Fix Java 17 type inference incompatibility with Spring JDBC queryForObject

[Copilot]

Java 17's stricter type inference cannot automatically infer the return type of jdbcTemplate.queryForObject() when used with older Spring Framework versions, causing 32 compilation errors across DAO test files.

Changes

Added explicit type casts to all queryForObject() calls returning Integer:

// Before
Integer count = jdbcTemplate.queryForObject(sqlStr, Integer.class);

// After  
Integer count = (Integer) jdbcTemplate.queryForObject(sqlStr, Integer.class);

Files Modified

• AlgorithmDAOTest.java (2 occurrences)
• StudyDAOTest.java (2 occurrences)
• UserDAOTest.java (3 occurrences)
• SubmissionDAOTest.java (3 occurrences)
• AnalyzedDataDAOTest.java (2 occurrences)
• PersonDAOTest.java (2 occurrences)
• MatrixDAOTest.java (3 occurrences)
• PhyloTreeDAOTest.java (15 occurrences)

Total: 32 fixes across 8 test files

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.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 org.codehaus.plexus.classworlds.launcher.Launcher clean compile -DskipTests (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 test-compile (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 org.codehaus.plexus.classworlds.launcher.Launcher clean compile -DskipTests (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 test-compile (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 org.codehaus.plexus.classworlds.launcher.Launcher clean compile -DskipTests (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 test-compile (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

Fix this:

Error:  COMPILATION ERROR : 
[INFO] -------------------------------------------------------------
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/study/AlgorithmDAOTest.java:[60,60] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/study/AlgorithmDAOTest.java:[93,60] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/study/StudyDAOTest.java:[267,60] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/study/StudyDAOTest.java:[277,66] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/admin/UserDAOTest.java:[87,60] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/admin/UserDAOTest.java:[96,66] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/admin/UserDAOTest.java:[133,66] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/study/SubmissionDAOTest.java:[106,60] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/study/SubmissionDAOTest.java:[139,60] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/study/SubmissionDAOTest.java:[162,60] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/study/AnalyzedDataDAOTest.java:[90,60] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/study/AnalyzedDataDAOTest.java:[126,60] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/admin/PersonDAOTest.java:[79,60] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/admin/PersonDAOTest.java:[88,66] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/matrix/MatrixDAOTest.java:[69,60] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/matrix/MatrixDAOTest.java:[79,52] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/matrix/MatrixDAOTest.java:[212,64] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/tree/PhyloTreeDAOTest.java:[122,68] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/tree/PhyloTreeDAOTest.java:[168,68] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/tree/PhyloTreeDAOTest.java:[211,64] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/tree/PhyloTreeDAOTest.java:[332,60] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/tree/PhyloTreeDAOTest.java:[340,66] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/tree/PhyloTreeDAOTest.java:[431,60] incompatible types: java.lang.Object cannot be converted to java.lang.Integer
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/...

</details>



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