Fix HQL member-of queries using redundant cross joins

[Copilot]

The testFindTaxonLabelSets test was failing because the HQL query returned empty results due to incorrect query syntax mixing cross joins with the member of operator.

Changes

• findTaxonLabelSets: Removed cross join, use parameter directly in member of clause
• findSubmissions: Applied same fix for consistency

Before

.createQuery("select tls from TaxonLabelSet tls, TaxonLabel tl where tl = :tl and tl member of tls.taxonLabelList")

After

.createQuery("select tls from TaxonLabelSet tls where :tl member of tls.taxonLabelList")

The original pattern created a Cartesian product and used the FROM clause variable tl with member of instead of the bound parameter :tl. The fix uses the standard HQL membership test pattern.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• download.java.net
  • Triggering command: /usr/lib/jvm/temurin-17-jdk-amd64/bin/java /usr/lib/jvm/temurin-17-jdk-amd64/bin/java --enable-native-access=ALL-UNNAMED -classpath /usr/share/apache-maven-3.9.11/boot/plexus-classworlds-2.9.0.jar -Dclassworlds.conf=/usr/share/apache-maven-3.9.11/bin/m2.conf -Dmaven.home=/usr/share/apache-maven-3.9.11 -Dlibrary.jansi.path=/usr/share/apache-maven-3.9.11/lib/jansi-native -Dmaven.multiModuleProjectDirectory=/home/REDACTED/work/treebase/treebase org.codehaus.plexus.classworlds.launcher.Launcher -f pom.xml -B -V -e -Dfindbugs.skip -Dcheckstyle.skip -Dpmd.skip=true -Dspotbugs.skip -Denforcer.skip -Dmaven.javadoc.skip (dns block)
• download.osgeo.org
  • Triggering command: /usr/lib/jvm/temurin-17-jdk-amd64/bin/java /usr/lib/jvm/temurin-17-jdk-amd64/bin/java --enable-native-access=ALL-UNNAMED -classpath /usr/share/apache-maven-3.9.11/boot/plexus-classworlds-2.9.0.jar -Dclassworlds.conf=/usr/share/apache-maven-3.9.11/bin/m2.conf -Dmaven.home=/usr/share/apache-maven-3.9.11 -Dlibrary.jansi.path=/usr/share/apache-maven-3.9.11/lib/jansi-native -Dmaven.multiModuleProjectDirectory=/home/REDACTED/work/treebase/treebase/treebase-core org.codehaus.plexus.classworlds.launcher.Launcher test -Dtest=TaxonLabelDAOTest#testFindTaxonLabelSets (dns block)
  • Triggering command: /usr/lib/jvm/temurin-17-jdk-amd64/bin/java /usr/lib/jvm/temurin-17-jdk-amd64/bin/java --enable-native-access=ALL-UNNAMED -classpath /usr/share/apache-maven-3.9.11/boot/plexus-classworlds-2.9.0.jar -Dclassworlds.conf=/usr/share/apache-maven-3.9.11/bin/m2.conf -Dmaven.home=/usr/share/apache-maven-3.9.11 -Dlibrary.jansi.path=/usr/share/apache-maven-3.9.11/lib/jansi-native -Dmaven.multiModuleProjectDirectory=/home/REDACTED/work/treebase/treebase org.codehaus.plexus.classworlds.launcher.Launcher -f pom.xml -B -V -e -Dfindbugs.skip -Dcheckstyle.skip -Dpmd.skip=true -Dspotbugs.skip -Denforcer.skip -Dmaven.javadoc.skip (dns block)
• hibernate.sourceforge.net
  • Triggering command: /opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/tools/linux64/java/bin/java /opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/tools/linux64/java/bin/java -jar /opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/xml/tools/xml-extractor.jar --fileList=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/working/files-to-index12474442815908407119.list --sourceArchiveDir=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/src --outputDir=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/trap/java (dns block)
• jakarta.apache.org
  • Triggering command: /opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/tools/linux64/java/bin/java /opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/tools/linux64/java/bin/java -jar /opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/xml/tools/xml-extractor.jar --fileList=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/working/files-to-index12474442815908407119.list --sourceArchiveDir=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/src --outputDir=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/trap/java (dns block)
• maven.indexdata.com
  • Triggering command: /usr/lib/jvm/temurin-17-jdk-amd64/bin/java /usr/lib/jvm/temurin-17-jdk-amd64/bin/java --enable-native-access=ALL-UNNAMED -classpath /usr/share/apache-maven-3.9.11/boot/plexus-classworlds-2.9.0.jar -Dclassworlds.conf=/usr/share/apache-maven-3.9.11/bin/m2.conf -Dmaven.home=/usr/share/apache-maven-3.9.11 -Dlibrary.jansi.path=/usr/share/apache-maven-3.9.11/lib/jansi-native -Dmaven.multiModuleProjectDirectory=/home/REDACTED/work/treebase/treebase org.codehaus.plexus.classworlds.launcher.Launcher -f pom.xml -B -V -e -Dfindbugs.skip -Dcheckstyle.skip -Dpmd.skip=true -Dspotbugs.skip -Denforcer.skip -Dmaven.javadoc.skip (dns block)
• nexml.github.io
