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Add support for filtering ACLs using subqueries #1617

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9179d6f
Add support for filtering ACLs using subqueries
arteymix Feb 15, 2026
eb86c8b
Merge branch 'hotfix-1.32.6' into improvements-for-denormalized-acl-q…
arteymix Feb 16, 2026
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8 changes: 4 additions & 4 deletions ...java/ubic/gemma/persistence/service/common/description/BibliographicReferenceDaoImpl.java
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Expand Up @@ -75,7 +75,7 @@ public long countDistinctWithRelatedExperiments() {
.createQuery( "select count(" + ( AclQueryUtils.requiresCountDistinct() ? "distinct " : "" ) + " b)" + " "
+ "from ExpressionExperiment e join e.primaryPublication b "
+ AclQueryUtils.formAclRestrictionClause( "e.id" ) );
AclQueryUtils.addAclParameters( q, ExpressionExperiment.class );
AclQueryUtils.setAclParameters( q, ExpressionExperiment.class );
return ( Long ) q.uniqueResult();
}

Expand All @@ -87,7 +87,7 @@ public long countWithRelatedExperiments() {
.createQuery( "select count(" + ( AclQueryUtils.requiresCountDistinct() ? "distinct " : "" ) + " e)" + " "
+ "from ExpressionExperiment e join e.primaryPublication b"
+ AclQueryUtils.formAclRestrictionClause( "e.id" ) );
AclQueryUtils.addAclParameters( q, ExpressionExperiment.class );
AclQueryUtils.setAclParameters( q, ExpressionExperiment.class );
return ( Long ) q.uniqueResult();
}

Expand All @@ -99,7 +99,7 @@ public LinkedHashMap<BibliographicReference, Set<ExpressionExperimentIdAndShortN
+ ( AclQueryUtils.requiresGroupBy() ? "group by b, e " : "" )
+ "order by b.authorList nulls last, b.title nulls last"
);
AclQueryUtils.addAclParameters( q, ExpressionExperiment.class );
AclQueryUtils.setAclParameters( q, ExpressionExperiment.class );
//noinspection unchecked
List<Object[]> os = q
.setFirstResult( offset )
Expand All @@ -126,7 +126,7 @@ public LinkedHashMap<BibliographicReference, Collection<ExpressionExperiment>> g
+ "and b in (:recs) "
+ ( AclQueryUtils.requiresGroupBy() ? "group by b, e " : "" )
+ "order by b.authorList nulls last, b.title nulls last" );
AclQueryUtils.addAclParameters( query, ExpressionExperiment.class );
AclQueryUtils.setAclParameters( query, ExpressionExperiment.class );
List<Object[]> os = QueryUtils.listByIdentifiableBatch( query, "recs", records, eeBatchSize );
LinkedHashMap<BibliographicReference, Collection<ExpressionExperiment>> result = new LinkedHashMap<>();
for ( Object[] o : os ) {
Expand Down
12 changes: 8 additions & 4 deletions ...rc/main/java/ubic/gemma/persistence/service/common/description/CharacteristicDaoImpl.java
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Expand Up @@ -29,6 +29,7 @@
import org.hibernate.engine.spi.SessionFactoryImplementor;
import org.hibernate.type.StandardBasicTypes;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.acls.domain.BasePermission;
import org.springframework.stereotype.Repository;
import org.springframework.util.Assert;
import ubic.gemma.core.ontology.OntologyUtils;
Expand All @@ -45,7 +46,7 @@
import ubic.gemma.model.genome.Taxon;
import ubic.gemma.model.genome.gene.GeneSet;
import ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao;
import ubic.gemma.persistence.util.EE2CAclQueryUtils;
import ubic.gemma.persistence.util.AclDenormalizedTableQueryUtils;
import ubic.gemma.persistence.util.IdentifiableUtils;
import ubic.gemma.persistence.util.QueryUtils;

