Skip to content

Fix HQL member-of queries using redundant cross joins #305

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
rvosa merged 2 commits into from
Dec 21, 2025
Merged

Fix HQL member-of queries using redundant cross joins #305

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
090e3fa
Initial plan
Copilot Dec 21, 2025
e78607a
Fix HQL queries in findTaxonLabelSets and findSubmissions methods
Copilot Dec 21, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -390,7 +390,7 @@

public Set<Submission> findSubmissions(TaxonLabel taxonLabel) {
Query q = getSession()
.createQuery("select s from Submission s, TaxonLabel tl where tl = :tl and tl member of s.submittedTaxonLabels");
.createQuery("select s from Submission s where :tl member of s.submittedTaxonLabels");
q.setParameter("tl", taxonLabel);
Set<Submission> result = new HashSet<Submission> ();
result.addAll(q.list());
Expand All @@ -402,10 +402,10 @@
*/
public Set<TaxonLabelSet> findTaxonLabelSets(TaxonLabel taxonLabel) {
Query q = getSession()
.createQuery("select tls from TaxonLabelSet tls, TaxonLabel tl where tl = :tl and tl member of tls.taxonLabelList");
.createQuery("select tls from TaxonLabelSet tls where :tl member of tls.taxonLabelList");
q.setParameter("tl", taxonLabel);
Set<TaxonLabelSet> result = new HashSet<TaxonLabelSet> ();
result.addAll(q.list());

Check failure on line 408 in treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java

View workflow job for this annotation

GitHub Actions / JUnit Test Results

org.cipres.treebase.dao.taxon.TaxonLabelDAOTest ► testFindTaxonLabelSets 

Failed test found in:
  treebase-core/target/surefire-reports/TEST-org.cipres.treebase.dao.taxon.TaxonLabelDAOTest.xml
Error:
  org.hibernate.exception.SQLGrammarException: could not execute query
Raw output 
org.hibernate.exception.SQLGrammarException: could not execute query
	at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:67)
	at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)
	at org.hibernate.loader.Loader.doList(Loader.java:2216)
	at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2104)
	at org.hibernate.loader.Loader.list(Loader.java:2099)
	at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:378)
	at org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:338)
	at org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:172)
	at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1121)
	at org.hibernate.impl.QueryImpl.list(QueryImpl.java:79)
	at org.cipres.treebase.dao.taxon.TaxonLabelDAO.findTaxonLabelSets(TaxonLabelDAO.java:408)
	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.$Proxy48.findTaxonLabelSets(Unknown Source)
	at org.cipres.treebase.dao.taxon.TaxonLabelDAOTest.testFindTaxonLabelSets(TaxonLabelDAOTest.java:35)
	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.GeneratedMethodAccessor24.invoke(Unknown Source)
	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: org.postgresql.util.PSQLException: ERROR: operator does not exist: bytea = bigint
  Hint: No operator matches the given name and argument types. You might need to add explicit type casts.
  Position: 231
	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:355)
	at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:490)
	at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:408)
	at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:166)
	at org.postgresql.jdbc.PgPreparedStatement.executeQuery(PgPreparedStatement.java:118)
	at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:76)
	at org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:186)
	at org.hibernate.loader.Loader.getResultSet(Loader.java:1787)
	at org.hibernate.loader.Loader.doQuery(Loader.java:674)
	at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:236)
	at org.hibernate.loader.Loader.doList(Loader.java:2213)
	... 43 more
return result;

}
Expand Down
Loading