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Copilot AI commented Dec 21, 2025

Fix AlgorithmDAOTest Failure

Root Cause

The test testFinalAllUniqueAlgorithmDescriptions was failing with "empty descriptions" because the algorithm table had no data during test execution.

Solution

Created database patch 0006_add-algorithm-types.sql that:

  • Adds six standard algorithm types as reference data
  • Is imported by init_db_uptodate.pg as part of the PostgreSQL initialization routine
  • Ensures algorithm data is available whenever the database is initialized

Algorithm types added:

  • Maximum likelihood (L)
  • Bayesian inference (B)
  • Parsimony (P)
  • Minimum evolution (E)
  • Neighbor joining (J)
  • UPGMA (U)

Changes Made

  • Analyzed the failing test and understood the root cause
  • Added algorithm reference data initialization to initTreebase.sql (for manual DB setup)
  • Created database patch 0006_add-algorithm-types.sql for PostgreSQL initialization
  • Updated init_db_uptodate.pg to include patches 0006 and 0007
  • Renumbered existing 0006_create-indices.sql to 0007_create-indices.sql
  • Removed redundant onSetUpBeforeTransaction() method from test (was causing duplicate key errors)
  • Ran code review (no issues - incorrectly flagged already-removed imports)
  • Ran CodeQL security check (no issues)

Security Summary

No security vulnerabilities detected. All CodeQL checks passed.

Original prompt

Why is this happening? Fix it:

Error:  org.cipres.treebase.dao.study.AlgorithmDAOTest.testFinalAllUniqueAlgorithmDescriptions -- Time elapsed: 0.010 s <<< FAILURE!
junit.framework.AssertionFailedError: empty descriptions.
	at junit.framework.Assert.fail(Assert.java:47)
	at junit.framework.Assert.assertTrue(Assert.java:20)
	at org.cipres.treebase.dao.study.AlgorithmDAOTest.testFinalAllUniqueAlgorithmDescriptions(AlgorithmDAOTest.java:51)
	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)

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Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
Copilot AI changed the title [WIP] Fix empty descriptions in AlgorithmDAOTest Add algorithm reference data to initTreebase.sql Dec 21, 2025
Copilot AI requested a review from rvosa December 21, 2025 21:27
@rvosa
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rvosa commented Dec 21, 2025

@copilot we're still getting this:

Error:  org.cipres.treebase.dao.study.AlgorithmDAOTest.testFinalAllUniqueAlgorithmDescriptions -- Time elapsed: 0.003 s <<< FAILURE!
junit.framework.AssertionFailedError: empty descriptions.
	at junit.framework.Assert.fail(Assert.java:47)
	at junit.framework.Assert.assertTrue(Assert.java:20)
	at org.cipres.treebase.dao.study.AlgorithmDAOTest.testFinalAllUniqueAlgorithmDescriptions(AlgorithmDAOTest.java:51)
	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)

Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
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Copilot AI commented Dec 21, 2025

@copilot we're still getting this:

...

The issue was that initTreebase.sql is for manual database setup, not automatically executed during tests. I've added programmatic test data initialization in AlgorithmDAOTest.onSetUpBeforeTransaction() that creates the six standard algorithm types before each test runs. This ensures the test has the required data. See commit 52ca4c0.

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Copilot AI changed the title Add algorithm reference data to initTreebase.sql Fix AlgorithmDAOTest failure by adding test data initialization Dec 21, 2025
@rvosa
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rvosa commented Dec 21, 2025

@copilot add a patch called patches/0006_add-algorithm-types.sql that is imported by treebase-core/db/schema/init_db_uptodate.pg in the same way as the other imports such that the six algorithm types are created as an integral part of the postgres initialization routine rather than by setting them up for individual tests.

Copilot AI and others added 2 commits December 21, 2025 21:47
Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
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Copilot AI commented Dec 21, 2025

@copilot add a patch called patches/0006_add-algorithm-types.sql that is imported by treebase-core/db/schema/init_db_uptodate.pg in the same way as the other imports such that the six algorithm types ...

Created patch 0006_add-algorithm-types.sql and added it to init_db_uptodate.pg. The patch adds the six standard algorithm types as reference data during database initialization. Also renumbered the existing 0006_create-indices.sql to 0007_create-indices.sql and included it in the init script. See commits 135053b and ac48026.

Copilot AI changed the title Fix AlgorithmDAOTest failure by adding test data initialization Fix AlgorithmDAOTest failure by adding database patch and test data initialization Dec 21, 2025
@rvosa
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rvosa commented Dec 21, 2025

@copilot new problem:

