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Fix Java 17 type inference incompatibility with Spring JDBC queryForObject #300

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

Fix Java 17 type inference incompatibility with Spring JDBC queryForObject #300

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08fb76b
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Copilot Dec 21, 2025
2552e3f
Fix jdbcTemplate.queryForObject type conversion errors by adding expl…
Copilot Dec 21, 2025
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4 changes: 2 additions & 2 deletions treebase-core/src/test/java/org/cipres/treebase/dao/admin/PersonDAOTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,7 @@

// 2. verify
String sqlStr = "select count(*) from Person where person_id=" + p.getId();
Integer count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = (Integer) jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue(count == 1);

// 3. delete
Expand All @@ -85,7 +85,7 @@
setComplete();

// 4. verify delete:
Integer countVerify = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer countVerify = (Integer) jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue(countVerify == 0);

if (logger.isInfoEnabled()) {
Expand All @@ -103,7 +103,7 @@
}

// 1. find a valid id first:
List<String> ids = jdbcTemplate.queryForList("select person_id from person", String.class);

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org.cipres.treebase.dao.admin.PersonDAOTest ► testFindByID 

Failed test found in:
  treebase-core/target/surefire-reports/TEST-org.cipres.treebase.dao.admin.PersonDAOTest.xml
Error:
  org.springframework.jdbc.BadSqlGrammarException:
Raw output 
org.springframework.jdbc.BadSqlGrammarException: 
StatementCallback; bad SQL grammar [select person_id from person]; nested exception is org.postgresql.util.PSQLException: ERROR: relation "person" does not exist
  Position: 23
Caused by: org.postgresql.util.PSQLException: ERROR: relation "person" does not exist
  Position: 23
	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.PgStatement.executeWithFlags(PgStatement.java:329)
	at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:315)
	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:291)
	at org.postgresql.jdbc.PgStatement.executeQuery(PgStatement.java:243)
	at com.mchange.v2.c3p0.impl.NewProxyStatement.executeQuery(NewProxyStatement.java:35)
	at org.springframework.jdbc.core.JdbcTemplate$1QueryStatementCallback.doInStatement(JdbcTemplate.java:390)
	at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:343)
	at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:405)
	at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:413)
	at org.springframework.jdbc.core.JdbcTemplate.queryForList(JdbcTemplate.java:440)
	at org.cipres.treebase.dao.admin.PersonDAOTest.testFindByID(PersonDAOTest.java:106)
	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)

if (ids.size() > 0) {
assertTrue("Empty Person table.", ids.size() > 0);
Expand Down Expand Up @@ -171,7 +171,7 @@
}

// 1. find a valid username first:
List<String> lastNames = jdbcTemplate.queryForList(

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org.cipres.treebase.dao.admin.PersonDAOTest ► testFindByLastName 

Failed test found in:
  treebase-core/target/surefire-reports/TEST-org.cipres.treebase.dao.admin.PersonDAOTest.xml
Error:
  org.springframework.jdbc.BadSqlGrammarException:
Raw output 
org.springframework.jdbc.BadSqlGrammarException: 
StatementCallback; bad SQL grammar [select lastname from person]; nested exception is org.postgresql.util.PSQLException: ERROR: relation "person" does not exist
  Position: 22
Caused by: org.postgresql.util.PSQLException: ERROR: relation "person" does not exist
  Position: 22
	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.PgStatement.executeWithFlags(PgStatement.java:329)
	at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:315)
	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:291)
	at org.postgresql.jdbc.PgStatement.executeQuery(PgStatement.java:243)
	at com.mchange.v2.c3p0.impl.NewProxyStatement.executeQuery(NewProxyStatement.java:35)
	at org.springframework.jdbc.core.JdbcTemplate$1QueryStatementCallback.doInStatement(JdbcTemplate.java:390)
	at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:343)
	at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:405)
	at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:413)
	at org.springframework.jdbc.core.JdbcTemplate.queryForList(JdbcTemplate.java:440)
	at org.cipres.treebase.dao.admin.PersonDAOTest.testFindByLastName(PersonDAOTest.java:174)
	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)
"select lastname from person",
String.class);