  • Triggering command: /usr/lib/jvm/temurin-17-jdk-amd64/bin/java /usr/lib/jvm/temurin-17-jdk-amd64/bin/java --enable-native-access=ALL-UNNAMED -classpath /usr/share/apache-maven-3.9.11/boot/plexus-classworlds-2.9.0.jar -Dclassworlds.conf=/usr/share/apache-maven-3.9.11/bin/m2.conf -Dmaven.home=/usr/share/apache-maven-3.9.11 -Dlibrary.jansi.path=/usr/share/apache-maven-3.9.11/lib/jansi-native -Dmaven.multiModuleProjectDirectory=/home/REDACTED/work/treebase/treebase org.codehaus.plexus.classworlds.launcher.Launcher -f pom.xml -B -V -e -Dfindbugs.skip -Dcheckstyle.skip -Dpmd.skip=true -Dspotbugs.skip -Denforcer.skip -Dmaven.javadoc.skip (dns block)
• repository.gbif.org
  • Triggering command: /usr/lib/jvm/temurin-17-jdk-amd64/bin/java /usr/lib/jvm/temurin-17-jdk-amd64/bin/java --enable-native-access=ALL-UNNAMED -classpath /usr/share/apache-maven-3.9.11/boot/plexus-classworlds-2.9.0.jar -Dclassworlds.conf=/usr/share/apache-maven-3.9.11/bin/m2.conf -Dmaven.home=/usr/share/apache-maven-3.9.11 -Dlibrary.jansi.path=/usr/share/apache-maven-3.9.11/lib/jansi-native -Dmaven.multiModuleProjectDirectory=/home/REDACTED/work/treebase/treebase/treebase-core org.codehaus.plexus.classworlds.launcher.Launcher test -Dtest=TaxonLabelDAOTest#testFindTaxonLabelSets (dns block)
  • Triggering command: /usr/lib/jvm/temurin-17-jdk-amd64/bin/java /usr/lib/jvm/temurin-17-jdk-amd64/bin/java --enable-native-access=ALL-UNNAMED -classpath /usr/share/apache-maven-3.9.11/boot/plexus-classworlds-2.9.0.jar -Dclassworlds.conf=/usr/share/apache-maven-3.9.11/bin/m2.conf -Dmaven.home=/usr/share/apache-maven-3.9.11 -Dlibrary.jansi.path=/usr/share/apache-maven-3.9.11/lib/jansi-native -Dmaven.multiModuleProjectDirectory=/home/REDACTED/work/treebase/treebase org.codehaus.plexus.classworlds.launcher.Launcher -f pom.xml -B -V -e -Dfindbugs.skip -Dcheckstyle.skip -Dpmd.skip=true -Dspotbugs.skip -Denforcer.skip -Dmaven.javadoc.skip (dns block)
• repository.jboss.org
  • Triggering command: /usr/lib/jvm/temurin-17-jdk-amd64/bin/java /usr/lib/jvm/temurin-17-jdk-amd64/bin/java --enable-native-access=ALL-UNNAMED -classpath /usr/share/apache-maven-3.9.11/boot/plexus-classworlds-2.9.0.jar -Dclassworlds.conf=/usr/share/apache-maven-3.9.11/bin/m2.conf -Dmaven.home=/usr/share/apache-maven-3.9.11 -Dlibrary.jansi.path=/usr/share/apache-maven-3.9.11/lib/jansi-native -Dmaven.multiModuleProjectDirectory=/home/REDACTED/work/treebase/treebase/treebase-core org.codehaus.plexus.classworlds.launcher.Launcher test -Dtest=TaxonLabelDAOTest#testFindTaxonLabelSets (dns block)
  • Triggering command: /usr/lib/jvm/temurin-17-jdk-amd64/bin/java /usr/lib/jvm/temurin-17-jdk-amd64/bin/java --enable-native-access=ALL-UNNAMED -classpath /usr/share/apache-maven-3.9.11/boot/plexus-classworlds-2.9.0.jar -Dclassworlds.conf=/usr/share/apache-maven-3.9.11/bin/m2.conf -Dmaven.home=/usr/share/apache-maven-3.9.11 -Dlibrary.jansi.path=/usr/share/apache-maven-3.9.11/lib/jansi-native -Dmaven.multiModuleProjectDirectory=/home/REDACTED/work/treebase/treebase org.codehaus.plexus.classworlds.launcher.Launcher -f pom.xml -B -V -e -Dfindbugs.skip -Dcheckstyle.skip -Dpmd.skip=true -Dspotbugs.skip -Denforcer.skip -Dmaven.javadoc.skip (dns block)
• treebase.github.io
  • Triggering command: /usr/lib/jvm/temurin-17-jdk-amd64/bin/java /usr/lib/jvm/temurin-17-jdk-amd64/bin/java --enable-native-access=ALL-UNNAMED -classpath /usr/share/apache-maven-3.9.11/boot/plexus-classworlds-2.9.0.jar -Dclassworlds.conf=/usr/share/apache-maven-3.9.11/bin/m2.conf -Dmaven.home=/usr/share/apache-maven-3.9.11 -Dlibrary.jansi.path=/usr/share/apache-maven-3.9.11/lib/jansi-native -Dmaven.multiModuleProjectDirectory=/home/REDACTED/work/treebase/treebase org.codehaus.plexus.classworlds.launcher.Launcher -f pom.xml -B -V -e -Dfindbugs.skip -Dcheckstyle.skip -Dpmd.skip=true -Dspotbugs.skip -Denforcer.skip -Dmaven.javadoc.skip (dns block)
• www.getahead.ltd.uk
  • Triggering command: /opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/tools/linux64/java/bin/java /opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/tools/linux64/java/bin/java -jar /opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/xml/tools/xml-extractor.jar --fileList=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/working/files-to-index12474442815908407119.list --sourceArchiveDir=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/src --outputDir=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/trap/java (dns block)
• www.springframework.org
  • Triggering command: /opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/tools/linux64/java/bin/java /opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/tools/linux64/java/bin/java -jar /opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/xml/tools/xml-extractor.jar --fileList=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/working/files-to-index12474442815908407119.list --sourceArchiveDir=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/src --outputDir=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/trap/java (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

