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Fix type mismatch in DAO tests from queryForInt to queryForObject migration #299

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

Fix type mismatch in DAO tests from queryForInt to queryForObject migration #299

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Copilot Dec 21, 2025
64b413d
Fix DAO test compilation errors by changing int to Integer for queryF…
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
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Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,7 @@ public void testDelete() {

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

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

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

if (logger.isInfoEnabled()) {
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6 changes: 3 additions & 3 deletions treebase-core/src/test/java/org/cipres/treebase/dao/admin/UserDAOTest.java
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Expand Up @@ -84,7 +84,7 @@ public void testCreateDelete() throws Exception {

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

// 3. delete
Expand All @@ -93,7 +93,7 @@ public void testCreateDelete() throws Exception {
setComplete();

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

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

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

if (logger.isInfoEnabled()) {
Expand Down
4 changes: 2 additions & 2 deletions treebase-core/src/test/java/org/cipres/treebase/dao/matrix/MatrixDAOTest.java
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Expand Up @@ -66,7 +66,7 @@ public void xtestAddDelete() {

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

// 3. delete:
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";
int countVeri = jdbcTemplate.queryForObject(treeCountStr, Integer.class);
Integer countVeri = jdbcTemplate.queryForObject(treeCountStr, Integer.class);
logger.debug("verify Count = " + countVeri);
assertTrue(countVeri == count);

Expand Down
6 changes: 3 additions & 3 deletions treebase-core/src/test/java/org/cipres/treebase/dao/matrix/RowSegmentDAOTest.java
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Expand Up @@ -223,15 +223,15 @@ public void testdeleteByMatrixAndColumnRange() throws Exception {

// 4. verify
String sqlStr = "select count(*) from ROWSEGMENT rs, MATRIXROW r where r.MATRIXROW_ID = rs.MATRIXROW_ID and r.MATRIX_ID =" + m.getId();
int count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue("verify succeed count", count == result.getSuccessfulCount());

//5 test:
int start = 5;
int end = 30;
String colSizeStr = "select count(*) from ROWSEGMENT rs, MATRIXROW r where r.MATRIXROW_ID = rs.MATRIXROW_ID and r.MATRIX_ID =" + m.getId()
+ " and rs.startIndex between " + start + " and " + end + " and rs.endIndex between " + start + " and " + end;
int colSizeJDBC = jdbcTemplate.queryForObject(colSizeStr, Integer.class);
Integer colSizeJDBC = jdbcTemplate.queryForObject(colSizeStr, Integer.class);

int deleteCount = getFixture().deleteByMatrixAndColumnRange(m.getId(), start, end);

Expand All @@ -248,7 +248,7 @@ public void testdeleteByMatrixAndColumnRange() throws Exception {
endTransaction();

// 6. verify delete:
int countVerify = jdbcTemplate.queryForObject(subSQL, Integer.class);
Integer countVerify = jdbcTemplate.queryForObject(subSQL, Integer.class);
assertTrue("Submission deletion failed.", countVerify == 0);
countVerify = jdbcTemplate.queryForObject(studySQL, Integer.class);
assertTrue("Study deletion failed.", countVerify == 0);
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";
int count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = 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";
int count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = 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();
int count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = 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();
int count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = 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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Expand Up @@ -264,7 +264,7 @@ public void testPersistNexusClob() {

// 2. verify
String sqlStr = "select count(*) from Study_nexusFile where study_id=" + s.getId();
int count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = 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:
int countVerify = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer countVerify = 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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Original file line number Diff line number Diff line change
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();
int count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = 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();
int count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = 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";
int count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue(count > 0);
assertTrue(s.size() == count);

Expand Down
18 changes: 9 additions & 9 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;
int count = jdbcTemplate.queryForObject(treeCountStr, Integer.class);
Integer count = 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;
int count = jdbcTemplate.queryForObject(treeCountStr, Integer.class);
Integer count = 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";
int countVeri = jdbcTemplate.queryForObject(treeCountStr, Integer.class);
Integer countVeri = 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();
int count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
Integer count = jdbcTemplate.queryForObject(sqlStr, Integer.class);
assertTrue(count == 1);

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

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

if (logger.isInfoEnabled()) {
Expand Down Expand Up @@ -428,7 +428,7 @@ 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();
int count = jdbcTemplate.queryForObject(treeSql, Integer.class);
Integer count = jdbcTemplate.queryForObject(treeSql, Integer.class);
assertTrue(count == 2);
count = jdbcTemplate.queryForObject(blockSql, Integer.class);
assertTrue(count == 1);
Expand Down Expand Up @@ -459,7 +459,7 @@ public void xtestCreateDeleteTreeBlock() throws Exception {
endTransaction();

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

if (logger.isInfoEnabled()) {
Expand Down
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