[main] ERROR org.hibernate.util.JDBCExceptionReporter - Batch entry 0 insert into ALGORITHM (VERSION, Description, PropertyName, PropertyValue, TYPE, ALGORITHM_ID) values (0, 'maximum likelihood', NULL, NULL, 'L', 1) was aborted: ERROR: duplicate key value violates unique constraint "algorithm_pkey"
  Detail: Key (algorithm_id)=(1) already exists.  Call getNextException to see other errors in the batch.
[main] WARN org.hibernate.util.JDBCExceptionReporter - SQL Error: 0, SQLState: 23505
[main] ERROR org.hibernate.util.JDBCExceptionReporter - ERROR: duplicate key value violates unique constraint "algorithm_pkey"
  Detail: Key (algorithm_id)=(1) already exists.
[main] ERROR org.hibernate.event.def.AbstractFlushingEventListener - Could not synchronize database state with session
org.hibernate.exception.ConstraintViolationException: Could not execute JDBC batch update
	at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:71)
	at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)
	at org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:253)
	at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:266)
	at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:167)
	at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298)
	at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27)
	at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
	at org.springframework.orm.hibernate3.HibernateAccessor.flushIfNecessary(HibernateAccessor.java:390)
	at org.springframework.orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java:373)
	at org.springframework.orm.hibernate3.HibernateTemplate.save(HibernateTemplate.java:632)
	at org.cipres.treebase.dao.study.AlgorithmDAOTest.onSetUpBeforeTransaction(AlgorithmDAOTest.java:72)
	at org.springframework.test.AbstractTransactionalSpringContextTests.onSetUp(AbstractTransactionalSpringContextTests.java:173)
	at org.springframework.test.AbstractSingleSpringContextTests.setUp(AbstractSingleSpringContextTests.java:89)
	at junit.framework.TestCase.runBare(TestCase.java:125)
	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)
Caused by: java.sql.BatchUpdateException: Batch entry 0 insert into ALGORITHM (VERSION, Description, PropertyName, PropertyValue, TYPE, ALGORITHM_ID) values (0, 'maximum likelihood', NULL, NULL, 'L', 1) was aborted: ERROR: duplicate key value violates unique constraint "algorithm_pkey"
  Detail: Key (algorithm_id)=(1) already exists.  Call getNextException to see other errors in the batch.
	at org.postgresql.jdbc.BatchResultHandler.handleCompletion(BatchResultHandler.java:186)
	at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:570)
	at org.postgresql.jdbc.PgStatement.internalExecuteBatch(PgStatement.java:887)
	at org.postgresql.jdbc.PgStatement.executeBatch(PgStatement.java:910)
	at org.postgresql.jdbc.PgPreparedStatement.executeBatch(PgPreparedStatement.java:1638)
	at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeBatch(NewProxyPreparedStatement.java:1723)
	at org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48)
	at org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:246)
	... 30 more
Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "algorithm_pkey"
  Detail: Key (algorithm_id)=(1) already exists.
	at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2675)
	at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2365)
	at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:559)
	... 36 more
Error:  Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.017 s <<< FAILURE! -- in org.cipres.treebase.dao.study.AlgorithmDAOTest
Error:  org.cipres.treebase.dao.study.AlgorithmDAOTest.testFinalAllUniqueAlgorithmDescriptions -- Time elapsed: 0.017 s <<< ERROR!
org.springframework.dao.DataIntegrityViolationException: Could not execute JDBC batch update; nested exception is org.hibernate.exception.ConstraintViolationException: Could not execute JDBC batch update
Caused by: org.hibernate.exception.ConstraintViolationException: Could not execute JDBC batch update
	at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:71)
	at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)
	at org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:253)
	at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:266)
	at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:167)
	at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298)
	at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27)
	at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
	at org.springframework.orm.hibernate3.HibernateAccessor.flushIfNecessary(HibernateAccessor.java:390)
	at org.springframework.orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java:373)
	at org.springframework.orm.hibernate3.HibernateTemplate.save(HibernateTemplate.java:632)
	at org.cipres.treebase.dao.study.AlgorithmDAOTest.onSetUpBeforeTransaction(AlgorithmDAOTest.java:72)
	at org.springframework.test.AbstractTransactionalSpringContextTests.onSetUp(AbstractTransactionalSpringContextTests.java:173)
	at org.springframework.test.AbstractSingleSpringContextTests.setUp(AbstractSingleSpringContextTests.java:89)
	at junit.framework.TestCase.runBare(TestCase.java:125)
	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)
Caused by: java.sql.BatchUpdateException: Batch entry 0 insert into ALGORITHM (VERSION, Description, PropertyName, PropertyValue, TYPE, ALGORITHM_ID) values (0, 'maximum likelihood', NULL, NULL, 'L', 1) was aborted: ERROR: duplicate key value violates unique constraint "algorithm_pkey"
  Detail: Key (algorithm_id)=(1) already exists.  Call getNextException to see other errors in the batch.
	at org.postgresql.jdbc.BatchResultHandler.handleCompletion(BatchResultHandler.java:186)
	at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:570)
	at org.postgresql.jdbc.PgStatement.internalExecuteBatch(PgStatement.java:887)
	at org.postgresql.jdbc.PgStatement.executeBatch(PgStatement.java:910)
	at org.postgresql.jdbc.PgPreparedStatement.executeBatch(PgPreparedStatement.java:1638)
	at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeBatch(NewProxyPreparedStatement.java:1723)
	at org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48)
	at org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:246)
	... 30 more
Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "algorithm_pkey"
  Detail: Key (algorithm_id)=(1) already exists.
	at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2675)
	at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2365)
	at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:559)
	... 36 more

Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
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Copilot AI commented Dec 21, 2025

@copilot new problem:

...

The duplicate key error was caused by the test's onSetUpBeforeTransaction() method trying to insert algorithm data that already exists from the database patch. Removed the redundant programmatic initialization from the test since the algorithm data now comes from the 0006_add-algorithm-types.sql patch. See commit 0bb40c8.

@rvosa rvosa marked this pull request as ready for review December 21, 2025 22:06
@rvosa rvosa merged commit a1e0d5d into master Dec 21, 2025
0 of 2 checks passed
@rvosa rvosa deleted the copilot/fix-empty-algorithm-descriptions branch December 21, 2025 22:08
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2 participants