Expand Down Expand Up @@ -207,7 +207,7 @@
}

// 1. find a valid email address:
List<String> emails = jdbcTemplate.queryForList(

Check failure on line 210 in treebase-core/src/test/java/org/cipres/treebase/dao/admin/PersonDAOTest.java

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org.cipres.treebase.dao.admin.PersonDAOTest ► testFindCompleteEmailAddress 

Failed test found in:
  treebase-core/target/surefire-reports/TEST-org.cipres.treebase.dao.admin.PersonDAOTest.xml
Error:
  org.springframework.jdbc.BadSqlGrammarException:
Raw output 
org.springframework.jdbc.BadSqlGrammarException: 
StatementCallback; bad SQL grammar [select email from person where email is not null]; nested exception is org.postgresql.util.PSQLException: ERROR: relation "person" does not exist
  Position: 19
Caused by: org.postgresql.util.PSQLException: ERROR: relation "person" does not exist
  Position: 19
	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.PgStatement.executeWithFlags(PgStatement.java:329)
	at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:315)
	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:291)
	at org.postgresql.jdbc.PgStatement.executeQuery(PgStatement.java:243)
	at com.mchange.v2.c3p0.impl.NewProxyStatement.executeQuery(NewProxyStatement.java:35)
	at org.springframework.jdbc.core.JdbcTemplate$1QueryStatementCallback.doInStatement(JdbcTemplate.java:390)
	at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:343)
	at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:405)
	at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:413)
	at org.springframework.jdbc.core.JdbcTemplate.queryForList(JdbcTemplate.java:440)
	at org.cipres.treebase.dao.admin.PersonDAOTest.testFindCompleteEmailAddress(PersonDAOTest.java:210)
	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)
"select email from person where email is not null",
String.class);

Expand Down
6 changes: 3 additions & 3 deletions treebase-core/src/test/java/org/cipres/treebase/dao/admin/UserDAOTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,7 @@

// 2. verify
String sqlStr = "select count(*) from public.user where user_id=" + user.getId();
Integer count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = (Integer) jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue(count == 1);

// 3. delete
Expand All @@ -93,7 +93,7 @@
setComplete();

// 4. verify delte:
Integer countVerify = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer countVerify = (Integer) jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue(countVerify == 0);

if (logger.isInfoEnabled()) {
Expand Down Expand Up @@ -130,7 +130,7 @@
fixture.delete(user);

// 4. verify delte:
Integer countVerify = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer countVerify = (Integer) jdbcTemplate.queryForObject(sqlStr, Integer.class);

Check failure on line 133 in treebase-core/src/test/java/org/cipres/treebase/dao/admin/UserDAOTest.java

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org.cipres.treebase.dao.admin.UserDAOTest ► testDelete_Negative 

Failed test found in:
  treebase-core/target/surefire-reports/TEST-org.cipres.treebase.dao.admin.UserDAOTest.xml
Error:
  org.springframework.jdbc.BadSqlGrammarException:
Raw output 
org.springframework.jdbc.BadSqlGrammarException: 
StatementCallback; bad SQL grammar [select count(*) from public.user where username='delete_negative test 0.9537393495033412']; nested exception is org.postgresql.util.PSQLException: ERROR: relation "public.user" does not exist
  Position: 22
Caused by: org.postgresql.util.PSQLException: ERROR: relation "public.user" does not exist
  Position: 22
	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.PgStatement.executeWithFlags(PgStatement.java:329)
	at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:315)
	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:291)
	at org.postgresql.jdbc.PgStatement.executeQuery(PgStatement.java:243)
	at com.mchange.v2.c3p0.impl.NewProxyStatement.executeQuery(NewProxyStatement.java:35)
	at org.springframework.jdbc.core.JdbcTemplate$1QueryStatementCallback.doInStatement(JdbcTemplate.java:390)
	at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:343)
	at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:405)
	at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:413)
	at org.springframework.jdbc.core.JdbcTemplate.queryForObject(JdbcTemplate.java:421)
	at org.springframework.jdbc.core.JdbcTemplate.queryForObject(JdbcTemplate.java:426)
	at org.cipres.treebase.dao.admin.UserDAOTest.testDelete_Negative(UserDAOTest.java:133)
	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)
assertTrue(countVerify == 0);

if (logger.isInfoEnabled()) {
Expand All @@ -150,7 +150,7 @@
}

// 1. find a valid username first:
List<String> usernames = jdbcTemplate.queryForList(