Expand All @@ -56,6 +57,7 @@

import static org.hibernate.criterion.Restrictions.like;
import static org.hibernate.criterion.Restrictions.not;
import static ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil.EE2C_IS_AUTHENTICATED_ANONYMOUSLY_MASK_COLUMN;
import static ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil.EE2C_QUERY_SPACE;
import static ubic.gemma.persistence.util.IdentifiableUtils.toIdentifiableSet;
import static ubic.gemma.persistence.util.QueryUtils.*;
Expand Down Expand Up @@ -242,11 +244,13 @@ public Map<Class<? extends Identifiable>, Map<String, Set<ExpressionExperiment>>
private Map<Class<? extends Identifiable>, Map<String, Set<Long>>> findExperimentsByUrisInternal( Collection<String> uris, boolean includeSubjects, boolean includePredicates, boolean includeObjects, @Nullable Taxon taxon, boolean rankByLevel, int limit ) {
String qs = "select T.`LEVEL`, T.VALUE_URI, T.PREDICATE_URI, T.OBJECT_URI, T.SECOND_PREDICATE_URI, T.SECOND_OBJECT_URI, T.EXPRESSION_EXPERIMENT_FK from EXPRESSION_EXPERIMENT2CHARACTERISTIC T"
+ ( taxon != null ? " join INVESTIGATION I on T.EXPRESSION_EXPERIMENT_FK = I.ID " : "" )
+ EE2CAclQueryUtils.formNativeAclJoinClause( "T.EXPRESSION_EXPERIMENT_FK" ) + " "
+ AclDenormalizedTableQueryUtils.formNativeAclJoinClause( "T.EXPRESSION_EXPERIMENT_FK", "IS_AUTHENTICATED_ANONYMOUSLY" ) + " "
+ "where "
+ createPredicates( "T", "uris", includeSubjects, includePredicates, includeObjects )
+ ( taxon != null ? " and I.TAXON_FK = :taxonId" : "" )
+ EE2CAclQueryUtils.formNativeAclRestrictionClause( ( SessionFactoryImplementor ) getSessionFactory(), "T.ACL_IS_AUTHENTICATED_ANONYMOUSLY_MASK" )
+ AclDenormalizedTableQueryUtils.formNativeAclRestrictionClause( ( SessionFactoryImplementor ) getSessionFactory(),
"IS_AUTHENTICATED_ANONYMOUSLY", "T." + EE2C_IS_AUTHENTICATED_ANONYMOUSLY_MASK_COLUMN,
BasePermission.READ )
+ ( rankByLevel ? " order by FIELD(T.LEVEL, :eeClass, :edClass, :bmClass)" : "" );

Query query = getSessionFactory().getCurrentSession().createSQLQuery( qs )
Expand Down Expand Up @@ -274,7 +278,7 @@ private Map<Class<? extends Identifiable>, Map<String, Set<Long>>> findExperimen
query.setParameter( "taxonId", taxon.getId() );
}

EE2CAclQueryUtils.addAclParameters( query, ExpressionExperiment.class );
AclDenormalizedTableQueryUtils.setAclParameters( query, "IS_AUTHENTICATED_ANONYMOUSLY", ExpressionExperiment.class );

query.setCacheable( true );

Expand Down
26 changes: 16 additions & 10 deletions ...c/main/java/ubic/gemma/persistence/service/expression/arrayDesign/ArrayDesignDaoImpl.java
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Expand Up @@ -25,6 +25,7 @@
import org.hibernate.engine.spi.SessionFactoryImplementor;
import org.hibernate.type.StandardBasicTypes;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.acls.domain.BasePermission;
import org.springframework.stereotype.Repository;
import org.springframework.util.Assert;
import ubic.gemma.model.common.auditAndSecurity.AuditEvent;
Expand All @@ -43,6 +44,7 @@
import ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation;
import ubic.gemma.model.genome.sequenceAnalysis.BlatResult;
import ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao;
import ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil;
import ubic.gemma.persistence.util.*;
import ubic.gemma.persistence.util.Filter;

Expand Down Expand Up @@ -492,7 +494,7 @@ public long countExpressionExperiments( ArrayDesign arrayDesign ) {
+ AclQueryUtils.formAclRestrictionClause( "ee.id" ) + " "
+ "and ad = :ad" )
.setParameter( "ad", arrayDesign );
AclQueryUtils.addAclParameters( query, ExpressionExperiment.class );
AclQueryUtils.setAclParameters( query, ExpressionExperiment.class );
return ( Long ) query.uniqueResult();
}

Expand All @@ -503,7 +505,7 @@ public Map<Taxon, Long> getPerTaxonCount() {
+ "join ad.primaryTaxon t "
+ AclQueryUtils.formAclRestrictionClause( "ad.id" ) + " "
+ "group by t" );
AclQueryUtils.addAclParameters( query, ArrayDesign.class );
AclQueryUtils.setAclParameters( query, ArrayDesign.class );
//noinspection unchecked
List<Object[]> csList = query.setCacheable( true ).list();
return csList.stream().collect( Collectors.toMap( row -> ( Taxon ) row[0], row -> ( Long ) row[1] ) );
Expand Down Expand Up @@ -536,7 +538,7 @@ public long countSwitchedExpressionExperiments( ArrayDesign arrayDesign ) {
+ AclQueryUtils.formAclRestrictionClause( "e.id" ) + " "
+ "and b.originalPlatform = :arrayDesign" )
.setParameter( "arrayDesign", arrayDesign );
AclQueryUtils.addAclParameters( query, ExpressionExperiment.class );
AclQueryUtils.setAclParameters( query, ExpressionExperiment.class );
return ( Long ) query
.setCacheable( true )
.uniqueResult();
Expand Down Expand Up @@ -1059,7 +1061,7 @@ private Query finishFilteringQuery( String queryString, @Nullable Filters filter

