Kpmp 4434 rp expression

src/main/java/org/kpmp/Query.java

@@ -13,9 +13,7 @@
 import org.kpmp.dataSummary.AtlasRepoSummaryResult;
 import org.kpmp.dataSummary.DataSummaryService;
 import org.kpmp.dataSummary.DataTypeSummary;
-import org.kpmp.geneExpression.RTExpressionByTissueType;
-import org.kpmp.geneExpression.RTExpressionData;
-import org.kpmp.geneExpression.RTExpressionDataService;
+import org.kpmp.geneExpression.*;
 import org.kpmp.geneExpressionSummary.GeneExpressionSummary;
 import org.kpmp.geneExpressionSummary.GeneExpressionSummaryService;
 import org.kpmp.participant.ParticipantDataTypeSummary;
@@ -43,14 +41,17 @@ public class Query implements GraphQLQueryResolver {
 	private UmapDataService umapService;
 	private ClusterHierarchyService clusterHierarchyService;
 	private RTExpressionDataService rtExpressionDataService;
+
+	private RPExpressionDataService rpExpressionDataService;
 	private ParticipantService participantService;
 	private Logger logger = LoggerFactory.getLogger(Query.class);
 
 	@Autowired
 	public Query(AutocompleteService autocompleteService, CellTypeService cellTypeService,
 			UmapDataService umapService, GeneExpressionSummaryService geneExpressionSummaryService,
 			DataSummaryService dataSummaryService, ClusterHierarchyService clusterHierarchyService,
-			RTExpressionDataService rtExpressionDataService, ParticipantService participantService) {
+			RTExpressionDataService rtExpressionDataService, RPExpressionDataService rpExpressionDataService,
+				 ParticipantService participantService) {
 
 		this.autocompleteService = autocompleteService;
 		this.cellTypeService = cellTypeService;
@@ -59,6 +60,7 @@ public Query(AutocompleteService autocompleteService, CellTypeService cellTypeSe
 		this.dataSummaryService = dataSummaryService;
 		this.clusterHierarchyService = clusterHierarchyService;
 		this.rtExpressionDataService = rtExpressionDataService;
+		this.rpExpressionDataService = rpExpressionDataService;
 		this.participantService = participantService;
 	}
 
@@ -142,6 +144,16 @@ public List<? extends RTExpressionData> getRTGeneExpressionByStructure(String st
 		}
 	}
 
+	public RPExpressionByTissueType getRPGeneExpressionByTissue(String geneSymbol)
+			throws Exception {
+		try {
+			return rpExpressionDataService.getByGeneSymbolPerTissue(geneSymbol);
+		} catch (Exception e) {
+			logger.error(e.getMessage());
+			throw e;
+		}
+	}
+
 	public ParticipantDataTypeSummary getDataTypeInformationByParticipant(String redcapId) {
 		return participantService.getExperimentCounts(redcapId);
 	}

src/main/java/org/kpmp/geneExpression/RPExpressionByTissueType.java

@@ -0,0 +1,53 @@
+package org.kpmp.geneExpression;
+
+import java.util.List;
+
+public class RPExpressionByTissueType {
+
+    private List<? extends RPExpressionData> all;
+    private List<? extends RPExpressionData> aki;
+    private List<? extends RPExpressionData> ckd;
+    private List<? extends RPExpressionData> hrt;
+    private List<? extends RPExpressionData> dmr;
+
+    public List<? extends RPExpressionData> getAll() {
+        return all;
+    }
+
+    public void setAll(List<? extends RPExpressionData> all) {
+        this.all = all;
+    }
+
+    public List<? extends RPExpressionData> getAki() {
+        return aki;
+    }
+
+    public void setAki(List<? extends RPExpressionData> aki) {
+        this.aki = aki;
+    }
+
+    public List<? extends RPExpressionData> getCkd() {
+        return ckd;
+    }
+
+    public void setCkd(List<? extends RPExpressionData> ckd) {
+        this.ckd = ckd;
+    }
+
+    public List<? extends RPExpressionData> getHrt() {
+        return hrt;
+    }
+
+    public void setHrt(List<? extends RPExpressionData> hrt) {
+        this.hrt = hrt;
+    }
+
+    public List<? extends RPExpressionData> getDmr() {
+        return dmr;
+    }
+
+    public void setDmr(List<? extends RPExpressionData> dmr) {
+        this.dmr = dmr;
+    }
+}
+

src/main/java/org/kpmp/geneExpression/RPExpressionData.java

@@ -40,7 +40,7 @@ public class RPExpressionData {
     @Column(name = "adj_p_val")
     private Double adjPVal;
 