Check failure on line 153 in treebase-core/src/test/java/org/cipres/treebase/dao/admin/UserDAOTest.java

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org.cipres.treebase.dao.admin.UserDAOTest ► testFindByUserName 

Failed test found in:
  treebase-core/target/surefire-reports/TEST-org.cipres.treebase.dao.admin.UserDAOTest.xml
Error:
  org.springframework.jdbc.BadSqlGrammarException:
Raw output 
org.springframework.jdbc.BadSqlGrammarException: 
StatementCallback; bad SQL grammar [select username from public.user]; nested exception is org.postgresql.util.PSQLException: ERROR: relation "public.user" does not exist
  Position: 22
Caused by: org.postgresql.util.PSQLException: ERROR: relation "public.user" does not exist
  Position: 22
	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.PgStatement.executeWithFlags(PgStatement.java:329)
	at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:315)
	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:291)
	at org.postgresql.jdbc.PgStatement.executeQuery(PgStatement.java:243)
	at com.mchange.v2.c3p0.impl.NewProxyStatement.executeQuery(NewProxyStatement.java:35)
	at org.springframework.jdbc.core.JdbcTemplate$1QueryStatementCallback.doInStatement(JdbcTemplate.java:390)
	at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:343)
	at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:405)
	at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:413)
	at org.springframework.jdbc.core.JdbcTemplate.queryForList(JdbcTemplate.java:440)
	at org.cipres.treebase.dao.admin.UserDAOTest.testFindByUserName(UserDAOTest.java:153)
	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)
"select username from public.user",
String.class);

Expand Down
6 changes: 3 additions & 3 deletions treebase-core/src/test/java/org/cipres/treebase/dao/matrix/MatrixDAOTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@ public void xtestAddDelete() {

// 2. verify
String matrixSQL = "select count(*) from matrix where matrix_id = " + m.getId();
Integer count = jdbcTemplate.queryForObject(matrixSQL, Integer.class);
Integer count = (Integer) jdbcTemplate.queryForObject(matrixSQL, Integer.class);
assertTrue(count == 1);

// 3. delete:
Expand All @@ -76,7 +76,7 @@ public void xtestAddDelete() {
endTransaction();

// 4. Verify delete:
count = jdbcTemplate.queryForObject(matrixSQL, Integer.class);
count = (Integer) jdbcTemplate.queryForObject(matrixSQL, Integer.class);
assertTrue("Matrix should be deleted", count == 0);

if (logger.isInfoEnabled()) {
Expand Down Expand Up @@ -209,7 +209,7 @@ public void testupdatePublishedFlagByStudy() throws Exception {
// 3. verify
String treeCountStr = "select count(m.matrix_id) from matrix m "
+ " where m.study_ID = " + s.getId() + " and m.published is true";
Integer countVeri = jdbcTemplate.queryForObject(treeCountStr, Integer.class);
Integer countVeri = (Integer) jdbcTemplate.queryForObject(treeCountStr, Integer.class);
logger.debug("verify Count = " + countVeri);
assertTrue(countVeri == count);

Expand Down
4 changes: 2 additions & 2 deletions treebase-core/src/test/java/org/cipres/treebase/dao/study/AlgorithmDAOTest.java
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Expand Up @@ -57,7 +57,7 @@ public void testFinalAllUniqueAlgorithmDescriptions() {
// 2. verify
String sqlStr = "select count (distinct lower(description)) from algorithm";
// String sqlStr = "select count (distinct description) from algorithm";
Integer count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = (Integer) jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue("description size has to match.", count == descriptions.size());

// assertTrue(result != null);
Expand Down Expand Up @@ -90,7 +90,7 @@ public void testFindAllUniqueOtherAlgorithmDescriptions(String pPartialValue) {
// 2. verify
String sqlStr = "select count (distinct lower(description)) from algorithm where type='O'";
// String sqlStr = "select count (distinct description) from algorithm";
Integer count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = (Integer) jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue("description size has to match.", count == descriptions.size());

