Move TestImportGenesetData to own class

cBioPortal · Apr 4, 2024 · 07906b8 · 07906b8
1 parent 0b48914
commit 07906b8
Showing 2 changed files with 72 additions and 56 deletions.
diff --git a/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportGenesetData.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportGenesetData.java
@@ -0,0 +1,72 @@
+package org.mskcc.cbio.portal.integrationTest.scripts;
+
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.mskcc.cbio.portal.dao.DaoGeneset;
+import org.mskcc.cbio.portal.model.Geneset;
+import org.mskcc.cbio.portal.scripts.ImportGenesetData;
+import org.mskcc.cbio.portal.util.ProgressMonitor;
+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 java.io.File;
+
+import static org.junit.Assert.assertEquals;
+
+@RunWith(SpringJUnit4ClassRunner.class)
+@ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" })
+@Rollback
+@Transactional
+public class TestImportGenesetData {
+
+    @Test
+    public void testImportGenesetData() throws Exception {
+        ProgressMonitor.setConsoleMode(false);
+
+        // Open genesets test data file
+        File file = new File("src/test/resources/genesets/unit-test1_genesets.gmt");
+        boolean updateInfo = false;
+        boolean newVersion = true;
+        int skippedGenes = ImportGenesetData.importData(file, updateInfo, newVersion);
+
+        // Open supplementary file
+        file = new File("src/test/resources/genesets/unit-test1_supp-genesets.txt");
+        ImportGenesetData.importSuppGenesetData(file);
+
+        // Test database entries
+        Geneset geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET5");
+        assertEquals("UNITTEST_GENESET5", geneset.getExternalId());
+        geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET10");
+        assertEquals("http://www.broadinstitute.org/gsea/msigdb/cards/GCNP_SHH_UP_EARLY.V1_UP", geneset.getRefLink());
+
+        // Test warning message
+        assertEquals(5, skippedGenes);
+
+        // Test database entries supplementary file
+        geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET2");
+        assertEquals("Genes up-regulated in RK3E cells (kidney epithelium) over-expressing GLI1 [GeneID=2735].", geneset.getDescription());
+        geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET8");
+        assertEquals("UNITTEST_GENESET8", geneset.getName());
+
+        // Test update of genes
+        // Open genesets test data file
+        file = new File("src/test/resources/genesets/unit-test2_genesets.gmt");
+        newVersion = false;
+        updateInfo = true;
+        skippedGenes = ImportGenesetData.importData(file, updateInfo, newVersion);
+
+        // Open supplementary file
+        file = new File("src/test/resources/genesets/unit-test2_supp-genesets.txt");
+        ImportGenesetData.importSuppGenesetData(file);
+
+        geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET2");
+        assertEquals("A made up description is suited for this a fake gene.", geneset.getDescription());
+        geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET1");
+        assertEquals("Thought of new nice name for this geneset", geneset.getName());
+        geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET1");
+        assertEquals("http://www.thehyve.nl/", geneset.getRefLink());
+
+    }
+}
diff --git a/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportTabDelimData.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/scripts/TestImportTabDelimData.java
@@ -527,60 +527,4 @@ private void addTestPatientAndSampleRecords(File file) throws FileNotFoundExcept
         }
         MySQLbulkLoader.flushAll();
     }
-
-    @RunWith(SpringJUnit4ClassRunner.class)
-    @ContextConfiguration(locations = { "classpath:/applicationContext-dao.xml" })
-    @Rollback
-    @Transactional
-    public static class TestImportGenesetData {
-
-        @Test
-        public void testImportGenesetData() throws Exception {
-            ProgressMonitor.setConsoleMode(false);
-
-            // Open genesets test data file
-            File file = new File("src/test/resources/genesets/unit-test1_genesets.gmt");
-            boolean updateInfo = false;
-            boolean newVersion = true;
-            int skippedGenes = ImportGenesetData.importData(file, updateInfo, newVersion);
-
-            // Open supplementary file
-            file = new File("src/test/resources/genesets/unit-test1_supp-genesets.txt");
-            ImportGenesetData.importSuppGenesetData(file);
-
-            // Test database entries
-            Geneset geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET5");
-            assertEquals("UNITTEST_GENESET5", geneset.getExternalId());
-            geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET10");
-            assertEquals("http://www.broadinstitute.org/gsea/msigdb/cards/GCNP_SHH_UP_EARLY.V1_UP", geneset.getRefLink());
-
-            // Test warning message
-            assertEquals(5, skippedGenes);
-
-            // Test database entries supplementary file
-            geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET2");
-            assertEquals("Genes up-regulated in RK3E cells (kidney epithelium) over-expressing GLI1 [GeneID=2735].", geneset.getDescription());
-            geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET8");
-            assertEquals("UNITTEST_GENESET8", geneset.getName());
-
-            // Test update of genes
-            // Open genesets test data file
-            file = new File("src/test/resources/genesets/unit-test2_genesets.gmt");
-            newVersion = false;
-            updateInfo = true;
-            skippedGenes = ImportGenesetData.importData(file, updateInfo, newVersion);
-
-            // Open supplementary file
-            file = new File("src/test/resources/genesets/unit-test2_supp-genesets.txt");
-            ImportGenesetData.importSuppGenesetData(file);
-
-            geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET2");
-            assertEquals("A made up description is suited for this a fake gene.", geneset.getDescription());
-            geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET1");
-            assertEquals("Thought of new nice name for this geneset", geneset.getName());
-            geneset = DaoGeneset.getGenesetByExternalId("UNITTEST_GENESET1");
-            assertEquals("http://www.thehyve.nl/", geneset.getRefLink());
-
-        }
-    }
 }