Replace wildcard imports in integrationTest folder

cBioPortal · Apr 3, 2024 · 04d49aa · 04d49aa
1 parent 993e6df
commit 04d49aa
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Showing 43 changed files with 423 additions and 218 deletions.
diff --git a/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoCancerStudy.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoCancerStudy.java
@@ -39,17 +39,18 @@
 import org.mskcc.cbio.portal.dao.DaoException;
 import org.mskcc.cbio.portal.dao.DaoTypeOfCancer;
 import org.mskcc.cbio.portal.model.CancerStudy;
-
-import java.io.IOException;
-import java.util.ArrayList;
-
 import org.mskcc.cbio.portal.model.ReferenceGenome;
 import org.springframework.test.annotation.Rollback;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
 
-import static org.junit.Assert.*;
+import java.io.IOException;
+import java.util.ArrayList;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
 
 /**
  * JUnit Tests for DaoCancer Study.

diff --git a/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoClinicalAttribute.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoClinicalAttribute.java
@@ -42,7 +42,8 @@
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
 
 @RunWith(SpringJUnit4ClassRunner.class)
 @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" })

diff --git a/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGenePanel.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGenePanel.java
@@ -37,16 +37,17 @@
 import org.mskcc.cbio.portal.dao.DaoException;
 import org.mskcc.cbio.portal.dao.DaoGeneOptimized;
 import org.mskcc.cbio.portal.dao.DaoGenePanel;
-import org.mskcc.cbio.portal.model.*;
-
+import org.mskcc.cbio.portal.model.CanonicalGene;
+import org.mskcc.cbio.portal.model.GenePanel;
 import org.springframework.test.annotation.Rollback;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
 
-import static org.junit.Assert.*;
+import java.util.HashSet;
 
-import java.util.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 /**
  * JUnit Tests for DaoGenePanel.

diff --git a/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGeneticAlteration.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGeneticAlteration.java
@@ -35,16 +35,28 @@
 import org.junit.Before;
 import org.junit.Test;
 import org.junit.runner.RunWith;
-import org.mskcc.cbio.portal.dao.*;
-import org.mskcc.cbio.portal.model.*;
+import org.mskcc.cbio.portal.dao.DaoCancerStudy;
+import org.mskcc.cbio.portal.dao.DaoException;
+import org.mskcc.cbio.portal.dao.DaoGeneticAlteration;
+import org.mskcc.cbio.portal.dao.DaoGeneticProfile;
+import org.mskcc.cbio.portal.dao.DaoGeneticProfileSamples;
+import org.mskcc.cbio.portal.dao.DaoPatient;
+import org.mskcc.cbio.portal.dao.DaoSample;
+import org.mskcc.cbio.portal.dao.MySQLbulkLoader;
+import org.mskcc.cbio.portal.model.CancerStudy;
+import org.mskcc.cbio.portal.model.CanonicalGene;
+import org.mskcc.cbio.portal.model.Patient;
+import org.mskcc.cbio.portal.model.Sample;
 import org.springframework.test.annotation.Rollback;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
 
-import static org.junit.Assert.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Set;
 
-import java.util.*;
+import static org.junit.Assert.assertEquals;
 
 /**
  * JUnit tests for DaoGeneticAlteration class.

diff --git a/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGeneticProfile.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGeneticProfile.java
@@ -32,19 +32,23 @@
 
 package org.mskcc.cbio.portal.integrationTest.dao;
 
-import java.util.ArrayList;
 import org.junit.Before;
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.mskcc.cbio.portal.dao.DaoCancerStudy;
 import org.mskcc.cbio.portal.dao.DaoException;
 import org.mskcc.cbio.portal.dao.DaoGeneticProfile;
-import org.mskcc.cbio.portal.model.*;
+import org.mskcc.cbio.portal.model.GeneticAlterationType;
+import org.mskcc.cbio.portal.model.GeneticProfile;
 import org.springframework.test.annotation.Rollback;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
-import static org.junit.Assert.*;
+
+import java.util.ArrayList;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 /**
  * JUnit tests for DaoGeneticProfile class.