// assertTrue(result != null);
Expand Down
4 changes: 2 additions & 2 deletions treebase-core/src/test/java/org/cipres/treebase/dao/study/AnalyzedDataDAOTest.java
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Expand Up @@ -87,7 +87,7 @@ public void testFindByMatrix_fixture_1() throws Exception {
long dataId = data.iterator().next().getId();
String sqlStr = "select count(*) from analyzedData where AnalyzedData_id = " + dataId
+ " and matrix_id = " + m.getId();
Integer count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = (Integer) jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue(count > 0);

if (logger.isInfoEnabled()) {
Expand Down Expand Up @@ -123,7 +123,7 @@ public void testFindByTree_fixture_1() throws Exception {
long dataId = data.iterator().next().getId();
String sqlStr = "select count(*) from analyzedData where AnalyzedData_id = " + dataId
+ " and phylotree_id = " + m.getId();
Integer count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = (Integer) jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue(count > 0);

if (logger.isInfoEnabled()) {
Expand Down
4 changes: 2 additions & 2 deletions treebase-core/src/test/java/org/cipres/treebase/dao/study/StudyDAOTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -264,7 +264,7 @@ public void testPersistNexusClob() {

// 2. verify
String sqlStr = "select count(*) from Study_nexusFile where study_id=" + s.getId();
Integer count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = (Integer) jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue(count == 1);

// assertTrue("need to return Analysis ID.", a1.getId() != null);
Expand All @@ -274,7 +274,7 @@ public void testPersistNexusClob() {
setComplete();

// 4. verify delte:
Integer countVerify = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer countVerify = (Integer) jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue("Deletion failed.", countVerify == 0);

if (logger.isInfoEnabled()) {
Expand Down
6 changes: 3 additions & 3 deletions treebase-core/src/test/java/org/cipres/treebase/dao/study/SubmissionDAOTest.java
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Expand Up @@ -103,7 +103,7 @@ public void testFindByMatrix() {
// 3. verify
String sqlStr = "select count(*) from sub_matrix where submission_id = " + s.getId()
+ " and matrix_id = " + m.getId();
Integer count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = (Integer) jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue(count == 1);

if (logger.isInfoEnabled()) {
Expand Down Expand Up @@ -136,7 +136,7 @@ public void testFindByTree() {
// 3. verify
String sqlStr = "select count(*) from sub_treeblock st, phylotree t where st.submission_id = " + s.getId()
+ " and st.treeblock_id = t.treeblock_id and t.phylotree_id = " + tree.getId();
Integer count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = (Integer) jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue(count == 1);

if (logger.isInfoEnabled()) {
Expand All @@ -159,7 +159,7 @@ public void testFindByReadyState() {

// 3. verify
String sqlStr = "select count(*) from study where studyStatus_ID = 2";
Integer count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = (Integer) jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue(count > 0);
assertTrue(s.size() == count);

Expand Down
30 changes: 15 additions & 15 deletions treebase-core/src/test/java/org/cipres/treebase/dao/tree/PhyloTreeDAOTest.java
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Expand Up @@ -119,7 +119,7 @@ public void testFindByAnyTaxonLabel() throws Exception {
String treeCountStr = "select count(tree.phylotree_id) from phylotree tree, phylotreenode node "
+ " where tree.PHYLOTREE_ID = node.PHYLOTREE_ID and node.TAXONLABEL_ID = "
+ label.getId() + " and tree.PHYLOTREE_ID = " + treeId;
Integer count = jdbcTemplate.queryForObject(treeCountStr, Integer.class);
Integer count = (Integer) jdbcTemplate.queryForObject(treeCountStr, Integer.class);
assertTrue(count > 0);
}

Expand Down Expand Up @@ -165,7 +165,7 @@ public void testFindByStudy() throws Exception {
long treeId = phyloTree.getId();
String treeCountStr = "select count(tree.phylotree_id) from phylotree tree "
+ " where tree.study_ID = " + s.getId() + " and tree.PHYLOTREE_ID = " + treeId;
Integer count = jdbcTemplate.queryForObject(treeCountStr, Integer.class);
Integer count = (Integer) jdbcTemplate.queryForObject(treeCountStr, Integer.class);
assertTrue(count > 0);
}

