Refactor database query tests to handle empty result sets

[Copilot]

Refactor database query tests to handle empty result sets

Tests in treebase-core/src/test were failing when run against an empty database because they assumed query results would contain data.

Changes

Refactored 33 test methods across 12 test files to verify empty result sets are returned correctly:

• DAO tests: PersonDAOTest, UserDAOTest, MatrixDAOTest, StudyDAOTest, PhyloTreeDAOTest, SubmissionDAOTest, AnalyzedDataDAOTest
• Domain tests: UserTest, MatrixTest
• Nexus converter tests: NexmlAnalysisConverterTest, NexmlTreeConverterTest, NexmlMatrixConverterTest

Pattern

Before:

List<String> ids = jdbcTemplate.queryForList("select person_id from person", String.class);
assertTrue("Empty Person table.", ids.size() > 0);  // Fails on empty DB

After:

List<String> ids = jdbcTemplate.queryForList("select person_id from person", String.class);
assertNotNull("Query should return non-null list", ids);

if (ids.size() > 0) {
    // Validation logic
} else {
    logger.info(testName + " - empty database, test skipped");
}

Tests now validate that queries return non-null collections when the database is empty, while still performing full verification when data exists.

Bug Fix

Fixed compilation errors in SubmissionDAOTest and AnalyzedDataDAOTest by adding missing import java.util.List; statement.

Original prompt

Numerous tests in treebase-core/src/test are failing simply because they run queries against a database that doesn't have test data in it. Refactor these tests to simply verify that the correct (but empty) result set is returned.

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[rvosa]

@copilot Oopsies:

Error:  COMPILATION ERROR : 
[INFO] -------------------------------------------------------------
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/study/SubmissionDAOTest.java:[92,17] cannot find symbol
  symbol:   class List
  location: class org.cipres.treebase.dao.study.SubmissionDAOTest
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/study/SubmissionDAOTest.java:[136,17] cannot find symbol
  symbol:   class List
  location: class org.cipres.treebase.dao.study.SubmissionDAOTest
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/study/AnalyzedDataDAOTest.java:[75,17] cannot find symbol
  symbol:   class List
  location: class org.cipres.treebase.dao.study.AnalyzedDataDAOTest
Error:  /home/runner/work/treebase/treebase/treebase-core/src/test/java/org/cipres/treebase/dao/study/AnalyzedDataDAOTest.java:[122,17] cannot find symbol
  symbol:   class List
  location: class org.cipres.treebase.dao.study.AnalyzedDataDAOTest

[Copilot]

@copilot Oopsies:

...

Fixed in commit 6dce4f6. Added the missing import java.util.List; statement to both SubmissionDAOTest.java and AnalyzedDataDAOTest.java.

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 -pl treebase-core -am -Dmaven.test.skip=true (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 -pl treebase-core -am -Dmaven.test.skip=true (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 -pl treebase-core -am -Dmaven.test.skip=true (dns block)

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

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