diff --git a/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGeneticProfileSamples.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGeneticProfileSamples.java
@@ -35,15 +35,22 @@
 import org.junit.Before;
 import org.junit.Test;
 import org.junit.runner.RunWith;
-import org.mskcc.cbio.portal.dao.*;
-import org.mskcc.cbio.portal.model.*;
+import org.mskcc.cbio.portal.dao.DaoCancerStudy;
+import org.mskcc.cbio.portal.dao.DaoException;
+import org.mskcc.cbio.portal.dao.DaoGeneticProfile;
+import org.mskcc.cbio.portal.dao.DaoGeneticProfileSamples;
+import org.mskcc.cbio.portal.dao.DaoPatient;
+import org.mskcc.cbio.portal.dao.DaoSample;
+import org.mskcc.cbio.portal.model.CancerStudy;
+import org.mskcc.cbio.portal.model.Patient;
+import org.mskcc.cbio.portal.model.Sample;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 
-import static org.junit.Assert.*;
-
 import java.util.ArrayList;
 
+import static org.junit.Assert.assertEquals;
+
 /**
  * JUnit Tests for the Dao Genetic Profile Cases Class.
  *

diff --git a/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGistic.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoGistic.java
@@ -32,8 +32,6 @@
 
 package org.mskcc.cbio.portal.integrationTest.dao;
 
-import java.util.Arrays;
-
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.mskcc.cbio.portal.dao.DaoException;
@@ -47,10 +45,12 @@
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
 
-import static org.junit.Assert.*;
-
 import java.sql.SQLException;
 import java.util.ArrayList;
+import java.util.Arrays;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 @RunWith(SpringJUnit4ClassRunner.class)
 @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" })

diff --git a/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoMutSig.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoMutSig.java
@@ -44,10 +44,11 @@
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
 
-import static org.junit.Assert.*;
-
 import java.io.IOException;
 
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
 /**
  * @author Lennart Bastian
  */

diff --git a/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoMutation.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoMutation.java
@@ -32,24 +32,33 @@
 
 package org.mskcc.cbio.portal.integrationTest.dao;
 
-import java.io.IOException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
 import org.junit.runner.RunWith;
-import org.mskcc.cbio.portal.dao.*;
-import org.mskcc.cbio.portal.model.*;
+import org.mskcc.cbio.portal.dao.DaoCancerStudy;
+import org.mskcc.cbio.portal.dao.DaoException;
+import org.mskcc.cbio.portal.dao.DaoGeneOptimized;
+import org.mskcc.cbio.portal.dao.DaoGeneticProfile;
+import org.mskcc.cbio.portal.dao.DaoMutation;
+import org.mskcc.cbio.portal.dao.DaoSample;
+import org.mskcc.cbio.portal.dao.MySQLbulkLoader;
+import org.mskcc.cbio.portal.model.CanonicalGene;
+import org.mskcc.cbio.portal.model.ExtendedMutation;
+import org.mskcc.cbio.portal.model.GeneticProfile;
 import org.springframework.test.annotation.Rollback;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
 
-import static org.junit.Assert.*;
-
-import java.util.*;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
 
-import org.junit.Assert;
+import static org.junit.Assert.assertEquals;
 
 /**
  * JUnit tests for DaoMutation class.

diff --git a/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoSampleList.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoSampleList.java
@@ -32,19 +32,27 @@
 
 package org.mskcc.cbio.portal.integrationTest.dao;
 
-import java.util.ArrayList;
-
 import org.junit.Before;
 import org.junit.Test;
 import org.junit.runner.RunWith;
-import org.mskcc.cbio.portal.dao.*;
-import org.mskcc.cbio.portal.model.*;
+import org.mskcc.cbio.portal.dao.DaoCancerStudy;
+import org.mskcc.cbio.portal.dao.DaoException;
+import org.mskcc.cbio.portal.dao.DaoPatient;
+import org.mskcc.cbio.portal.dao.DaoSample;
+import org.mskcc.cbio.portal.dao.DaoSampleList;
+import org.mskcc.cbio.portal.model.CancerStudy;
+import org.mskcc.cbio.portal.model.Patient;
+import org.mskcc.cbio.portal.model.Sample;
+import org.mskcc.cbio.portal.model.SampleList;
+import org.mskcc.cbio.portal.model.SampleListCategory;
 import org.springframework.test.annotation.Rollback;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
 
-import static org.junit.Assert.*;
+import java.util.ArrayList;
+
+import static org.junit.Assert.assertEquals;
 
 /**
  * JUnit test for DaoCase List.

diff --git a/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoSampleProfile.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoSampleProfile.java
@@ -32,20 +32,32 @@
 
 package org.mskcc.cbio.portal.integrationTest.dao;
 
