From 8ab2d02396a2194db358e38c3e460a513c235bf2 Mon Sep 17 00:00:00 2001
From: HaneenT <haneen@umich.edu>
Date: Thu, 29 Feb 2024 08:50:11 -0500
Subject: [PATCH 1/2] KPMP-5154: add additional geneExpressionValues to feature
 data

---
 .../java/org/kpmp/umap/SCMetadataRepository.java |  2 ++
 src/main/java/org/kpmp/umap/UmapDataService.java | 16 ++++++++++++++++
 2 files changed, 18 insertions(+)

diff --git a/src/main/java/org/kpmp/umap/SCMetadataRepository.java b/src/main/java/org/kpmp/umap/SCMetadataRepository.java
index cbcad2e..8f83782 100755
--- a/src/main/java/org/kpmp/umap/SCMetadataRepository.java
+++ b/src/main/java/org/kpmp/umap/SCMetadataRepository.java
@@ -32,6 +32,8 @@ public interface SCMetadataRepository extends CrudRepository<SCMetadata, String>
 
 	List<SCMetadata> findByTissueType(String tissueType);
 
+	SCMetadata findByBarcode(String barcode);
+
 	@Cacheable("scMetadataWithTissue")
 	@Query(value = "SELECT "
 						+ "umap_x, "
diff --git a/src/main/java/org/kpmp/umap/UmapDataService.java b/src/main/java/org/kpmp/umap/UmapDataService.java
index f3dc921..7d6bc2f 100755
--- a/src/main/java/org/kpmp/umap/UmapDataService.java
+++ b/src/main/java/org/kpmp/umap/UmapDataService.java
@@ -5,6 +5,7 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Iterator;
 
 import org.json.JSONException;
 import org.json.JSONObject;
@@ -78,6 +79,21 @@ public PlotData getPlotData(String dataType, String geneSymbol, String requestTi
             }
 		}
 
+		if (dataTypeEnum.equals(DataTypeEnum.SINGLE_CELL) 
+			&& featureDataWithExpressionValues.getExpression().size() == 0 
+			&& geneExpressionValues.length() <= 200) {
+			Iterator<String> keys = geneExpressionValues.keys();
+			while(keys.hasNext()) {
+				String barcode = keys.next();
+				Double expressionValue = geneExpressionValues.getDouble(barcode);
+				UmapPoint umapPoint = scMetadataRepo.findByBarcode(barcode);
+				featureDataWithExpressionValues.addXValue(umapPoint.getUmapX());
+				featureDataWithExpressionValues.addYValue(umapPoint.getUmapY());
+				featureDataWithExpressionValues.addExpression(expressionValue);
+				featureDataWithExpressionValues.addHoverDisplay(Double.toString(expressionValue) + "<br>" + umapPoint.getClusterName());
+			}
+		}
+
 		List<ReferenceCluster> referenceClusterList = new ArrayList<>(referenceClusters.values());
 		return new PlotData(referenceClusterList,
 				Arrays.asList(featureDataWithExpressionValues, featureDataWithNoExpressionValues));

From fde222d80dbba55dfec7db22b239ce4c73009095 Mon Sep 17 00:00:00 2001
From: HaneenT <haneen@umich.edu>
Date: Thu, 29 Feb 2024 09:02:29 -0500
Subject: [PATCH 2/2] fix linkinformation type

---
 src/main/resources/knowledge_environment.graphqls | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/main/resources/knowledge_environment.graphqls b/src/main/resources/knowledge_environment.graphqls
index 69712fd..6840d47 100755
--- a/src/main/resources/knowledge_environment.graphqls
+++ b/src/main/resources/knowledge_environment.graphqls
@@ -41,10 +41,10 @@ type AtlasRepoSummaryRow {
   hrtCount: Long
   dmrCount: Long
   omicsType: String
-  linkInformation: AtlasRepositoryLinkInformationInformation
+  linkInformation: AtlasRepositoryLinkInformation
 }
 
-type AtlasRepositoryLinkInformationInformation {
+type AtlasRepositoryLinkInformation {
   linkType: String
   linkValue: String
 }
@@ -74,7 +74,7 @@ type ParticipantRepoDataTypeSummary {
 type ParticipantRepoDataTypeInformation {
   dataType: String
   count: Long
-  linkInformation: AtlasRepositoryLinkInformationInformation
+  linkInformation: AtlasRepositoryLinkInformation
 }
 
 type DataTypeSummaryInformation {