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Fix BeanInstantiationException when searching for blacklisted entities #1649

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Merged
ppavlidis merged 2 commits into from
Apr 28, 2026
+10 −0
Merged

Fix BeanInstantiationException when searching for blacklisted entities #1649

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7cc5c3c
Initial plan
Copilot Apr 27, 2026
f489643
Fix error when searching for a blacklisted entity by checking for abs…
Copilot Apr 27, 2026
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4 changes: 4 additions & 0 deletions gemma-core/src/main/java/ubic/gemma/persistence/util/EntityUrlBuilder.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@
import ubic.gemma.model.genome.Taxon;

import javax.annotation.Nullable;
import java.lang.reflect.Modifier;
import java.net.URI;
import java.util.Collection;
import java.util.List;
Expand Down Expand Up @@ -105,6 +106,9 @@ public <T extends Identifiable> EntityUrl<T> entity( T entity ) {
}

public <T extends Identifiable> EntityUrl<T> entity( Class<T> entityType, Long id ) {
if ( Modifier.isAbstract( entityType.getModifiers() ) ) {
throw new UnsupportedEntityUrlException( "Cannot generate a URL for abstract entity type " + entityType.getSimpleName() + ".", entityType );
}
T entity = BeanUtils.instantiate( entityType );
if ( entity instanceof AbstractIdentifiable ) {
( ( AbstractIdentifiable ) entity ).setId( id );
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6 changes: 6 additions & 0 deletions gemma-core/src/test/java/ubic/gemma/persistence/util/EntityUrlBuilderTest.java
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@@ -1,6 +1,7 @@
package ubic.gemma.persistence.util;

import org.junit.Test;
import ubic.gemma.model.blacklist.BlacklistedEntity;
import ubic.gemma.model.common.description.Characteristic;
import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
import ubic.gemma.model.expression.experiment.ExpressionExperiment;
Expand Down Expand Up @@ -81,4 +82,9 @@ public void testFactorValueOntologyUrl() {
c.setValueUri( "http://purl.obolibrary.org/ont/NCBITaxon_9606" );
assertThrows( UnsupportedEntityUrlException.class, () -> entityUrlBuilder.fromHostUrl().entity( c ).ont().toUriString() );
}

@Test
public void testAbstractEntityType() {
assertThrows( UnsupportedEntityUrlException.class, () -> entityUrlBuilder.fromHostUrl().entity( BlacklistedEntity.class, 1L ) );
}
}