Atlas Q1 2026 release

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

@@ -6,7 +6,7 @@ on:
 jobs:
   build-gradle-project:
     env:
-      IMAGE_TAG: 3.1.0
+      IMAGE_TAG: 3.3.0
     runs-on: ubuntu-latest
     steps:
       - name: Get branch names

.java-version

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

Dockerfile

@@ -1,4 +1,4 @@
-FROM --platform=linux/amd64 alpine:3.19.1
+FROM --platform=linux/amd64 alpine:3.21.6
 
 RUN apk update
 RUN apk add openjdk21

build.gradle

@@ -13,7 +13,7 @@ plugins {
 }
 
 group = 'kingstonduo'
-version = '3.1.0'
+version = '3.3.0'
 
 apply plugin: 'java'
 apply plugin: 'eclipse'
@@ -45,6 +45,7 @@ dependencies {
     implementation 'org.springframework.graphql:spring-graphql'
     implementation 'org.springframework.boot:spring-boot-starter-cache'
     implementation 'com.hazelcast:hazelcast-all:4.2.5'
+    implementation 'com.graphql-java:graphql-java-extended-scalars:21.0'
 
     testImplementation('org.mockito:mockito-junit-jupiter:3.12.4')
     testImplementation 'org.springframework.boot:spring-boot-starter-test'

changelog.md

@@ -1,7 +1,13 @@
 # Changelog
 
-## Release 3.2 (unreleased)
+## Release 3.3 (unreleased)
+
+---
+
+## Release 3.2 
 Brief summary:
+- return HUBMAP cell type ontology ID 
+- fixed duplicate data being returned for Regional Transcriptomics data
 
 ### Breaking changes
 

src/main/java/org/kpmp/Application.java

@@ -9,6 +9,9 @@
 import org.springframework.web.servlet.config.annotation.CorsRegistry;
 import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
 
+import graphql.scalars.ExtendedScalars;
+import org.springframework.graphql.execution.RuntimeWiringConfigurer;
+
 @Configuration
 @EnableCaching
 @SpringBootApplication
@@ -28,4 +31,9 @@ public void addCorsMappings(CorsRegistry registry) {
 			}
 		};
 	}
+
+    @Bean
+    public RuntimeWiringConfigurer runtimeWiringConfigurer() {
+        return wiringBuilder -> wiringBuilder.scalar(ExtendedScalars.Json);
+    }
 }

src/main/java/org/kpmp/QueryController.java

@@ -3,33 +3,26 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
 
 import org.kpmp.atlasMessage.AtlasMessage;
 import org.kpmp.atlasMessage.AtlasMessageService;
 import org.kpmp.autocomplete.AutocompleteResult;
 import org.kpmp.autocomplete.AutocompleteService;
 import org.kpmp.cellType.CellTypeHierarchy;
 import org.kpmp.cellType.CellTypeService;
+import org.kpmp.cellType.HubmapCellTypeMappingService;
+import org.kpmp.cellType.HubmapOntologyCellType;
 import org.kpmp.cellTypeSummary.ClusterHierarchy;
 import org.kpmp.cellTypeSummary.ClusterHierarchyService;
 import org.kpmp.dataSummary.AtlasRepoSummaryResult;
 import org.kpmp.dataSummary.DataSummaryService;
 import org.kpmp.dataSummary.DataTypeSummary;
 import org.kpmp.geneExpression.*;
 import org.kpmp.geneExpressionSummary.GeneExpressionSummary;
-import org.kpmp.geneExpressionSummary.GeneExpressionSummaryService;
 import org.kpmp.geneExpressionSummary.GeneExpressionSummaryService2025;
-import org.kpmp.participant.ParticipantClinicalDataset;
-import org.kpmp.participant.ParticipantDataTypeSummary;
-import org.kpmp.participant.ParticipantDataTypeSummary2025;
-import org.kpmp.participant.ParticipantRepoDataTypeInformation;
-import org.kpmp.participant.ParticipantRepoDataTypeSummary;
-import org.kpmp.participant.ParticipantService;
-import org.kpmp.participant.ParticipantService2025;
-import org.kpmp.participant.ParticipantSummaryDataset;
-import org.kpmp.participant.ParticipantEnrollmentCategorySummary;
+import org.kpmp.participant.*;
 import org.kpmp.umap.PlotData;
-import org.kpmp.umap.UmapDataService;
 import org.kpmp.umap.UmapDataService2025;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -45,71 +38,47 @@ public class QueryController implements GraphQLQueryResolver {
 