Query query = this.getSessionFactory().getCurrentSession().createQuery( queryString );

AclQueryUtils.addAclParameters( query, ArrayDesign.class );
AclQueryUtils.setAclParameters( query, ArrayDesign.class );
FilterQueryUtils.addRestrictionParameters( query, filters );

return query;
Expand Down Expand Up @@ -1136,10 +1138,12 @@ private void populateBlacklisted( Collection<ArrayDesignValueObject> vos ) {
private void populateExpressionExperimentCount( Collection<ArrayDesignValueObject> entities ) {
Query query = this.getSessionFactory().getCurrentSession()
.createSQLQuery( "select ee2ad.ARRAY_DESIGN_FK as ID, count(distinct ee2ad.EXPRESSION_EXPERIMENT_FK) as EE_COUNT from EXPRESSION_EXPERIMENT2ARRAY_DESIGN ee2ad "
+ EE2CAclQueryUtils.formNativeAclJoinClause( "ee2ad.EXPRESSION_EXPERIMENT_FK" ) + " "
+ AclDenormalizedTableQueryUtils.formNativeAclJoinClause( "ee2ad.EXPRESSION_EXPERIMENT_FK", "IS_AUTHENTICATED_ANONYMOUSLY" ) + " "
+ "where ee2ad.ARRAY_DESIGN_FK in :ids "
+ "and not ee2ad.IS_ORIGINAL_PLATFORM"
+ EE2CAclQueryUtils.formNativeAclRestrictionClause( ( SessionFactoryImplementor ) getSessionFactory(), "ee2ad.ACL_IS_AUTHENTICATED_ANONYMOUSLY_MASK" )
+ AclDenormalizedTableQueryUtils.formNativeAclRestrictionClause( ( SessionFactoryImplementor ) getSessionFactory(),
"IS_AUTHENTICATED_ANONYMOUSLY", "ee2ad." + TableMaintenanceUtil.EE2AD_IS_AUTHENTICATED_ANONYMOUSLY_MASK_COLUMN,
BasePermission.READ )
+ formNativeNonTroubledClause( "ee2ad.EXPRESSION_EXPERIMENT_FK", ExpressionExperiment.class )
+ " group by ee2ad.ARRAY_DESIGN_FK" )
.addScalar( "ID", StandardBasicTypes.LONG )
Expand All @@ -1150,7 +1154,7 @@ private void populateExpressionExperimentCount( Collection<ArrayDesignValueObjec
.addSynchronizedEntityClass( ExpressionExperiment.class )
.addSynchronizedEntityClass( ArrayDesign.class )
.setCacheable( true );
EE2CAclQueryUtils.addAclParameters( query, ExpressionExperiment.class );
AclDenormalizedTableQueryUtils.setAclParameters( query, "IS_AUTHENTICATED_ANONYMOUSLY", ExpressionExperiment.class );
Map<Long, Long> countById = QueryUtils.<Long, Object[]>streamByBatch( query, "ids", IdentifiableUtils.getIds( entities ), 2048 )
.collect( Collectors.toMap( o -> ( Long ) o[0], o -> ( Long ) o[1] ) );
for ( ArrayDesignValueObject vo : entities ) {
Expand All @@ -1162,12 +1166,14 @@ private void populateExpressionExperimentCount( Collection<ArrayDesignValueObjec
private void populateSwitchedExpressionExperimentCount( Collection<ArrayDesignValueObject> entities ) {
Query query = this.getSessionFactory().getCurrentSession()
.createSQLQuery( "select ee2ad.ARRAY_DESIGN_FK as ID, count(distinct ee2ad.EXPRESSION_EXPERIMENT_FK) as EE_COUNT from EXPRESSION_EXPERIMENT2ARRAY_DESIGN ee2ad "
+ EE2CAclQueryUtils.formNativeAclJoinClause( "ee2ad.EXPRESSION_EXPERIMENT_FK" ) + " "
+ AclDenormalizedTableQueryUtils.formNativeAclJoinClause( "ee2ad.EXPRESSION_EXPERIMENT_FK", "IS_AUTHENTICATED_ANONYMOUSLY" ) + " "
+ "where ee2ad.ARRAY_DESIGN_FK in :ids "
+ "and ee2ad.IS_ORIGINAL_PLATFORM "
// ignore noop switches