Expand Down Expand Up @@ -208,7 +208,7 @@ public void testupdatePublishedFlagByStudy() throws Exception {
// 3. verify
String treeCountStr = "select count(tree.phylotree_id) from phylotree tree "
+ " where tree.study_ID = " + s.getId() + " and tree.published is true";
Integer countVeri = jdbcTemplate.queryForObject(treeCountStr, Integer.class);
Integer countVeri = (Integer) jdbcTemplate.queryForObject(treeCountStr, Integer.class);
logger.debug("verify Count = " + countVeri);
assertTrue(countVeri == count);

Expand Down Expand Up @@ -329,15 +329,15 @@ public void testCreateDelete() throws Exception {

// 2. verify
String sqlStr = "select count(*) from phylotree where phylotree_id=" + tree.getId();
Integer count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = (Integer) jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue(count == 1);

// 3. delete
getFixture().delete(tree);
setComplete();

// 4. verify delete:
Integer countVerify = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer countVerify = (Integer) jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue(countVerify == 0);

if (logger.isInfoEnabled()) {
Expand Down Expand Up @@ -428,13 +428,13 @@ public void xtestCreateDeleteTreeBlock() throws Exception {
String analyzedDataSql = "select count(*) from analyzedData where analysisstep_id="
+ step1.getId();
String a1Sql = "select count(*) from analysis where analysis_id=" + a1.getId();
Integer count = jdbcTemplate.queryForObject(treeSql, Integer.class);
Integer count = (Integer) jdbcTemplate.queryForObject(treeSql, Integer.class);
assertTrue(count == 2);
count = jdbcTemplate.queryForObject(blockSql, Integer.class);
count = (Integer) jdbcTemplate.queryForObject(blockSql, Integer.class);
assertTrue(count == 1);
count = jdbcTemplate.queryForObject(a1Sql, Integer.class);
count = (Integer) jdbcTemplate.queryForObject(a1Sql, Integer.class);
assertTrue(count == 1);
count = jdbcTemplate.queryForObject(analyzedDataSql, Integer.class);
count = (Integer) jdbcTemplate.queryForObject(analyzedDataSql, Integer.class);
assertTrue(count == 1);

onSetUp();
Expand All @@ -459,13 +459,13 @@ public void xtestCreateDeleteTreeBlock() throws Exception {
endTransaction();

// 4. verify delete:
Integer countVerify = jdbcTemplate.queryForObject(blockSql, Integer.class);
Integer countVerify = (Integer) jdbcTemplate.queryForObject(blockSql, Integer.class);
assertTrue(countVerify == 0);
countVerify = jdbcTemplate.queryForObject(treeSql, Integer.class);
countVerify = (Integer) jdbcTemplate.queryForObject(treeSql, Integer.class);
assertTrue(countVerify == 0);
countVerify = jdbcTemplate.queryForObject(a1Sql, Integer.class);
countVerify = (Integer) jdbcTemplate.queryForObject(a1Sql, Integer.class);
assertTrue(countVerify == 0);
countVerify = jdbcTemplate.queryForObject(analyzedDataSql, Integer.class);
countVerify = (Integer) jdbcTemplate.queryForObject(analyzedDataSql, Integer.class);
assertTrue(countVerify == 0);

if (logger.isInfoEnabled()) {
Expand Down Expand Up @@ -497,7 +497,7 @@ public void xxtestDeleteByID() throws Exception {

// 2. verify
String sqlStr = "select count(*) from phylotree where phylotree_id=" + tree.getId();
Integer count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = (Integer) jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue(count == 1);

// 3. delete
Expand All @@ -506,7 +506,7 @@ public void xxtestDeleteByID() throws Exception {
endTransaction();

// 4. verify delete:
Integer countVerify = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer countVerify = (Integer) jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue(countVerify == 0);

if (logger.isInfoEnabled()) {
Expand Down
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