Increase test independence

Adding or removing profile/sample should break only one test
cBioPortal · Jun 27, 2024 · 9afe6bc · 9afe6bc
1 parent aa80b0e
commit 9afe6bc
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Showing 2 changed files with 15 additions and 19 deletions.
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
@@ -72,7 +72,7 @@ public void setUp() throws DaoException
 	public void testDaoGetAllGeneticProfiles() throws DaoException {
 
 		ArrayList<GeneticProfile> list = DaoGeneticProfile.getAllGeneticProfiles(studyId);
-		assertEquals(9, list.size());
+		assertEquals(11, list.size());
 	}
 
 	@Test
@@ -134,12 +134,12 @@ public void testDaoDeleteGeneticProfile() throws DaoException {
 
 		GeneticProfile geneticProfile = DaoGeneticProfile.getGeneticProfileById(2);
 
-		assertEquals(9, DaoGeneticProfile.getCount());
+		int numberOfProfiles = DaoGeneticProfile.getCount();
 		DaoGeneticProfile.deleteGeneticProfile(geneticProfile);
-		assertEquals(8, DaoGeneticProfile.getCount());
+		assertEquals(numberOfProfiles - 1, DaoGeneticProfile.getCount());
 
 		ArrayList<GeneticProfile> list = DaoGeneticProfile.getAllGeneticProfiles(studyId);
-		assertEquals(8, list.size());
+		assertEquals(numberOfProfiles - 1, list.size());
 		geneticProfile = list.get(0);
 		assertEquals(studyId, geneticProfile.getCancerStudyId());
 		assertEquals("mRNA expression (microarray)", geneticProfile.getProfileName());
@@ -154,12 +154,10 @@ public void testDaoUpdateGeneticProfile() throws DaoException {
 		assertTrue(DaoGeneticProfile.updateNameAndDescription(
 				geneticProfile.getGeneticProfileId(), "Updated Name",
 				"Updated Description"));
-		ArrayList<GeneticProfile> list = DaoGeneticProfile.getAllGeneticProfiles(studyId);
-		assertEquals(9, list.size());
-		geneticProfile = list.get(0);
-		assertEquals(studyId, geneticProfile.getCancerStudyId());
-		assertEquals("Updated Name", geneticProfile.getProfileName());
-		assertEquals(GeneticAlterationType.COPY_NUMBER_ALTERATION, geneticProfile.getGeneticAlterationType());
-		assertEquals("Updated Description", geneticProfile.getProfileDescription());
+		GeneticProfile updatedGeneticProfile = DaoGeneticProfile.getGeneticProfileById(geneticProfile.getGeneticProfileId());
+		assertEquals(studyId, updatedGeneticProfile.getCancerStudyId());
+		assertEquals("Updated Name", updatedGeneticProfile.getProfileName());
+		assertEquals(GeneticAlterationType.COPY_NUMBER_ALTERATION, updatedGeneticProfile.getGeneticAlterationType());
+		assertEquals("Updated Description", updatedGeneticProfile.getProfileDescription());
 	}
 }
diff --git a/...est/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportCnaDiscreteLongData.java b/...est/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportCnaDiscreteLongData.java
@@ -29,7 +29,6 @@
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 import org.junit.After;
-import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
 import org.junit.runner.RunWith;
@@ -178,7 +177,6 @@ public void testImportCnaDiscreteLongDataAddsCnaEvents() throws Exception {
     @Test
     public void testImportCnaDiscreteLongDataAddsGeneticAlterations() throws Exception {
         List<TestGeneticAlteration> beforeGeneticAlterations = getAllGeneticAlterations();
-        assertEquals(57, beforeGeneticAlterations.size());
 
         File file = new File("src/test/resources/data_cna_discrete_import_test.txt");
         new ImportCnaDiscreteLongData(
@@ -202,7 +200,6 @@ public void testImportCnaDiscreteLongDataAddsGeneticAlterations() throws Excepti
     @Test
     public void testImportCnaDiscreteLongDataAddsMissingGeneticAlterations() throws Exception {
         List<TestGeneticAlteration> beforeGeneticAlterations = getAllGeneticAlterations();
-        assertEquals(57, beforeGeneticAlterations.size());
 
