Skip database-dependent tests when test database is empty #309

Copilot · 2025-12-21T22:15:48Z

Fifteen unit tests were failing with AssertionFailedError when run against an empty test database. These tests now detect empty data conditions and skip gracefully with informational log messages.

Changes

TaxonLabelTest: Added skip checks to testFindBySubstring, testFindStudies, and testTaxonLabelLengthSorting
PhyloTreeTest: Added skip check to testUpdateNewickString
MatrixServiceImplTest: Added skip check to testFindSomethingByRangeExpression
TaxonLabelServiceImplTest: Added skip checks to testFindStudiesByTaxon and testFindTreesByTaxon
SearchResultsTest: Added skip checks to testTrivial, testSearchService, testQuickCheck, testConvertToMatrices, testConvertFromMatrices, testConvertToTrees, and testConvertFromTrees. Also removed assertion in getTestData() helper method that prevented tests from running when database is empty.
PhyloTreeServiceImplTest: Added skip check to testFindSomethingByRangeExpression. Also fixed bug where assertion range (37..100) didn't match query range (37..40).

Implementation

Follows existing skip pattern from testFindMatricesByTaxonVariant and testBuildNewickStringPerf:

public void testFindBySubstring() {
    Collection<TaxonLabel> res = findHomoSapiensTL();
    assertNotNull(res);
    
    // Skip test if database is empty
    if (res.isEmpty()) {
        LOGGER.info("SKIPPED: testFindBySubstring - No TaxonLabel data found in database. Test requires populated database.");
        return;
    }
    
    for (TaxonLabel tl : res) {
        assertTrue(tl.getTaxonLabel().toLowerCase().contains("homo"));
    }
}

Checks use isEmpty() for collections and null checks for single objects, consistent with codebase conventions.

Original prompt

We're getting numerous AssertionFailedErrors in the unit tests. If these are because the
test database is empty, skip the tests and emit an informational message. Otherwise,
proceed with the tests as intended:

org.cipres.treebase.domain.taxon.TaxonLabelTest ► testFindStudies: treebase-core/src/test/java/org/cipres/treebase/domain/taxon/TaxonLabelTest.java#L59
Failed test found in: treebase-core/target/surefire-reports/TEST-org.cipres.treebase.domain.taxon.TaxonLabelTest.xml Error: junit.framework.AssertionFailedError
org.cipres.treebase.domain.taxon.TaxonLabelTest ► testFindBySubstring: treebase-core/src/test/java/org/cipres/treebase/domain/taxon/TaxonLabelTest.java#L48
Failed test found in: treebase-core/target/surefire-reports/TEST-org.cipres.treebase.domain.taxon.TaxonLabelTest.xml Error: junit.framework.AssertionFailedError
org.cipres.treebase.domain.taxon.TaxonLabelTest ► testTaxonLabelLengthSorting: treebase-core/src/test/java/org/cipres/treebase/domain/taxon/TaxonLabelTest.java#L152
Failed test found in: treebase-core/target/surefire-reports/TEST-org.cipres.treebase.domain.taxon.TaxonLabelTest.xml Error: junit.framework.AssertionFailedError
org.cipres.treebase.domain.tree.PhyloTreeTest ► testUpdateNewickString: treebase-core/src/test/java/org/cipres/treebase/domain/tree/PhyloTreeTest.java#L202
Failed test found in: treebase-core/target/surefire-reports/TEST-org.cipres.treebase.domain.tree.PhyloTreeTest.xml Error: junit.framework.AssertionFailedError: Study deletion failed.
org.cipres.treebase.service.matrix.MatrixServiceImplTest ► testFindSomethingByRangeExpression: treebase-core/src/test/java/org/cipres/treebase/service/matrix/MatrixServiceImplTest.java#L145
Failed test found in: treebase-core/target/surefire-reports/TEST-org.cipres.treebase.service.matrix.MatrixServiceImplTest.xml Error: junit.framework.AssertionFailedError
org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest ► testFindStudiesByTaxon: treebase-core/src/test/java/org/cipres/treebase/service/taxon/TaxonLabelServiceImplTest.java#L81
Failed test found in: treebase-core/target/surefire-reports/TEST-org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest.xml Error: junit.framework.AssertionFailedError
org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest ► testFindTreesByTaxon: treebase-core/src/test/java/org/cipres/treebase/service/taxon/TaxonLabelServiceImplTest.java#L107
Failed test found in: treebase-core/target/surefire-reports/TEST-org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest.xml Error: junit.framework.AssertionFailedError

✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.

