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Patient $everything operation with _offset query parameter throws exception - draft implementation

This commit is contained in:
volodymyr 2024-07-05 14:01:29 -06:00
parent dcf164bdb8
commit de43553fb6
3 changed files with 174 additions and 82 deletions
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1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaResourceDaoPatient.java
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@ -19,7 +19,6 @@
*/
package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoPatient;
import ca.uhn.fhir.jpa.api.dao.PatientEverythingParameters;

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java
View File

@ -1477,6 +1477,11 @@ public class QueryStack {
mySqlBuilder.getSelect().addGroupings(firstPredicateBuilder.getResourceIdColumn());
}
public void addOrdering() {
BaseJoiningPredicateBuilder firstPredicateBuilder = mySqlBuilder.getOrCreateFirstPredicateBuilder();
mySqlBuilder.getSelect().addOrderings(firstPredicateBuilder.getResourceIdColumn());
}
public Condition createPredicateReferenceForEmbeddedChainedSearchResource(
@Nullable DbColumn theSourceJoinColumn,
String theResourceName,

250
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java
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@ -136,6 +136,7 @@ import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Set;
import java.util.TreeSet;
import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.model.util.JpaConstants.UNDESIRED_RESOURCE_LINKAGES_FOR_EVERYTHING_ON_PATIENT_INSTANCE;
@ -571,8 +572,7 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
*
* @param theTargetPids
*/
private void extractTargetPidsFromIdParams(
HashSet<Long> theTargetPids, List<ISearchQueryExecutor> theSearchQueryExecutors) {
private void extractTargetPidsFromIdParams(Set<Long> theTargetPids) {
// get all the IQueryParameterType objects
// for _id -> these should all be StringParam values
HashSet<String> ids = new HashSet<>();
@ -601,10 +601,6 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
for (JpaPid pid : idToPid.values()) {
theTargetPids.add(pid.getId());
}
// add the target pids to our executors as the first
// results iterator to go through
theSearchQueryExecutors.add(new ResolvedSearchQueryExecutor(new ArrayList<>(theTargetPids)));
}
private void createChunkedQuery(
@ -616,13 +612,29 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
RequestDetails theRequest,
List<Long> thePidList,
List<ISearchQueryExecutor> theSearchQueryExecutors) {
String sqlBuilderResourceName = myParams.getEverythingMode() == null ? myResourceName : null;
if (myParams.getEverythingMode() != null) {
createChunkedQueryForEverything(
theParams, theOffset, theMaximumResults, theCountOnlyFlag, thePidList, theSearchQueryExecutors);
} else {
createChunkedQueryGeneral(
theParams, sort, theOffset, theCountOnlyFlag, theRequest, thePidList, theSearchQueryExecutors);
}
}
private void createChunkedQueryGeneral(
SearchParameterMap theParams,
SortSpec sort,
Integer theOffset,
boolean theCountOnlyFlag,
RequestDetails theRequest,
List<Long> thePidList,
List<ISearchQueryExecutor> theSearchQueryExecutors) {
SearchQueryBuilder sqlBuilder = new SearchQueryBuilder(
myContext,
myStorageSettings,
myPartitionSettings,
myRequestPartitionId,
sqlBuilderResourceName,
myResourceName,
mySqlBuilderFactory,
myDialectProvider,
theCountOnlyFlag);
@ -640,67 +652,22 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
}
}
JdbcTemplate jdbcTemplate = new JdbcTemplate(myEntityManagerFactory.getDataSource());
jdbcTemplate.setFetchSize(myFetchSize);
if (theMaximumResults != null) {
jdbcTemplate.setMaxRows(theMaximumResults);
/*
* If we're doing a filter, always use the resource table as the root - This avoids the possibility of
* specific filters with ORs as their root from working around the natural resource type / deletion
* status / partition IDs built into queries.
*/
if (theParams.containsKey(Constants.PARAM_FILTER)) {
Condition partitionIdPredicate = sqlBuilder
.getOrCreateResourceTablePredicateBuilder()
.createPartitionIdPredicate(myRequestPartitionId);
if (partitionIdPredicate != null) {
sqlBuilder.addPredicate(partitionIdPredicate);
}
}
if (myParams.getEverythingMode() != null) {
HashSet<Long> targetPids = new HashSet<>();
if (myParams.get(IAnyResource.SP_RES_ID) != null) {
// will add an initial search executor for
// _id params
extractTargetPidsFromIdParams(targetPids, theSearchQueryExecutors);
} else {
// For Everything queries, we make the query root by the ResourceLink table, since this query
// is basically a reverse-include search. For type/Everything (as opposed to instance/Everything)
// the one problem with this approach is that it doesn't catch Patients that have absolutely
// nothing linked to them. So we do one additional query to make sure we catch those too.
