Release 3.1

.github/workflows/build-gradle-project.yml

@@ -6,7 +6,7 @@ on:
 jobs:
   build-gradle-project:
     env:
-      IMAGE_TAG: 3.0.0
+      IMAGE_TAG: 3.1.0
     runs-on: ubuntu-latest
     steps:
       - name: Get branch names

.java-version

@@ -1 +1 @@
-21.0.4
+11

build.gradle

@@ -13,7 +13,7 @@ plugins {
 }
 
 group = 'kingstonduo'
-version = '3.0.0'
+version = '3.1.0'
 
 apply plugin: 'java'
 apply plugin: 'eclipse'

changelog.md

@@ -1,13 +1,32 @@
 # Changelog
 
-## Release 2.9 (unreleased)
+## Release 3.2 (unreleased)
+Brief summary:
+
+### Breaking changes
+
+---
+
+## Release 3.1 
+Brief summary:
+
+- Fixed issue with gene expression tables not showing up for some UMAPs
+
+---
+
+## Release 3.0 (11/13/2025)
 Breief summary:
 - Created new Objects for Single-Cell & Single-Nuc data
 - Created new Endpoints to retrieve new SN / SC data
 - Dynamic count returning for cluster counts
 - Use a Union instead of Union All for ClusterHierarchy Endpoint
 - Use a Set for ClusterHierarchy
 
+### Breaking changes
+N/A
+
+---
+
 ## Release 2.8 (6/30/2025)
 Brief summary:
 - Updates to how we calculate the numbers for the tables so it is more data driven

src/main/java/org/kpmp/dataSummary/DataSummaryRepository.java

@@ -66,6 +66,10 @@ public interface DataSummaryRepository extends CrudRepository<DataSummaryValue,
 	@Query(value = "SELECT count(*) from sv_file_v WHERE data_type= :data_type AND redcap_id= :redcap_id", nativeQuery = true)
 	Integer getParticipantSvFileDataTypeCount(@Param("redcap_id") String redcapId, @Param("data_type") String dataType);
 
+    @Cacheable("dataParticipantSvFileConfigTypeCount")
+    @Query(value = "SELECT count(*) from sv_file_v WHERE config_type= :config_type AND redcap_id= :redcap_id", nativeQuery = true)
+    Integer getParticipantSegmentationConfigTypeCount(@Param("redcap_id") String redcapId, @Param("config_type") String configType);
+
 	@Cacheable("dataParticipantSvLinkDataTypeCount")
 	@Query(value = "SELECT count(*) from sv_link_v WHERE data_type= :data_type AND redcap_id= :redcap_id", nativeQuery = true)
 	Integer getParticipantSvLinkDataTypeCount(@Param("redcap_id") String redcapId, @Param("data_type") String dataType);

src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService2025.java

@@ -4,9 +4,9 @@
 import java.util.List;
 import java.util.stream.Collectors;
 
+import org.kpmp.EnrollmentCategoryEnum;
 import org.kpmp.FullDataTypeEnum;
 import org.kpmp.OmicsTypeEnum;
-import org.kpmp.EnrollmentCategoryEnum;
 import org.kpmp.dataSummary.DataTypeSummary;
 import org.kpmp.geneExpression.RPExpressionDataRepository;
 import org.kpmp.geneExpression.RTExpressionDataAllSegmentsRepository;
@@ -165,6 +165,12 @@ public List<DataTypeSummary> getDataTypeSummaryInformation() {
 				rpParticipantRepository.getCountByEnrollmentCategory(EnrollmentCategoryEnum.DMR.getParticipantEnrollmentCategory()),
 				rpParticipantRepository.getParticipantCount(),
 				rpParticipantRepository.getParticipantCount()));
+		// dataTypeSummary.add(new DataTypeSummary(
+		// 	OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), 
+		// 	FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS.getFullName(), 
+		// 	FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS.getAbbreviation(), 
+		// 	1000L, 1000L, 1000L, 
+		// 	1000L, 1000L, 1000L));
 		return dataTypeSummary;
 	}
 

src/main/java/org/kpmp/participant/ParticipantService2025.java

@@ -195,7 +195,9 @@ private List<ParticipantDataTypeInformation2025> getSpatialViewerCounts(String r
 				Integer count = dataSummaryRepo.getParticipantSvFileDataTypeCount(redcapId, dataType);
 				ParticipantDataTypeInformation2025 dataTypeInfo = new ParticipantDataTypeInformation2025(dataType, count,
 						false);
+
 				spatialViewerExperiments.add(dataTypeInfo);
+
 			} else if (spatialViewerDataType.getTableName().equals(SPATIAL_VIEWER_LINK_VIEW)) {
 				Integer count = dataSummaryRepo.getParticipantSvLinkDataTypeCount(redcapId, dataType);
 				ParticipantDataTypeInformation2025 dataTypeInfo = new ParticipantDataTypeInformation2025(dataType, count,
@@ -205,6 +207,10 @@ private List<ParticipantDataTypeInformation2025> getSpatialViewerCounts(String r
 				logger.error("Unable to query for data type: " + dataType + ". Need to change code to handle.");
 			}
 		}
+        Integer segmentationCount = dataSummaryRepo.getParticipantSegmentationConfigTypeCount(redcapId, "Segmentation Masks & Pathomics Vectors");
+        ParticipantDataTypeInformation2025 segmentationDataTypeInfo = new ParticipantDataTypeInformation2025("Segmentation Masks & Pathomics Vectors", segmentationCount,
+                        false);
+                spatialViewerExperiments.add(segmentationDataTypeInfo);
 		return spatialViewerExperiments;
 	}
 

src/main/java/org/kpmp/umap/SCMetadataRepository2025.java

@@ -9,11 +9,11 @@
 
 public interface SCMetadataRepository2025 extends CrudRepository<SCMetadata2025, String> {
 
-	@Cacheable("scMetadataAll")
+	@Cacheable("scMetadataAll2025")
 	@Override
 	List<SCMetadata2025> findAll();
 
-	@Cacheable("scMetadataLimited")
+	@Cacheable("scMetadataLimited2025")
 	@Query(value = "SELECT "
 			+ "umap_x, umap_y, cluster_abbreviation, cluster_name, cluster_color, barcode, enrollment_category "
 			+ "FROM sc_umap_point_2025_v "
@@ -35,15 +35,15 @@ public interface SCMetadataRepository2025 extends CrudRepository<SCMetadata2025,
 			+ "limit :largeClusterLimit) ", nativeQuery = true)
 	List<SCMetadata2025> findLimited(@Param("mediumClusterLimit") int mediumClusterLimit, @Param("largeClusterLimit") int largeClusterLimit);
 
-	@Cacheable("scMetadataCount")
+	@Cacheable("scMetadataCount2025")
 	@Query(value = "SELECT COUNT(umap_x) FROM sc_umap_point_2025_v;", nativeQuery = true)
 	int findCount();
 
 	List<SCMetadata2025> findByEnrollmentCategory(String enrollmentCategory);
 
-	SCMetadata findByBarcode(String barcode);
+	SCMetadata2025 findByBarcode(String barcode);
 
-	@Cacheable("scMetadataWithEnrollment")
+	@Cacheable("scMetadataWithEnrollment2025")
 	@Query(value = "SELECT "
 			+ "umap_x, umap_y, cluster_abbreviation, cluster_name, cluster_color, barcode, enrollment_category "
 			+ "FROM sc_umap_point_2025_v "