From ba79b0a2faecbf7eb4516b889c4e88382b91a652 Mon Sep 17 00:00:00 2001 From: rlreamy <34109594+rlreamy@users.noreply.github.com> Date: Mon, 17 Nov 2025 11:32:24 -0500 Subject: [PATCH 01/10] Update changelog.md --- changelog.md | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/changelog.md b/changelog.md index 4c35a21..d9d0bde 100644 --- a/changelog.md +++ b/changelog.md @@ -1,6 +1,13 @@ # Changelog -## Release 2.9 (unreleased) +## Release 2.10 (unreleased) +Brief summary: + +### Breaking changes + +--- + +## Release 2.9 (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 +15,11 @@ 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 From 9c5163a43b89b8979ac396449688b62c7769f924 Mon Sep 17 00:00:00 2001 From: rlreamy <34109594+rlreamy@users.noreply.github.com> Date: Mon, 17 Nov 2025 11:33:26 -0500 Subject: [PATCH 02/10] Update build.gradle --- build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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' From 1b517c22bf3ce31a401ceceb4a49f3705d237c0f Mon Sep 17 00:00:00 2001 From: rlreamy <34109594+rlreamy@users.noreply.github.com> Date: Mon, 17 Nov 2025 11:33:53 -0500 Subject: [PATCH 03/10] Update changelog.md --- changelog.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/changelog.md b/changelog.md index d9d0bde..0d2174e 100644 --- a/changelog.md +++ b/changelog.md @@ -1,13 +1,13 @@ # Changelog -## Release 2.10 (unreleased) +## Release 3.1 (unreleased) Brief summary: ### Breaking changes --- -## Release 2.9 (11/13/2025) +## 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 From eb1dd4bc28aa1059184ddc62e8bbf2a643f4b5be Mon Sep 17 00:00:00 2001 From: rlreamy <34109594+rlreamy@users.noreply.github.com> Date: Mon, 17 Nov 2025 11:34:08 -0500 Subject: [PATCH 04/10] Update build-gradle-project.yml --- .github/workflows/build-gradle-project.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From 4de6e09c1a85d9f9670b81673b7239e2e186fc00 Mon Sep 17 00:00:00 2001 From: dert1129 Date: Mon, 17 Nov 2025 14:46:22 -0500 Subject: [PATCH 05/10] shove a config type with the data types manually --- .../java/org/kpmp/dataSummary/DataSummaryRepository.java | 4 ++++ .../java/org/kpmp/participant/ParticipantService2025.java | 6 ++++++ 2 files changed, 10 insertions(+) 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 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; } From 390a5e26f0ddefb3a8ffab98076c569ba9341247 Mon Sep 17 00:00:00 2001 From: HaneenT Date: Mon, 17 Nov 2025 16:02:18 -0500 Subject: [PATCH 06/10] KPMP-6119: return dummy data for ST dataTypeSummaryInformation --- .../GeneExpressionSummaryService2025.java | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService2025.java b/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService2025.java index 7c190fe..1e97229 100755 --- a/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService2025.java +++ b/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 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)); return dataTypeSummary; } From 08da2394da14a5a5597d2cff7679f99ca86e31d1 Mon Sep 17 00:00:00 2001 From: HaneenT Date: Wed, 19 Nov 2025 14:30:18 -0500 Subject: [PATCH 07/10] add totalCount --- .../geneExpressionSummary/GeneExpressionSummaryService2025.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService2025.java b/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService2025.java index 1e97229..e4a86f0 100755 --- a/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService2025.java +++ b/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService2025.java @@ -170,7 +170,7 @@ public List getDataTypeSummaryInformation() { FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS.getFullName(), FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS.getAbbreviation(), 1000L, 1000L, 1000L, - 1000L, 1000L)); + 1000L, 1000L, 1000L)); return dataTypeSummary; } From 39a5647f459c611635c65f202aa9e9b76f03967b Mon Sep 17 00:00:00 2001 From: dert1129 Date: Thu, 11 Dec 2025 13:26:59 -0500 Subject: [PATCH 08/10] fix type error and name caches differently --- .../java/org/kpmp/umap/SCMetadataRepository2025.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) 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 " From ea03fd0a916024646561e0ef71aaedc5819d99eb Mon Sep 17 00:00:00 2001 From: Becky Reamy Date: Fri, 12 Dec 2025 11:37:04 -0500 Subject: [PATCH 09/10] KPMP-6410: Commented out returning dummy data for ST --- .java-version | 2 +- .../GeneExpressionSummaryService2025.java | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) 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/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService2025.java b/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService2025.java index e4a86f0..967578a 100755 --- a/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService2025.java +++ b/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService2025.java @@ -165,12 +165,12 @@ public List 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)); + // dataTypeSummary.add(new DataTypeSummary( + // OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), + // FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS.getFullName(), + // FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS.getAbbreviation(), + // 1000L, 1000L, 1000L, + // 1000L, 1000L, 1000L)); return dataTypeSummary; } From b8630468d84403269233bb3c0243c6dfcabb1b3d Mon Sep 17 00:00:00 2001 From: Zach Wright Date: Mon, 15 Dec 2025 12:32:38 -0500 Subject: [PATCH 10/10] Update changelog.md --- changelog.md | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/changelog.md b/changelog.md index 0d2174e..39269a7 100644 --- a/changelog.md +++ b/changelog.md @@ -1,12 +1,19 @@ # Changelog -## Release 3.1 (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