-    @Column(name = "fold_chane")
+    @Column(name = "fold_change")
     private Double foldChange;
 
     @Column(name = "tissue_type")
@@ -49,6 +49,8 @@ public class RPExpressionData {
     @Column(name = "region")
     private String region;
 
+    @Column(name = "sample_count")
+    private Integer sampleCount;
     public Integer getId() {
         return id;
     }
@@ -153,4 +155,11 @@ public void setRegion(String region) {
         this.region = region;
     }
 
+    public Integer getSampleCount() {
+        return sampleCount;
+    }
+
+    public void setSampleCount(Integer sampleCount) {
+        this.sampleCount = sampleCount;
+    }
 }

src/main/java/org/kpmp/geneExpression/RPExpressionDataRepository.java

@@ -5,8 +5,16 @@
 import org.springframework.data.repository.CrudRepository;
 import org.springframework.data.repository.query.Param;
 
+import java.util.List;
+
 public interface RPExpressionDataRepository extends CrudRepository<RPExpressionData, Integer> {
 
+
+    @Query(value = "SELECT rpe.*, count(*) as sample_count FROM rp_expression rpe " +
+            "JOIN rp_metadata rpm ON LOWER(rpe.region) = LOWER(rpm.tissue_region) " +
+            "WHERE rpe.gene_symbol = :geneSymbol AND rpe.tissue_type = :tissueType " +
+            "GROUP BY rpe.region", nativeQuery = true)
+    List<RPExpressionData> findByGeneSymbolAndTissueTypeWithCounts(String geneSymbol, String tissueType);
     @Cacheable("rpExpCountByGene")
     @Query(value = "SELECT COUNT(*) FROM rp_expression WHERE gene_symbol = :gene", nativeQuery = true)
     long getCountByGene(@Param("gene") String gene);

src/main/java/org/kpmp/geneExpression/RPExpressionDataService.java

@@ -0,0 +1,29 @@
+package org.kpmp.geneExpression;
+
+import org.kpmp.TissueTypeEnum;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+@Service
+public class RPExpressionDataService {
+
+    RPExpressionDataRepository rpExpressionDataRepository;
+
+    @Autowired
+    public RPExpressionDataService(RPExpressionDataRepository rpExpressionDataRepository) {
+        this.rpExpressionDataRepository = rpExpressionDataRepository;
+    }
+
+    public RPExpressionByTissueType getByGeneSymbolPerTissue(String geneSymbol) {
+        RPExpressionByTissueType rpExpressionByTissueType = new RPExpressionByTissueType();
+
+        rpExpressionByTissueType.setAki(rpExpressionDataRepository.findByGeneSymbolAndTissueTypeWithCounts(geneSymbol, TissueTypeEnum.AKI.getParticipantTissueType()));
+        rpExpressionByTissueType.setCkd(rpExpressionDataRepository.findByGeneSymbolAndTissueTypeWithCounts(geneSymbol, TissueTypeEnum.CKD.getParticipantTissueType()));
+        rpExpressionByTissueType.setDmr(rpExpressionDataRepository.findByGeneSymbolAndTissueTypeWithCounts(geneSymbol, TissueTypeEnum.DMR.getParticipantTissueType()));
+        rpExpressionByTissueType.setHrt(rpExpressionDataRepository.findByGeneSymbolAndTissueTypeWithCounts(geneSymbol, TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType()));
+        rpExpressionByTissueType.setAll(rpExpressionDataRepository.findByGeneSymbolAndTissueTypeWithCounts(geneSymbol, TissueTypeEnum.ALL.getParticipantTissueType()));
+
+        return rpExpressionByTissueType;
+
+    }
+}

src/main/resources/knowledge_environment.graphqls

@@ -7,6 +7,7 @@ type Query {
   dataTypesForConcept(geneSymbol: String, clusterName: String): [String]
   getDataTypeSummaryInformation: [DataTypeSummaryInformation]
   getRTGeneExpressionByTissue(comparisonType: String, geneSymbol: String): RTGeneExpressionByTissue
+  getRPGeneExpressionByTissue(geneSymbol: String): RPGeneExpressionByTissue
   getRTGeneExpressionByStructure(structure: String): [RTGeneExpression]
   getSummaryData: [DataTypeSummaryInformation]
   getDataTypeInformationByParticipant(redcapId: String!): ParticipantDataTypeSummary
@@ -74,6 +75,7 @@ type DataTypeSummaryInformation {
   participantCount: Long
 }
 