Original prompt

Failing unit test in treebase-core/src/test/org/cipres/treebase/dao/taxon/TaxonLabelDAOTest.java:

junit.framework.AssertionFailedError
	at junit.framework.Assert.fail(Assert.java:47)
	at junit.framework.Assert.assertTrue(Assert.java:20)
	at junit.framework.Assert.assertFalse(Assert.java:34)
	at junit.framework.Assert.assertFalse(Assert.java:41)
	at org.cipres.treebase.dao.taxon.TaxonLabelDAOTest.testFindTaxonLabelSets(TaxonLabelDAOTest.java:36)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at junit.framework.TestCase.runTest(TestCase.java:154)
	at junit.framework.TestCase.runBare(TestCase.java:127)
	at org.springframework.test.ConditionalTestCase.runBare(ConditionalTestCase.java:69)
	at junit.framework.TestResult$1.protect(TestResult.java:106)
	at junit.framework.TestResult.runProtected(TestResult.java:124)
	at junit.framework.TestResult.run(TestResult.java:109)
	at junit.framework.TestCase.run(TestCase.java:118)
	at junit.framework.TestSuite.runTest(TestSuite.java:208)
	at junit.framework.TestSuite.run(TestSuite.java:203)
	at sun.reflect.GeneratedMethodAccessor24.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.apache.maven.surefire.junit.JUnitTestSetExecutor.execute(JUnitTestSetExecutor.java:81)
	at org.apache.maven.surefire.junit.JUnit3Provider.executeTestSet(JUnit3Provider.java:131)
	at org.apache.maven.surefire.junit.JUnit3Provider.invoke(JUnit3Provider.java:93)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)

Why? Fix this.

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