diff --git a/.github/workflows/build-gradle-project.yml b/.github/workflows/build-gradle-project.yml index ae9e73b..73c43fe 100644 --- a/.github/workflows/build-gradle-project.yml +++ b/.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 diff --git a/.java-version b/.java-version index f222bf6..b4de394 100644 --- a/.java-version +++ b/.java-version @@ -1 +1 @@ -21.0.4 +11 diff --git a/build.gradle b/build.gradle index f74c376..7732656 100755 --- a/build.gradle +++ b/build.gradle @@ -13,7 +13,7 @@ plugins { } group = 'kingstonduo' -version = '3.0.0' +version = '3.1.0' apply plugin: 'java' apply plugin: 'eclipse' diff --git a/changelog.md b/changelog.md index 4c35a21..39269a7 100644 --- a/changelog.md +++ b/changelog.md @@ -1,6 +1,20 @@ # 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 @@ -8,6 +22,11 @@ Breief summary: - 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 diff --git a/src/main/java/org/kpmp/dataSummary/DataSummaryRepository.java b/src/main/java/org/kpmp/dataSummary/DataSummaryRepository.java index cbd9ae4..b7d4703 100755 --- a/src/main/java/org/kpmp/dataSummary/DataSummaryRepository.java +++ b/src/main/java/org/kpmp/dataSummary/DataSummaryRepository.java @@ -66,6 +66,10 @@ public interface DataSummaryRepository extends CrudRepository 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; } diff --git a/src/main/java/org/kpmp/participant/ParticipantService2025.java b/src/main/java/org/kpmp/participant/ParticipantService2025.java index 65a44d6..733b336 100755 --- a/src/main/java/org/kpmp/participant/ParticipantService2025.java +++ b/src/main/java/org/kpmp/participant/ParticipantService2025.java @@ -195,7 +195,9 @@ private List 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 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; } diff --git a/src/main/java/org/kpmp/umap/SCMetadataRepository2025.java b/src/main/java/org/kpmp/umap/SCMetadataRepository2025.java index a45cf98..fc19dd1 100755 --- a/src/main/java/org/kpmp/umap/SCMetadataRepository2025.java +++ b/src/main/java/org/kpmp/umap/SCMetadataRepository2025.java @@ -9,11 +9,11 @@ public interface SCMetadataRepository2025 extends CrudRepository { - @Cacheable("scMetadataAll") + @Cacheable("scMetadataAll2025") @Override List 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 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 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 "