+
 type AutoCompleteResult {
   value: String
   name: String
@@ -170,6 +172,31 @@ type RTGeneExpressionByTissue {
     aki: [RTGeneExpression]
 }
 
+type RPGeneExpression {
+    id: ID
+    geneSymbol: String
+    fdrConfidence: String
+    accession: String
+    description: String
+    coveragePct: Int
+    numPeptides: Int
+    numUniquePeptides: Int
+    comparison: String
+    region: String
+    foldChange: Float
+    adjPVal: Float
+    tissueType: String
+    sampleCount: Int
+}
+
+type RPGeneExpressionByTissue {
+    all: [RPGeneExpression]
+    hrt: [RPGeneExpression]
+    ckd: [RPGeneExpression]
+    dmr: [RPGeneExpression]
+    aki: [RPGeneExpression]
+}
+
 type ParticipantSummaryDataset {
   participantId: String
   redcapId: String

src/test/java/org/kpmp/QueryTest.java

@@ -24,6 +24,7 @@
 import org.kpmp.dataSummary.AtlasRepoSummaryResult;
 import org.kpmp.dataSummary.DataSummaryService;
 import org.kpmp.dataSummary.DataTypeSummary;
+import org.kpmp.geneExpression.RPExpressionDataService;
 import org.kpmp.geneExpression.RTExpressionByTissueType;
 import org.kpmp.geneExpression.RTExpressionDataAllSegments;
 import org.kpmp.geneExpression.RTExpressionDataService;
@@ -64,11 +65,14 @@ public class QueryTest {
 	@Mock
 	private ParticipantTissueTypeSummary participantTissueTypeSummary;
 
+	@Mock
+	private RPExpressionDataService rpExpressionDataService;
+
 	@Before
 	public void setUp() throws Exception {
 		MockitoAnnotations.openMocks(this);
 		query = new Query(autocompleteService, cellTypeService, umapDataService, geneExpressionService,
-				dataSummaryService, clusterHierarchyService, rtExpressionDataService, participantService);
+				dataSummaryService, clusterHierarchyService, rtExpressionDataService, rpExpressionDataService, participantService);
 	}
 
 	@After

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

@@ -0,0 +1,71 @@
+package org.kpmp.geneExpression;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.util.Arrays;
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+public class RPExpressionDataByTissueTypeTest {
+
+    private RPExpressionByTissueType rpExpressionByTissueType;
+
+    @Before
+    public void setUp() throws Exception {
+        rpExpressionByTissueType = new RPExpressionByTissueType();
+    }
+
+    @After
+    public void tearDown() throws Exception {
+        rpExpressionByTissueType = null;
+    }
+
+    @Test
+    public void setAll() {
+        RPExpressionData allData = new RPExpressionData();
+        List<? extends RPExpressionData> allataList = Arrays.asList(allData);
+        rpExpressionByTissueType.setAll(allataList);
+        List<? extends RPExpressionData> actual = rpExpressionByTissueType.getAll();
+        assertEquals(allataList, actual);
+    }
+
+    @Test
+    public void setAki() {
+        RPExpressionData allAkiData = new RPExpressionData();
+        List<? extends RPExpressionData> allAkiDataList = Arrays.asList(allAkiData);
+        rpExpressionByTissueType.setAki(allAkiDataList);
+        List<? extends RPExpressionData> actual = rpExpressionByTissueType.getAki();
+        assertEquals(allAkiDataList, actual);
+    }
+
+    @Test
+    public void setCkd() {
+        RPExpressionData allCkdData = new RPExpressionData();
+        List<? extends RPExpressionData> allCkdDataList = Arrays.asList(allCkdData);
+        rpExpressionByTissueType.setCkd(allCkdDataList);
+        List<? extends RPExpressionData> actual = rpExpressionByTissueType.getCkd();
+        assertEquals(allCkdDataList, actual);
+    }
+
+    @Test
+    public void setHrt() {
+        RPExpressionData allHrtData = new RPExpressionData();
+        List<? extends RPExpressionData> allHrtDataList = Arrays.asList(allHrtData);
+        rpExpressionByTissueType.setHrt(allHrtDataList);
+        List<? extends RPExpressionData> actual = rpExpressionByTissueType.getHrt();
+        assertEquals(allHrtDataList, actual);
+    }
+
+    @Test
+    public void setDmr() {
+        RPExpressionData allDmrData = new RPExpressionData();
+        List<? extends RPExpressionData> allDmrDataList = Arrays.asList(allDmrData);
+        rpExpressionByTissueType.setDmr(allDmrDataList);
+        List<? extends RPExpressionData> actual = rpExpressionByTissueType.getDmr();
+        assertEquals(allDmrDataList, actual);
+    }
+
+}