 	private AutocompleteService autocompleteService;
 	private CellTypeService cellTypeService;
-	private GeneExpressionSummaryService geneExpressionSummaryService;
     private GeneExpressionSummaryService2025 geneExpressionSummaryService2025;
 	private DataSummaryService dataSummaryService;
-	private UmapDataService umapService;
     private UmapDataService2025 umapService2025;
 	private ClusterHierarchyService clusterHierarchyService;
 	private RTExpressionDataService rtExpressionDataService;
-
 	private RPExpressionDataService rpExpressionDataService;
-	private ParticipantService participantService;
     private ParticipantService2025 participantService2025;
     private AtlasMessageService atlasMessageService;
+	private HubmapCellTypeMappingService hubmapCellTypeMappingService;
 	private Logger logger = LoggerFactory.getLogger(QueryController.class);
 
 	@Autowired
-	public QueryController(AutocompleteService autocompleteService, CellTypeService cellTypeService,
-			UmapDataService umapService, UmapDataService2025 umapService2025, GeneExpressionSummaryService geneExpressionSummaryService, 
+	public QueryController(AutocompleteService autocompleteService, CellTypeService cellTypeService, UmapDataService2025 umapService2025,
             GeneExpressionSummaryService2025 geneExpressionService2025,
 			DataSummaryService dataSummaryService, ClusterHierarchyService clusterHierarchyService,
-			RTExpressionDataService rtExpressionDataService, RPExpressionDataService rpExpressionDataService,
-      ParticipantService participantService, ParticipantService2025 participantService2025, AtlasMessageService atlasMessageService) {
+			RTExpressionDataService rtExpressionDataService, RPExpressionDataService rpExpressionDataService, ParticipantService2025 participantService2025,
+                           AtlasMessageService atlasMessageService, HubmapCellTypeMappingService hubmapCellTypeMappingService) {
 
 		this.autocompleteService = autocompleteService;
 		this.cellTypeService = cellTypeService;
-		this.umapService = umapService;
         this.umapService2025 = umapService2025;
-		this.geneExpressionSummaryService = geneExpressionSummaryService;
         this.geneExpressionSummaryService2025 = geneExpressionService2025;
 		this.dataSummaryService = dataSummaryService;
 		this.clusterHierarchyService = clusterHierarchyService;
 		this.rtExpressionDataService = rtExpressionDataService;
 		this.rpExpressionDataService = rpExpressionDataService;
-		this.participantService = participantService;
         this.participantService2025 = participantService2025;
         this.atlasMessageService = atlasMessageService;
+		this.hubmapCellTypeMappingService = hubmapCellTypeMappingService;
 	}
 
     @QueryMapping
 	public List<AutocompleteResult> autocomplete(@Argument String searchTerm) throws IOException, Exception {
 		return autocompleteService.query(searchTerm);
 	}
 
-    @QueryMapping
-	public CellTypeHierarchy cellTypeHierarchy() throws IOException {
-		return cellTypeService.getCellTypeHierarchy();
-	}
-
     @QueryMapping
     public CellTypeHierarchy cellTypeHierarchy2025() throws IOException {
         return cellTypeService.getCellTypeHierarchy2025();
     }
 
-    @QueryMapping
-	public List<? extends GeneExpressionSummary> geneExpressionSummary(@Argument String dataType, @Argument String geneSymbol,
-        @Argument String cellType, @Argument String enrollmentCategory) throws IOException {
-		List<? extends GeneExpressionSummary> results = new ArrayList<>();
-		if (cellType.isEmpty()) {
-			results = geneExpressionSummaryService.getByDataTypeEnrollmentCategoryAndGene(dataType, geneSymbol, enrollmentCategory);
-		} else if (geneSymbol.isEmpty()) {
-			results = geneExpressionSummaryService.getExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory(dataType,
-					cellType, enrollmentCategory);
-		}
-		return results;
-	}
-
     @QueryMapping
 	public List<? extends GeneExpressionSummary> geneExpressionSummary2025(@Argument String dataType, @Argument String geneSymbol,
         @Argument String cellType, @Argument String enrollmentCategory) throws IOException {
@@ -123,26 +92,11 @@ public List<? extends GeneExpressionSummary> geneExpressionSummary2025(@Argument
 		return results;
 	}
 
-    @QueryMapping
-	public List<ClusterHierarchy> getClusterHieararchies(@Argument String cellType) throws IOException {
-		return clusterHierarchyService.findClustersByCellType(cellType);
-	}
-
     @QueryMapping
     public List<ClusterHierarchy> getClusterHieararchies2025(@Argument String cellType) throws IOException {
         return clusterHierarchyService.findClustersByCellType2025(cellType);
     }
 
