Merge pull request #110 from KPMP/TI_Fix

Ti fix

src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchyService.java

@@ -1,11 +1,6 @@
 package org.kpmp.cellTypeSummary;
 
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 import org.kpmp.DataTypeEnum;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -39,7 +34,16 @@ public List<ClusterHierarchy> findClustersByCellType(String cellType) {
 				clusterToHierarchy.put(clusterName, clusterHierarchy);
 			}
 		}
-
+		if (cellType.equals("Tubules") || cellType.equals("Interstitium")) {
+			ClusterHierarchy tiCluster = new ClusterHierarchy();
+			tiCluster.setStructureRegion("Tubulo-interstitium");
+			tiCluster.setIsSingleCellCluster("N");
+			tiCluster.setIsSingleNucCluster("N");
+			tiCluster.setIsRegionalProteomics("Y");
+			tiCluster.setIsRegionalTranscriptomics("Y");
+			tiCluster.setCellTypeOrder(0.01);
+			result.add(tiCluster);
+		}
 		result.addAll(clusterToHierarchy.values());
         Collections.sort(result, new Comparator<ClusterHierarchy>() {
             @Override
@@ -52,18 +56,23 @@ public int compare(ClusterHierarchy a, ClusterHierarchy b) {
 
 	public List<String> findDataTypesByClusterName(String clusterName) {
 		List<String> dataTypesRepresented = new ArrayList<>();
-		ClusterHierarchy clustersInDataTypes = clusterHierarchyRepo.findFirstByClusterOrRegion(clusterName);
-		if (clustersInDataTypes.getIsSingleCellCluster().equalsIgnoreCase("Y")) {
-			dataTypesRepresented.add(DataTypeEnum.SINGLE_CELL.getAbbreviation());
-		}
-		if (clustersInDataTypes.getIsSingleNucCluster().equalsIgnoreCase("Y")) {
-			dataTypesRepresented.add(DataTypeEnum.SINGLE_NUCLEUS.getAbbreviation());
-		}
-		if (clustersInDataTypes.getIsRegionalTranscriptomics().equalsIgnoreCase("Y")) {
-			dataTypesRepresented.add(DataTypeEnum.REGIONAL_TRANSCRIPTOMICS.getAbbreviation());
-		}
-		if (clustersInDataTypes.getIsRegionalProteomics().equalsIgnoreCase("Y")) {
+		if (clusterName.equals("Tubulo-interstitium")) {
 			dataTypesRepresented.add(DataTypeEnum.REGIONAL_PROTEOMICS.getAbbreviation());
+			dataTypesRepresented.add(DataTypeEnum.REGIONAL_TRANSCRIPTOMICS.getAbbreviation());
+		} else {
+			ClusterHierarchy clustersInDataTypes = clusterHierarchyRepo.findFirstByClusterOrRegion(clusterName);
+			if (clustersInDataTypes.getIsSingleCellCluster().equalsIgnoreCase("Y")) {
+				dataTypesRepresented.add(DataTypeEnum.SINGLE_CELL.getAbbreviation());
+			}
+			if (clustersInDataTypes.getIsSingleNucCluster().equalsIgnoreCase("Y")) {
+				dataTypesRepresented.add(DataTypeEnum.SINGLE_NUCLEUS.getAbbreviation());
+			}
+			if (clustersInDataTypes.getIsRegionalTranscriptomics().equalsIgnoreCase("Y")) {
+				dataTypesRepresented.add(DataTypeEnum.REGIONAL_TRANSCRIPTOMICS.getAbbreviation());
+			}
+			if (clustersInDataTypes.getIsRegionalProteomics().equalsIgnoreCase("Y")) {
+				dataTypesRepresented.add(DataTypeEnum.REGIONAL_PROTEOMICS.getAbbreviation());
+			}
 		}
 		return dataTypesRepresented;
 	}

src/test/java/org/kpmp/cellTypeSummary/ClusterHierarchyServiceTest.java

@@ -1,9 +1,10 @@
 package org.kpmp.cellTypeSummary;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.*;
 import static org.mockito.Mockito.verify;
 import static org.mockito.Mockito.when;
 
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
@@ -190,4 +191,24 @@ public void testFindDataTypesByClusterNameWhenRPY() throws Exception {
 		assertEquals(Arrays.asList("rp"), dataTypes);
 		verify(clusterHierarchyRepo).findFirstByClusterOrRegion("cluster");
 	}
+
+	@Test
+	public void testFindClustersByCellTypeTubulesOrInterstitium() throws Exception {
+		List<ClusterHierarchy> clusterHierarchies = new ArrayList<>();
+		when(clusterHierarchyRepo.findByCellType("Tubules")).thenReturn(clusterHierarchies);
+		when(clusterHierarchyRepo.findByCellType("Interstitium")).thenReturn(clusterHierarchies);
+		List<ClusterHierarchy> clusters = service.findClustersByCellType("Tubules");
+		assertEquals("Tubulo-interstitium", clusters.get(0).getStructureRegion());
+		List<ClusterHierarchy> clusters2 = service.findClustersByCellType("Interstitium");
+		assertEquals("Tubulo-interstitium", clusters2.get(0).getStructureRegion());
+	}
+
+	@Test
+	public void testFindDataTypesByClusterNameTi() throws Exception {
+		List<String> dataTypes = service.findDataTypesByClusterName("Tubulo-interstitium");
+		assertTrue(dataTypes.contains(DataTypeEnum.REGIONAL_PROTEOMICS.getAbbreviation()));
+		assertTrue(dataTypes.contains(DataTypeEnum.REGIONAL_TRANSCRIPTOMICS.getAbbreviation()));
+		assertFalse(dataTypes.contains(DataTypeEnum.SINGLE_CELL.getAbbreviation()));
+		assertFalse(dataTypes.contains(DataTypeEnum.SINGLE_NUCLEUS.getAbbreviation()));
+	}
 }

src/test/java/org/kpmp/geneExpression/RPAccessionGroupTest.java

@@ -0,0 +1,41 @@
+package org.kpmp.geneExpression;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+public class RPAccessionGroupTest {
+
+    private RPAccessionGroup rpAccessionGroup;
+
+    @Before
+    public void setUp() throws Exception {
+        rpAccessionGroup = new RPAccessionGroup();
+    }
+
+    @After
+    public void tearDown() throws Exception {
+        rpAccessionGroup = null;
+    }
+
+    @Test
+    public void testConstructor() throws Exception {
+        RPExpressionByTissueType rpExpressionByTissueType = new RPExpressionByTissueType();
+        RPAccessionGroup rpAccessionGroup1 = new RPAccessionGroup("accession", rpExpressionByTissueType);
+        assertEquals(rpExpressionByTissueType, rpAccessionGroup1.getRpExpressionByTissueType());
+        assertEquals("accession", rpAccessionGroup1.getAccession());
+    }
+
+    @Test
+    public void testSetters() throws Exception {
+        RPExpressionByTissueType rpExpressionByTissueType = new RPExpressionByTissueType();
+        rpAccessionGroup.setAccession("1234");
+        rpAccessionGroup.setRpExpressionByTissueType(rpExpressionByTissueType);
+        assertEquals("1234", rpAccessionGroup.getAccession());
+        assertEquals(rpExpressionByTissueType, rpAccessionGroup.getRpExpressionByTissueType());
+    }
+
+
+}