SearchQueryBuilder fetchPidsSqlBuilder = new SearchQueryBuilder(
myContext,
myStorageSettings,
myPartitionSettings,
myRequestPartitionId,
myResourceName,
mySqlBuilderFactory,
myDialectProvider,
theCountOnlyFlag);
GeneratedSql allTargetsSql = fetchPidsSqlBuilder.generate(theOffset, myMaxResultsToFetch);
String sql = allTargetsSql.getSql();
Object[] args = allTargetsSql.getBindVariables().toArray(new Object[0]);
List<Long> output = jdbcTemplate.query(sql, args, new SingleColumnRowMapper<>(Long.class));
// we add a search executor to fetch unlinked patients first
theSearchQueryExecutors.add(new ResolvedSearchQueryExecutor(output));
}
List<String> typeSourceResources = new ArrayList<>();
if (myParams.get(Constants.PARAM_TYPE) != null) {
typeSourceResources.addAll(extractTypeSourceResourcesFromParams());
}
queryStack3.addPredicateEverythingOperation(
myResourceName, typeSourceResources, targetPids.toArray(new Long[0]));
} else {
/*
* If we're doing a filter, always use the resource table as the root - This avoids the possibility of
* specific filters with ORs as their root from working around the natural resource type / deletion
* status / partition IDs built into queries.
*/
if (theParams.containsKey(Constants.PARAM_FILTER)) {
Condition partitionIdPredicate = sqlBuilder
.getOrCreateResourceTablePredicateBuilder()
.createPartitionIdPredicate(myRequestPartitionId);
if (partitionIdPredicate != null) {
sqlBuilder.addPredicate(partitionIdPredicate);
}
}
// Normal search
searchForIdsWithAndOr(sqlBuilder, queryStack3, myParams, theRequest);
}
// Normal search
searchForIdsWithAndOr(sqlBuilder, queryStack3, myParams, theRequest);
// If we haven't added any predicates yet, we're doing a search for all resources. Make sure we add the
// partition ID predicate in that case.
@ -778,6 +745,109 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
}
}
private void createChunkedQueryForEverything(
SearchParameterMap theParams,
Integer theOffset,
Integer theMaximumResults,
boolean theCountOnlyFlag,
List<Long> thePidList,
List<ISearchQueryExecutor> theSearchQueryExecutors) {
SearchQueryBuilder sqlBuilder = new SearchQueryBuilder(
myContext,
myStorageSettings,
myPartitionSettings,
myRequestPartitionId,
null,
mySqlBuilderFactory,
myDialectProvider,
theCountOnlyFlag);
QueryStack queryStack3 = new QueryStack(
theParams, myStorageSettings, myContext, sqlBuilder, mySearchParamRegistry, myPartitionSettings);
JdbcTemplate jdbcTemplate = initializeJdbcTemplate(theMaximumResults);
Set<Long> targetPids = new TreeSet<>();
if (myParams.get(IAnyResource.SP_RES_ID) != null) {
extractTargetPidsFromIdParams(targetPids);
// add the target pids to our executors as the first
// results iterator to go through
theSearchQueryExecutors.add(new ResolvedSearchQueryExecutor(new ArrayList<>(targetPids)));
} else {
// For Everything queries, we make the query root by the ResourceLink table, since this query
// is basically a reverse-include search. For type/Everything (as opposed to instance/Everything)
// the one problem with this approach is that it doesn't catch Patients that have absolutely
// nothing linked to them. So we do one additional query to make sure we catch those too.