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

@@ -0,0 +1,64 @@
+package org.kpmp.geneExpression;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.kpmp.TissueTypeEnum;
+import org.mockito.Mock;
+import org.mockito.MockitoAnnotations;
+
+import java.util.Arrays;
+import java.util.List;
+
+import static org.mockito.Mockito.when;
+
+public class RPExpressionDataServiceTest {
+
+    @Mock
+    RPExpressionDataRepository rpExpressionDataRepository;
+
+    RPExpressionDataService rpExpressionDataService;
+
+    @Before
+    public void setUp() throws Exception {
+        MockitoAnnotations.openMocks(this);
+        rpExpressionDataService = new RPExpressionDataService(rpExpressionDataRepository);
+    }
+
+    @After
+    public void tearDown() throws Exception {
+        MockitoAnnotations.openMocks(this).close();
+        rpExpressionDataService = null;
+    }
+
+    @Test
+    public void testGetByGeneSymbolPerTissue() throws Exception {
+        List<RPExpressionData> rpExpressionDataAki = Arrays.asList(new RPExpressionData[]{new RPExpressionData()});
+        List<RPExpressionData>  rpExpressionDataCkd = Arrays.asList(new RPExpressionData[]{new RPExpressionData()});
+        List<RPExpressionData>  rpExpressionDataHrt = Arrays.asList(new RPExpressionData[]{new RPExpressionData()});
+        List<RPExpressionData>  rpExpressionDataDmr = Arrays.asList(new RPExpressionData[]{new RPExpressionData()});
+        List<RPExpressionData>  rpExpressionDataAll = Arrays.asList(new RPExpressionData[]{new RPExpressionData()});
+
+        when(rpExpressionDataRepository.findByGeneSymbolAndTissueTypeWithCounts("gene", TissueTypeEnum.AKI.getParticipantTissueType())).
+                thenReturn(rpExpressionDataAki);
+        when(rpExpressionDataRepository.findByGeneSymbolAndTissueTypeWithCounts("gene", TissueTypeEnum.CKD.getParticipantTissueType())).
+                thenReturn(rpExpressionDataCkd);
+        when(rpExpressionDataRepository.findByGeneSymbolAndTissueTypeWithCounts("gene", TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType())).
+                thenReturn(rpExpressionDataHrt);
+        when(rpExpressionDataRepository.findByGeneSymbolAndTissueTypeWithCounts("gene", TissueTypeEnum.DMR.getParticipantTissueType())).
+                thenReturn(rpExpressionDataDmr);
+        when(rpExpressionDataRepository.findByGeneSymbolAndTissueTypeWithCounts("gene", TissueTypeEnum.ALL.getParticipantTissueType())).
+                thenReturn(rpExpressionDataAll);
+
+        RPExpressionByTissueType rpExpressionByTissueType = rpExpressionDataService.getByGeneSymbolPerTissue("gene");
+
+        assertEquals(rpExpressionByTissueType.getAki(), rpExpressionDataAki);
+        assertEquals(rpExpressionByTissueType.getHrt(), rpExpressionDataHrt);
+        assertEquals(rpExpressionByTissueType.getCkd(), rpExpressionDataCkd);
+        assertEquals(rpExpressionByTissueType.getAll(), rpExpressionDataAll);
+        assertEquals(rpExpressionByTissueType.getDmr(), rpExpressionDataDmr);
+
+    }
+}