-    @QueryMapping
-	public PlotData getUmapPlotData(@Argument String dataType, @Argument String geneSymbol, @Argument String enrollmentCategory) throws Exception {
-		try {
-			return umapService.getPlotData(dataType, geneSymbol, enrollmentCategory);
-		} catch (Exception e) {
-			logger.error(e.getMessage());
-			throw e;
-		}
-	}
-
     @QueryMapping
 	public PlotData getUmapPlotData2025(@Argument String dataType, @Argument String geneSymbol, @Argument String enrollmentCategory) throws Exception {
 		try {
@@ -153,16 +107,6 @@ public PlotData getUmapPlotData2025(@Argument String dataType, @Argument String
 		}
 	}
 
-    @QueryMapping
-	public List<DataTypeSummary> getDataTypeSummaryInformation() throws Exception {
-		try {
-            return geneExpressionSummaryService.getDataTypeSummaryInformation();
-		} catch (Exception e) {
-			logger.error(e.getMessage());
-			throw e;
-		}
-	}
-
     @QueryMapping
     public List<DataTypeSummary> getDataTypeSummaryInformation2025() throws Exception {
 		try {
@@ -183,21 +127,10 @@ public List<DataTypeSummary> getSummaryData() throws Exception {
 		}
 	}
 
-    @QueryMapping
-	public List<String> dataTypesForConcept(@Argument String geneSymbol, @Argument String clusterName) throws Exception {
-		if (geneSymbol != null && !geneSymbol.isEmpty()) {
-			return geneExpressionSummaryService.findDataTypesByGene(geneSymbol);
-		} else if (clusterName != null && !clusterName.isEmpty()) {
-			return clusterHierarchyService.findDataTypesByClusterName(clusterName);
-		}
-		throw new Exception("Must provide either a cluster or a gene symbol.");
-
-	}
-
     @QueryMapping
     public List<String> dataTypesForConcept2025(@Argument String geneSymbol, @Argument String clusterName) throws Exception {
         if (geneSymbol != null && !geneSymbol.isEmpty()) {
-            return geneExpressionSummaryService.findDataTypesByGene(geneSymbol);
+            return geneExpressionSummaryService2025.findDataTypesByGene(geneSymbol);
         } else if (clusterName != null && !clusterName.isEmpty()) {
             return clusterHierarchyService.findDataTypesByClusterName2025(clusterName);
         }
@@ -260,32 +193,27 @@ public List<RPAccessionGroup> getRPGeneExpressionByEnrollment(@Argument String g
     @QueryMapping
     public ParticipantClinicalDataset getParticipantClinicalDataset(@Argument String redcapId) {
         try{
-            return participantService.getParticipantClinicalDataset(redcapId);
+            return participantService2025.getParticipantClinicalDataset(redcapId);
         }catch (Exception e) {
             logger.error(e.getMessage());
             throw e;
         }
     }
 
-    @QueryMapping
-	public ParticipantDataTypeSummary getDataTypeInformationByParticipant(@Argument String redcapId) {
-		return participantService.getExperimentCounts(redcapId);
-	}
-
     @QueryMapping
 	public ParticipantDataTypeSummary2025 getDataTypeInformationByParticipant2025(@Argument String redcapId) {
 		return participantService2025.getExperimentCounts(redcapId);
 	}
 
     @QueryMapping
-	public ParticipantRepoDataTypeSummary getRepoDataTypeInformationByParticipant(@Argument String redcapId) {
-		return participantService.getDataTypeCounts(redcapId);
-	}
+    public ParticipantRepoDataTypeSummary getRepoDataTypeInformationByParticipant(@Argument String redcapId) {
+        return participantService2025.getDataTypeCounts(redcapId);
+    }
 
     @QueryMapping
 	public ParticipantSummaryDataset participantSummaryDataset(@Argument String redcapId) throws Exception {
 		try {
-			return participantService.getParticipantSummaryDataset(redcapId);
+			return participantService2025.getParticipantSummaryDataset(redcapId);
 		} catch (Exception e) {
 			logger.error(e.getMessage());
 			ParticipantSummaryDataset emptyResult = new ParticipantSummaryDataset();
@@ -298,7 +226,7 @@ public ParticipantSummaryDataset participantSummaryDataset(@Argument String redc
     @QueryMapping
 	public ParticipantRepoDataTypeInformation getTotalParticipantFilesCount(@Argument String redcapId) throws Exception {
 		try {
-			return this.participantService.getTotalFilesCount(redcapId);
+			return this.participantService2025.getTotalFilesCount(redcapId);
 		} catch (Exception e) {
 			logger.error(e.getMessage());
 			throw e;
@@ -308,7 +236,7 @@ public ParticipantRepoDataTypeInformation getTotalParticipantFilesCount(@Argumen
     @QueryMapping
 	public List<ParticipantEnrollmentCategorySummary> getEnrollmentCategorySummaryData() throws Exception {
 		try {
-			return participantService.getEnrollmentData();
+			return participantService2025.getEnrollmentData();
 		} catch (Exception e) {
 			logger.error(e.getMessage());
 			throw e;
@@ -337,6 +265,11 @@ public List<AtlasMessage> getAtlasMessages() throws Exception {
 