SearchQueryBuilder fetchPidsSqlBuilder = new SearchQueryBuilder(
myContext,
myStorageSettings,
myPartitionSettings,
myRequestPartitionId,
myResourceName,
mySqlBuilderFactory,
myDialectProvider,
theCountOnlyFlag);
GeneratedSql allTargetsSql = fetchPidsSqlBuilder.generate(theOffset, myMaxResultsToFetch);
String sql = allTargetsSql.getSql();
Object[] args = allTargetsSql.getBindVariables().toArray(new Object[0]);
List<Long> output = jdbcTemplate.query(sql, args, new SingleColumnRowMapper<>(Long.class));
// we add a search executor to fetch unlinked patients first
theSearchQueryExecutors.add(new ResolvedSearchQueryExecutor(output));
}
List<String> typeSourceResources = new ArrayList<>();
if (myParams.get(Constants.PARAM_TYPE) != null) {
typeSourceResources.addAll(extractTypeSourceResourcesFromParams());
}
queryStack3.addPredicateEverythingOperation(
myResourceName, typeSourceResources, targetPids.toArray(new Long[0]));
// Add PID list predicate for full text search and/or lastn operation
if (thePidList != null && !thePidList.isEmpty()) {
sqlBuilder.addResourceIdsPredicate(thePidList);
}
// Last updated
DateRangeParam lu = myParams.getLastUpdated();
if (lu != null && !lu.isEmpty()) {
Condition lastUpdatedPredicates = sqlBuilder.addPredicateLastUpdated(lu);
sqlBuilder.addPredicate(lastUpdatedPredicates);
}
/*
* If offset is present, we want deduplicate the results by using GROUP BY
*/
if (theOffset != null) {
queryStack3.addGrouping();
queryStack3.addOrdering();
queryStack3.setUseAggregate(true);
}
/*
* Now perform the search
*/
GeneratedSql generatedSql = sqlBuilder.generate(theOffset, myMaxResultsToFetch);
if (!generatedSql.isMatchNothing()) {
SearchQueryExecutor executor =
mySqlBuilderFactory.newSearchQueryExecutor(generatedSql, myMaxResultsToFetch);
theSearchQueryExecutors.add(executor);
}
}
private JdbcTemplate initializeJdbcTemplate(Integer theMaximumResults) {
JdbcTemplate jdbcTemplate = new JdbcTemplate(myEntityManagerFactory.getDataSource());
jdbcTemplate.setFetchSize(myFetchSize);
if (theMaximumResults != null) {
jdbcTemplate.setMaxRows(theMaximumResults);
}
return jdbcTemplate;
}
private Collection<String> extractTypeSourceResourcesFromParams() {
List<List<IQueryParameterType>> listOfList = myParams.get(Constants.PARAM_TYPE);
@ -2275,6 +2345,10 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
if (myMaxResultsToFetch == null) {
if (myParams.getLoadSynchronousUpTo() != null) {
myMaxResultsToFetch = myParams.getLoadSynchronousUpTo();
} else if (myParams.getOffset() != null
&& myParams.getCount() != null
&& myParams.getEverythingMode() != null) {
myMaxResultsToFetch = myParams.getOffset() + myParams.getCount();
} else if (myParams.getOffset() != null && myParams.getCount() != null) {
myMaxResultsToFetch = myParams.getCount();
} else {
@ -2286,7 +2360,11 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
* assigns the results iterator
* and populates the myQueryList.
*/
initializeIteratorQuery(myOffset, myMaxResultsToFetch);
if (myParams.getEverythingMode() != null) {
initializeIteratorQuery(0, myMaxResultsToFetch);
} else {
initializeIteratorQuery(myOffset, myMaxResultsToFetch);
}
}
if (myNext == null) {
@ -2305,22 +2383,21 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
Long nextLong = myResultsIterator.next();
if (myHavePerfTraceFoundIdHook) {
HookParams params = new HookParams()
.add(Integer.class, System.identityHashCode(this))
.add(Object.class, nextLong);
CompositeInterceptorBroadcaster.doCallHooks(
myInterceptorBroadcaster,
myRequest,
Pointcut.JPA_PERFTRACE_SEARCH_FOUND_ID,
params);
callPerformanceTracingHook(nextLong);
}
if (nextLong != null) {
JpaPid next = JpaPid.fromId(nextLong);
if (myPidSet.add(next)) {
myNext = next;
myNonSkipCount++;
break;
if (myParams.getEverythingMode() != null
&& myOffset != null
&& myOffset >= myPidSet.size()) {
mySkipCount++;
} else {
myNext = next;
myNonSkipCount++;
break;
}
} else {
mySkipCount++;
}
@ -2352,8 +2429,11 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
JpaPid next = myIncludesIterator.next();
if (next != null)
if (myPidSet.add(next)) {
myNext = next;
break;
if (myParams.getEverythingMode() == null
|| (myOffset != null && myOffset < myPidSet.size())) {
myNext = next;
break;
}
}
}
if (myNext == null) {
@ -2393,6 +2473,14 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
}
}
private void callPerformanceTracingHook(Long theNextLong) {
HookParams params = new HookParams()
.add(Integer.class, System.identityHashCode(this))
.add(Object.class, theNextLong);
CompositeInterceptorBroadcaster.doCallHooks(
myInterceptorBroadcaster, myRequest, Pointcut.JPA_PERFTRACE_SEARCH_FOUND_ID, params);
}
private void sendProcessingMsgAndFirePerformanceHook() {
String msg = "Pass completed with no matching results seeking rows "
+ myPidSet.size() + "-" + mySkipCount