         File file = new File("src/test/resources/data_cna_discrete_import_test_with_cna_events_missing.txt");
         new ImportCnaDiscreteLongData(
@@ -229,7 +226,6 @@ public void testImportCnaDiscreteLongDataAddsMissingGeneticAlterations() throws
     @Test
     public void testImportCnaDiscreteLongDataAddsGeneticAlterationsAndProfileSamplesInCorrectOrder() throws Exception {
         List<TestGeneticAlteration> beforeGeneticAlterations = getAllGeneticAlterations();
-        assertEquals(57, beforeGeneticAlterations.size());
 
         File file = new File("src/test/resources/data_cna_discrete_import_test.txt");
         new ImportCnaDiscreteLongData(
@@ -255,7 +251,6 @@ public void testImportCnaDiscreteLongDataAddsGeneticAlterationsAndProfileSamples
     @Test
     public void testImportCnaDiscreteLongDataHandlesEntriesWithoutEntrezButWithHugo() throws Exception {
         List<TestGeneticAlteration> beforeGeneticAlterations = getAllGeneticAlterations();
-        assertEquals(57, beforeGeneticAlterations.size());
 
         File file = new File("src/test/resources/data_cna_discrete_import_test_without_entrez_with_hugo.txt");
         new ImportCnaDiscreteLongData(
@@ -277,7 +272,6 @@ public void testImportCnaDiscreteLongDataHandlesEntriesWithoutEntrezButWithHugo(
     @Test
     public void testImportCnaDiscreteLongDataHandlesEntriesWithWrongEntrezAndCorrectHugo() throws Exception {
         List<TestGeneticAlteration> beforeGeneticAlterations = getAllGeneticAlterations();
-        assertEquals(57, beforeGeneticAlterations.size());
 
         File file = new File("src/test/resources/data_cna_discrete_import_test_with_wrong_entrez_and_correct_hugo.txt");
         new ImportCnaDiscreteLongData(
@@ -299,7 +293,6 @@ public void testImportCnaDiscreteLongDataHandlesEntriesWithWrongEntrezAndCorrect
     @Test
     public void testImportCnaDiscreteLongDataAddsGeneticAlterationsFromNonCnaEvents() throws Exception {
         List<TestGeneticAlteration> beforeGeneticAlterations = getAllGeneticAlterations();
-        assertEquals(57, beforeGeneticAlterations.size());
 
         File file = new File("src/test/resources/data_cna_discrete_import_test.txt");
         new ImportCnaDiscreteLongData(
@@ -326,7 +319,6 @@ public void testImportCnaDiscreteLongDataAddsGeneticAlterationsFromNonCnaEvents(
     @Test
     public void testImportCnaDiscreteLongDataIgnoresLineWithDuplicateGene() throws Exception {
         List<TestGeneticAlteration> beforeGeneticAlterations = getAllGeneticAlterations();
-        assertEquals(57, beforeGeneticAlterations.size());
 
         File file = new File("src/test/resources/data_cna_discrete_import_test.txt");
         new ImportCnaDiscreteLongData(
@@ -544,6 +536,12 @@ public void testImportCnaDiscreteLongDataImportsCustomNamespaceColumnsAsNullWhen
         String expectedAnnotationJson = null;
         assertEquals(expectedAnnotationJson, results.get(0).annotationJson);
     }
+
+    @Test
+    public void GetAllGeneticAlterations() throws DaoException {
+        List<TestGeneticAlteration> geneticAlterations = getAllGeneticAlterations();
+        assertEquals(59, geneticAlterations.size());
+    }
 
     private List<TestPdAnnotationPK> createPrimaryKeys(String sample, List<CnaEvent.Event> cnaEvents) {
         return cnaEvents.stream().map(e -> {