     @QueryMapping
 	public List<ParticipantRepoDataTypeInformation> getExperimentalStrategyCountsByParticipant(@Argument String redcapId) {
-		return participantService.getExperimentalStrategyCountsByParticipant(redcapId);
+		return participantService2025.getExperimentalStrategyCountsByParticipant(redcapId);
+	}
+
+	@QueryMapping
+	public List<HubmapOntologyCellType>  getHubmapTermMap() {
+		return hubmapCellTypeMappingService.buildHubmapIdToCellTypeMap();
 	}
 }

src/main/java/org/kpmp/cellType/CellTypeRepository.java

@@ -19,9 +19,6 @@ public interface CellTypeRepository extends CrudRepository<CellType, Integer> {
 			+ "    WHERE ct.cell_type LIKE %:searchTerm% ", nativeQuery = true)
 	List<CellType> findByCellTypeContainingOrSynonymContaining(@Param("searchTerm") String searchTerm);
 
-	@Cacheable("cellTypeIsNotNullOrderByCellTypeOrdering")
-	List<CellType> findAllByCellTypeIsNotNullOrderByCellTypeOrdering();
-
     @Cacheable("cellTypeIsNotNullOrderByCellTypeOrdering2025")
     @Query(value = "SELECT * FROM cell_type_2025 WHERE cell_type IS NOT NULL ORDER BY cell_type_order ASC", nativeQuery = true)
     List<CellType> findAllByCellTypeIsNotNullOrderByCellTypeOrdering2025();

src/main/java/org/kpmp/cellType/CellTypeService.java

@@ -15,21 +15,6 @@ public CellTypeService(CellTypeRepository cellTypeRepo) {
 		this.cellTypeRepo = cellTypeRepo;
 	}
 
-	public CellTypeHierarchy getCellTypeHierarchy() {
-		List<CellType> cellTypes = cellTypeRepo.findAllByCellTypeIsNotNullOrderByCellTypeOrdering();
-		CellTypeHierarchy hierarchy = new CellTypeHierarchy();
-
-		for (CellType cellType : cellTypes) {
-			CellTypeStructureSubregion subregion = new CellTypeStructureSubregion(cellType.getStructureSubregion());
-			subregion.addCellType(cellType);
-			CellTypeStructureRegion region = new CellTypeStructureRegion(cellType.getStructureRegion());
-			region.addCellTypeSubregion(subregion);
-			hierarchy.addCellTypeStructureRegion(region);
-		}
-
-		return hierarchy;
-	}
-
     public CellTypeHierarchy getCellTypeHierarchy2025() {
         List<CellType> cellTypes = cellTypeRepo.findAllByCellTypeIsNotNullOrderByCellTypeOrdering2025();
         CellTypeHierarchy hierarchy = new CellTypeHierarchy();

src/main/java/org/kpmp/cellType/HubmapCellTypeMappingService.java

@@ -0,0 +1,18 @@
+package org.kpmp.cellType;
+
+import java.util.List;
+import org.springframework.stereotype.Service;
+
+@Service
+public class HubmapCellTypeMappingService {
+
+    private final HubmapOnotologyCellTypeRepository repo;
+
+    public HubmapCellTypeMappingService(HubmapOnotologyCellTypeRepository repo) {
+        this.repo = repo;
+    }
+
+    public List<HubmapOntologyCellType> buildHubmapIdToCellTypeMap() {
+        return repo.findAll();
+    }
+}

src/main/java/org/kpmp/cellType/HubmapOnotologyCellTypeRepository.java

@@ -0,0 +1,16 @@
+package org.kpmp.cellType;
+
+import org.jetbrains.annotations.NotNull;
+import org.springframework.cache.annotation.Cacheable;
+import org.springframework.data.repository.CrudRepository;
+import org.springframework.stereotype.Repository;
+
+import java.util.List;
+
+@Repository
+public interface HubmapOnotologyCellTypeRepository extends CrudRepository<HubmapOntologyCellType, String> {
+
+    @NotNull
+    @Cacheable("hubmapOntologyCellTypeMap")
+    List<HubmapOntologyCellType> findAll();
+}