+ "and ee2ad.ARRAY_DESIGN_FK not in (select ARRAY_DESIGN_FK from EXPRESSION_EXPERIMENT2ARRAY_DESIGN where EXPRESSION_EXPERIMENT_FK = ee2ad.EXPRESSION_EXPERIMENT_FK and ARRAY_DESIGN_FK = ee2ad.ARRAY_DESIGN_FK and not IS_ORIGINAL_PLATFORM)"
+ EE2CAclQueryUtils.formNativeAclRestrictionClause( ( SessionFactoryImplementor ) getSessionFactory(), "ee2ad.ACL_IS_AUTHENTICATED_ANONYMOUSLY_MASK" )
+ AclDenormalizedTableQueryUtils.formNativeAclRestrictionClause( ( SessionFactoryImplementor ) getSessionFactory(),
"IS_AUTHENTICATED_ANONYMOUSLY", "ee2ad." + TableMaintenanceUtil.EE2AD_IS_AUTHENTICATED_ANONYMOUSLY_MASK_COLUMN,
BasePermission.READ )
+ formNativeNonTroubledClause( "ee2ad.EXPRESSION_EXPERIMENT_FK", ExpressionExperiment.class )
+ " group by ee2ad.ARRAY_DESIGN_FK" )
.addScalar( "ID", StandardBasicTypes.LONG )
Expand All @@ -1178,7 +1184,7 @@ private void populateSwitchedExpressionExperimentCount( Collection<ArrayDesignVa
.addSynchronizedEntityClass( ExpressionExperiment.class )
.addSynchronizedEntityClass( ArrayDesign.class )
.setCacheable( true );
EE2CAclQueryUtils.addAclParameters( query, ExpressionExperiment.class );
AclDenormalizedTableQueryUtils.setAclParameters( query, "IS_AUTHENTICATED_ANONYMOUSLY", ExpressionExperiment.class );
Map<Long, Long> switchedCountById = QueryUtils.<Long, Object[]>streamByBatch( query, "ids", IdentifiableUtils.getIds( entities ), 2048 )
.collect( Collectors.toMap( row -> ( Long ) row[0], row -> ( Long ) row[1] ) );
for ( ArrayDesignValueObject vo : entities ) {
Expand Down
6 changes: 3 additions & 3 deletions ...ava/ubic/gemma/persistence/service/expression/designElement/CompositeSequenceDaoImpl.java
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Expand Up @@ -99,7 +99,7 @@ protected Query getFilteringQuery( @Nullable Filters filters, @Nullable Sort sor
+ ( !SecurityUtil.isUserAdmin() ? " and ad.curationDetails.troubled = false" : "" )
+ FilterQueryUtils.formRestrictionClause( filters )
+ FilterQueryUtils.formOrderByClause( sort ) );
AclQueryUtils.addAclParameters( query, ArrayDesign.class );
AclQueryUtils.setAclParameters( query, ArrayDesign.class );
FilterQueryUtils.addRestrictionParameters( query, filters );
return query;
}
Expand All @@ -119,7 +119,7 @@ protected Query getFilteringIdQuery( @Nullable Filters filters, @Nullable Sort s
+ ( !SecurityUtil.isUserAdmin() ? " and ad.curationDetails.troubled = false" : "" )
+ FilterQueryUtils.formRestrictionClause( filters )
+ FilterQueryUtils.formOrderByClause( sort ) );
AclQueryUtils.addAclParameters( query, ArrayDesign.class );
AclQueryUtils.setAclParameters( query, ArrayDesign.class );
FilterQueryUtils.addRestrictionParameters( query, filters );
return query;
}
Expand All @@ -132,7 +132,7 @@ protected Query getFilteringCountQuery( @Nullable Filters filters ) {
+ AclQueryUtils.formAclRestrictionClause( "ad.id" )
+ ( !SecurityUtil.isUserAdmin() ? " and ad.curationDetails.troubled = false" : "" )
+ FilterQueryUtils.formRestrictionClause( filters ) );
AclQueryUtils.addAclParameters( query, ArrayDesign.class );
AclQueryUtils.setAclParameters( query, ArrayDesign.class );
FilterQueryUtils.addRestrictionParameters( query, filters );
return query;
}
Expand Down
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