-import org.mskcc.cbio.portal.dao.*;
-import org.mskcc.cbio.portal.model.*;
-
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.mskcc.cbio.portal.dao.DaoCancerStudy;
+import org.mskcc.cbio.portal.dao.DaoException;
+import org.mskcc.cbio.portal.dao.DaoGeneOptimized;
+import org.mskcc.cbio.portal.dao.DaoGenePanel;
+import org.mskcc.cbio.portal.dao.DaoGeneticProfile;
+import org.mskcc.cbio.portal.dao.DaoPatient;
+import org.mskcc.cbio.portal.dao.DaoSample;
+import org.mskcc.cbio.portal.dao.DaoSampleProfile;
+import org.mskcc.cbio.portal.model.CancerStudy;
+import org.mskcc.cbio.portal.model.CanonicalGene;
+import org.mskcc.cbio.portal.model.GenePanel;
+import org.mskcc.cbio.portal.model.Patient;
+import org.mskcc.cbio.portal.model.Sample;
 import org.springframework.test.annotation.Rollback;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
 
-import org.junit.Test;
-import org.junit.Before;
-import org.junit.runner.RunWith;
-import static org.junit.Assert.*;
+import java.util.ArrayList;
+import java.util.HashSet;
 
-import java.util.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 /**
  * JUnit test for DaoSample class

diff --git a/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoUser.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoUser.java
@@ -32,10 +32,6 @@
 
 package org.mskcc.cbio.portal.integrationTest.dao;
 
-import static org.junit.Assert.*;
-
-import java.util.ArrayList;
-
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.mskcc.cbio.portal.dao.DaoUser;
@@ -45,7 +41,14 @@
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
 
-import static org.hamcrest.CoreMatchers.*;
+import java.util.ArrayList;
+
+import static org.hamcrest.CoreMatchers.is;
+import static org.hamcrest.CoreMatchers.not;
+import static org.hamcrest.CoreMatchers.notNullValue;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertThat;
 
 /**
  * JUnit test for DaoUser class.

diff --git a/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoUserAuthorities.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoUserAuthorities.java
@@ -33,12 +33,6 @@
 package org.mskcc.cbio.portal.integrationTest.dao;
 
 // imports
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.util.Arrays;
 
 import org.junit.Test;
 import org.junit.runner.RunWith;
@@ -50,6 +44,13 @@
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
 
+import java.util.Arrays;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
 /**
  * JUnit test for DaoUserAuthorities class.
  */

diff --git a/src/test/java/org/mskcc/cbio/portal/integrationTest/pancancer/LargeTestSetGenerator.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/pancancer/LargeTestSetGenerator.java
@@ -1,7 +1,15 @@
 package org.mskcc.cbio.portal.integrationTest.pancancer;
 
-import java.io.*;
-import java.util.*;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 
 /**

diff --git a/...java/org/mskcc/cbio/portal/integrationTest/pancancer/TestPanCancerStudySummaryImport.java b/...java/org/mskcc/cbio/portal/integrationTest/pancancer/TestPanCancerStudySummaryImport.java
@@ -5,8 +5,19 @@
 import org.junit.Ignore;
 import org.junit.Test;
 import org.junit.runner.RunWith;
-import org.mskcc.cbio.portal.dao.*;
-import org.mskcc.cbio.portal.model.*;
+import org.mskcc.cbio.portal.dao.DaoCancerStudy;
+import org.mskcc.cbio.portal.dao.DaoClinicalData;
+import org.mskcc.cbio.portal.dao.DaoException;
+import org.mskcc.cbio.portal.dao.DaoGeneOptimized;
+import org.mskcc.cbio.portal.dao.DaoGeneticProfile;
+import org.mskcc.cbio.portal.dao.DaoPatient;
+import org.mskcc.cbio.portal.dao.DaoSample;
+import org.mskcc.cbio.portal.dao.DaoTypeOfCancer;
+import org.mskcc.cbio.portal.model.CancerStudy;
+import org.mskcc.cbio.portal.model.CanonicalGene;
+import org.mskcc.cbio.portal.model.ClinicalAttribute;
+import org.mskcc.cbio.portal.model.Sample;
+import org.mskcc.cbio.portal.model.TypeOfCancer;
 import org.mskcc.cbio.portal.scripts.ImportCancerStudy;
 import org.mskcc.cbio.portal.scripts.ImportClinicalData;
 import org.mskcc.cbio.portal.scripts.ImportProfileData;