…ssages Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>

Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>

…plTest Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>

Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>

…udies' Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>

rvosa · 2025-12-21T22:36:39Z

@copilot there are more failures of the same type:

❌ org.cipres.treebase.domain.search.SearchResultsTest
❌ testTrivial
	junit.framework.AssertionFailedError
❌ testQuickCheck
	junit.framework.AssertionFailedError
❌ testSearchService
	junit.framework.AssertionFailedError
❌ testConvertToMatrices
	junit.framework.AssertionFailedError
❌ testConvertFromMatrices
	junit.framework.AssertionFailedError
❌ testConvertToTrees
	junit.framework.AssertionFailedError
❌ testConvertFromTrees
	junit.framework.AssertionFailedError
	
❌ org.cipres.treebase.domain.tree.PhyloTreeTest
❌ testUpdateNewickString
	junit.framework.AssertionFailedError: Study deletion failed.	

❌ org.cipres.treebase.service.tree.PhyloTreeServiceImplTest
❌ testFindSomethingByRangeExpression
	junit.framework.AssertionFailedError

…plTest Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>

Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>

…ery range Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>

Copilot · 2025-12-21T22:44:51Z

@copilot there are more failures of the same type:

...

I've added database empty checks to all the failing tests you mentioned:

SearchResultsTest (7 tests):

testTrivial, testSearchService, testQuickCheck
testConvertToMatrices, testConvertFromMatrices
testConvertToTrees, testConvertFromTrees
Also removed assertion in getTestData() helper method

PhyloTreeServiceImplTest (1 test):

testFindSomethingByRangeExpression
Fixed bug: assertion range now matches query range (37..40 instead of 37..100)

PhyloTreeTest.testUpdateNewickString: Already has skip check for empty User data (commit 243aeb6). The "Study deletion failed" error occurs during test cleanup, not due to empty database.

Commits: d459e02, 1b31713, b7a5541

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 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-index12223092218108206524.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-index12223092218108206524.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 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 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-index12223092218108206524.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-index12223092218108206524.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)

Initial plan

3231278

Copilot AI assigned Copilot and rvosa Dec 21, 2025

Copilot started work on behalf of rvosa December 21, 2025 22:16 View session

Copilot AI and others added 5 commits December 21, 2025 22:19

Add database empty checks to skip failing tests with informational me…

243aeb6

…ssages Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>

Remove redundant assertions after database empty checks

ae983e7

Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>

Use isEmpty() instead of null check for collection in MatrixServiceIm…

cd9fe73

…plTest Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>

Use isEmpty() for collection checks consistently

90dbdb3

Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>

Fix log message in testFindTreesByTaxon to say 'trees' instead of 'st…

3c0cbab

…udies' Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>

Copilot AI changed the title ~~[WIP] Skip tests if database is empty and log message~~ Skip database-dependent tests when test database is empty Dec 21, 2025

Copilot AI requested a review from rvosa December 21, 2025 22:31

Copilot finished work on behalf of rvosa December 21, 2025 22:31

Copilot started work on behalf of rvosa December 21, 2025 22:37 View session

Copilot AI and others added 3 commits December 21, 2025 22:39

Add database empty checks to SearchResultsTest and PhyloTreeServiceIm…

d459e02

…plTest Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>

Remove assertion from getTestData that fails when database is empty

1b31713

Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>

Fix assertion range in testFindSomethingByRangeExpression to match qu…

b7a5541

…ery range Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>

rvosa marked this pull request as ready for review December 21, 2025 22:45

rvosa merged commit 090ab55 into master Dec 21, 2025
0 of 2 checks passed

rvosa deleted the copilot/skip-tests-if-empty-db branch December 21, 2025 22:45

Copilot AI restored the copilot/skip-tests-if-empty-db branch December 21, 2025 22:45

Copilot stopped work on behalf of rvosa due to an error December 21, 2025 22:45
Copilot has encountered an error. See logs for additional details.

rvosa deleted the copilot/skip-tests-if-empty-db branch December 21, 2025 23:10

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

Skip database-dependent tests when test database is empty #309

Skip database-dependent tests when test database is empty #309

Uh oh!

Copilot AI commented Dec 21, 2025 •

edited

Loading

Uh oh!

rvosa commented Dec 21, 2025

Uh oh!

Copilot AI commented Dec 21, 2025 •

edited

Loading

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

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Skip database-dependent tests when test database is empty #309

Skip database-dependent tests when test database is empty #309

Uh oh!

Conversation

Copilot AI commented Dec 21, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Changes

Implementation

Uh oh!

rvosa commented Dec 21, 2025

Uh oh!

Copilot AI commented Dec 21, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

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

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Copilot AI commented Dec 21, 2025 •

edited

Loading

Copilot AI commented Dec 21, 2025 •

edited

Loading