From 0440874431654c68c8638ea2f328a75e2d70def7 Mon Sep 17 00:00:00 2001
From: HaneenT <haneen@umich.edu>
Date: Tue, 5 Mar 2024 11:38:00 -0500
Subject: [PATCH] KPMP-5178: added query to fetch biomarker counts

---
 .../dataSummary/DataSummaryRepository.java    |  4 ++
 .../kpmp/dataSummary/DataSummaryService.java  | 72 ++++++++++++-------
 .../dataSummary/DataSummaryServiceTest.java   | 12 ++--
 3 files changed, 56 insertions(+), 32 deletions(-)

diff --git a/src/main/java/org/kpmp/dataSummary/DataSummaryRepository.java b/src/main/java/org/kpmp/dataSummary/DataSummaryRepository.java
index 0d13df8..b393fc4 100755
--- a/src/main/java/org/kpmp/dataSummary/DataSummaryRepository.java
+++ b/src/main/java/org/kpmp/dataSummary/DataSummaryRepository.java
@@ -20,6 +20,10 @@ public interface DataSummaryRepository extends CrudRepository<DataSummaryValue,
 	@Cacheable("repoDataSummaryCount")
 	@Query(value = "select count(distinct(dl_file_id)) from repo_file_v where experimental_strategy = :exp_strat and tissue_type = :tissue_type", nativeQuery = true)
 	Long getRepoDataSummaryCount(@Param("tissue_type") String tissue_type, @Param("exp_strat") String exp_strat);
+	
+	@Cacheable("repoBiomarkerSummaryCount")
+	@Query(value = "select count(distinct(dl_file_id)) from repo_file_v where data_category = 'Biomarker' and tissue_type = :tissue_type", nativeQuery = true)
+	Long getRepoBiomarkerSummaryCount(@Param("tissue_type") String tissue_type);
 
 	@Cacheable("dataSummaryLinkCount")
 	@Query(value = "select count(distinct(redcap_id)) " + "from sv_link_v " + "where data_type = :data_type "
diff --git a/src/main/java/org/kpmp/dataSummary/DataSummaryService.java b/src/main/java/org/kpmp/dataSummary/DataSummaryService.java
index a332e5d..3e241fc 100755
--- a/src/main/java/org/kpmp/dataSummary/DataSummaryService.java
+++ b/src/main/java/org/kpmp/dataSummary/DataSummaryService.java
@@ -89,30 +89,54 @@ private AtlasRepositoryLinkInformation getLinkInformation(ExperimentalStrategyVa
 
 	private void setCounts(ExperimentalStrategyValue experimentalStrategyValue, AtlasRepoSummaryRow atlasRepoSummaryRow)
 			throws Exception {
-		atlasRepoSummaryRow.setAkiCount(
-			dataSummaryRepository.getRepoDataSummaryCount(
-				TissueTypeEnum.AKI.getParticipantTissueType(), 
-				experimentalStrategyValue.getExperimentalStrategy()
-			)
-		);
-		atlasRepoSummaryRow.setCkdCount(
-			dataSummaryRepository.getRepoDataSummaryCount(
-				TissueTypeEnum.CKD.getParticipantTissueType(), 
-				experimentalStrategyValue.getExperimentalStrategy()
-			)
-		);
-		atlasRepoSummaryRow.setHrtCount(
-			dataSummaryRepository.getRepoDataSummaryCount(
-				TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(), 
-				experimentalStrategyValue.getExperimentalStrategy()
-			)
-		);
-		atlasRepoSummaryRow.setDmrCount(
-			dataSummaryRepository.getRepoDataSummaryCount(
-				TissueTypeEnum.DMR.getParticipantTissueType(), 
-				experimentalStrategyValue.getExperimentalStrategy()
-			)
-		);
+		if (experimentalStrategyValue.getDataCategory().equalsIgnoreCase(BIOMARKER)) {
+			atlasRepoSummaryRow.setAkiCount(
+				dataSummaryRepository.getRepoBiomarkerSummaryCount(
+					TissueTypeEnum.AKI.getParticipantTissueType()
+				)
+			);
+			atlasRepoSummaryRow.setCkdCount(
+				dataSummaryRepository.getRepoBiomarkerSummaryCount(
+					TissueTypeEnum.CKD.getParticipantTissueType()
+				)
+			);
+			atlasRepoSummaryRow.setHrtCount(
+				dataSummaryRepository.getRepoBiomarkerSummaryCount(
+					TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType()
+				)
+			);
+			atlasRepoSummaryRow.setDmrCount(
+				dataSummaryRepository.getRepoBiomarkerSummaryCount(
+					TissueTypeEnum.DMR.getParticipantTissueType()
+				)
+			);
+		}
+		else {
+			atlasRepoSummaryRow.setAkiCount(
+				dataSummaryRepository.getRepoDataSummaryCount(
+					TissueTypeEnum.AKI.getParticipantTissueType(), 
+					experimentalStrategyValue.getExperimentalStrategy()
+				)
+			);
+			atlasRepoSummaryRow.setCkdCount(
+				dataSummaryRepository.getRepoDataSummaryCount(
+					TissueTypeEnum.CKD.getParticipantTissueType(), 
+					experimentalStrategyValue.getExperimentalStrategy()
+				)
+			);
+			atlasRepoSummaryRow.setHrtCount(
+				dataSummaryRepository.getRepoDataSummaryCount(
+					TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(), 
+					experimentalStrategyValue.getExperimentalStrategy()
+				)
+			);
+			atlasRepoSummaryRow.setDmrCount(
+				dataSummaryRepository.getRepoDataSummaryCount(
+					TissueTypeEnum.DMR.getParticipantTissueType(), 
+					experimentalStrategyValue.getExperimentalStrategy()
+				)
+			);
+		}
 	}
 
 	public List<DataTypeSummary> getSummaryData() {
diff --git a/src/test/java/org/kpmp/dataSummary/DataSummaryServiceTest.java b/src/test/java/org/kpmp/dataSummary/DataSummaryServiceTest.java
index bb0299b..d80b38a 100755
--- a/src/test/java/org/kpmp/dataSummary/DataSummaryServiceTest.java
+++ b/src/test/java/org/kpmp/dataSummary/DataSummaryServiceTest.java
@@ -70,14 +70,10 @@ public void testGetAtlasRepoSummary() throws Exception {
 		strategies.get(3).setDataType("datatype");
 
 		when(atlasRepoSummaryRepository.findAll()).thenReturn(strategies);
-		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.AKI.getParticipantTissueType(),
-				"abcd")).thenReturn(Long.valueOf(1));
-		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.CKD.getParticipantTissueType(),
-				"abcd")).thenReturn(Long.valueOf(2));
-		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(),
-				"abcd")).thenReturn(Long.valueOf(3));
-		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.DMR.getParticipantTissueType(),
-				"abcd")).thenReturn(4l);
+		when(dataSummaryRepository.getRepoBiomarkerSummaryCount(TissueTypeEnum.AKI.getParticipantTissueType())).thenReturn(Long.valueOf(1));
+		when(dataSummaryRepository.getRepoBiomarkerSummaryCount(TissueTypeEnum.CKD.getParticipantTissueType())).thenReturn(Long.valueOf(2));
+		when(dataSummaryRepository.getRepoBiomarkerSummaryCount(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType())).thenReturn(Long.valueOf(3));
+		when(dataSummaryRepository.getRepoBiomarkerSummaryCount(TissueTypeEnum.DMR.getParticipantTissueType())).thenReturn(4l);
 
 		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.AKI.getParticipantTissueType(),
 				"")).thenReturn(Long.valueOf(5));