.closeQuietly(resp);
|
||||
}
|
||||
|
||||
return bundle;
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue