Fix testfindRowAsString ObjectNotFoundException on empty database #304

Copilot · 2025-12-21T19:28:07Z

The test fails with ObjectNotFoundException when matrix ID 265 doesn't exist because Hibernate's load() returns a lazy proxy that only throws when properties are accessed.

Changes

Query database first to verify matrix existence before loading proxy object
Skip test with log message if matrix not found
Follows existing pattern from testfindByNexusFileName in same file

// Before: proxy throws on first property access
CharacterMatrix m = (CharacterMatrix) loadObject(CharacterMatrix.class, matrixId);
if (m != null) {  // ineffective - proxy is never null
    List<String> rowStrings = getFixture().findRowAsString(m, start, end);  // throws here
}

// After: check existence first
List<Long> result = jdbcTemplate.queryForList(
    "select matrix_id from matrix where matrix_id = " + matrixId + " fetch first rows only", Long.class);
if (!result.isEmpty()) {
    CharacterMatrix m = (CharacterMatrix) loadObject(CharacterMatrix.class, matrixId);
    List<String> rowStrings = getFixture().findRowAsString(m, start, end);  // safe
}

Warning

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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 compiler:testCompile (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
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jakarta.apache.org
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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 compiler:testCompile (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 compiler:testCompile (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-index15218700111393466483.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-index15218700111393466483.list --sourceArchiveDir=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/src --outputDir=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/trap/java (dns block)

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Original prompt

A unit test is failing in treebase-core/src/test/org/cipres/treebase/dao/matrix/MatrixDAOTest.java:

Error:  org.cipres.treebase.dao.matrix.MatrixDAOTest.testfindRowAsString -- Time elapsed: 0.019 s <<< ERROR!
org.hibernate.ObjectNotFoundException: No row with the given identifier exists: [org.cipres.treebase.domain.matrix.CharacterMatrix#265]
	at org.hibernate.impl.SessionFactoryImpl$1.handleEntityNotFound(SessionFactoryImpl.java:377)
	at org.hibernate.proxy.AbstractLazyInitializer.checkTargetState(AbstractLazyInitializer.java:79)
	at org.hibernate.proxy.AbstractLazyInitializer.initialize(AbstractLazyInitializer.java:68)
	at org.hibernate.proxy.AbstractLazyInitializer.getImplementation(AbstractLazyInitializer.java:111)
	at org.hibernate.proxy.pojo.cglib.CGLIBLazyInitializer.invoke(CGLIBLazyInitializer.java:150)
	at org.cipres.treebase.domain.matrix.CharacterMatrix$$EnhancerByCGLIB$$4ad8dd0b.getRowsReadOnly(<generated>)
	at org.cipres.treebase.dao.matrix.MatrixDAO.findRowAsString(MatrixDAO.java:504)
	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 org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
	at com.sun.proxy.$Proxy58.findRowAsString(Unknown Source)
	at org.cipres.treebase.dao.matrix.MatrixDAOTest.testfindRowAsString(MatrixDAOTest.java:160)
	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.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 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)

Fix this under the assumption that the database may be empty. If empty: skip, otherwise proceed as the test intends.

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Query database first to check if matrix exists before loading the proxy object. This prevents ObjectNotFoundException when database is empty, following the same pattern as testfindByNexusFileName. Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>

Copilot AI assigned Copilot and rvosa Dec 21, 2025

Initial plan

d43a08e

Copilot started work on behalf of rvosa December 21, 2025 19:28 View session

Copilot AI changed the title ~~[WIP] Fix failing unit test in MatrixDAOTest~~ Fix testfindRowAsString ObjectNotFoundException on empty database Dec 21, 2025

Copilot finished work on behalf of rvosa December 21, 2025 19:35

Copilot AI requested a review from rvosa December 21, 2025 19:35

rvosa marked this pull request as ready for review December 21, 2025 19:37

rvosa merged commit 25d62d0 into master Dec 21, 2025
0 of 2 checks passed

rvosa deleted the copilot/fix-matrixdao-test-error branch December 21, 2025 19:38

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Fix testfindRowAsString ObjectNotFoundException on empty database #304

Fix testfindRowAsString ObjectNotFoundException on empty database #304

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Copilot AI commented Dec 21, 2025 •

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Fix testfindRowAsString ObjectNotFoundException on empty database #304

Fix testfindRowAsString ObjectNotFoundException on empty database #304

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Copilot AI commented Dec 21, 2025 •

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