KPMP-6538: added code to return the ontology id to cell type mapping

.java-version

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

build.gradle

@@ -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'

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

@@ -3,13 +3,16 @@
 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;
@@ -43,14 +46,15 @@ public class QueryController implements GraphQLQueryResolver {
 	private RPExpressionDataService rpExpressionDataService;
     private ParticipantService2025 participantService2025;
     private AtlasMessageService atlasMessageService;
+	private HubmapCellTypeMappingService hubmapCellTypeMappingService;
 	private Logger logger = LoggerFactory.getLogger(QueryController.class);
 
 	@Autowired
 	public QueryController(AutocompleteService autocompleteService, CellTypeService cellTypeService, UmapDataService2025 umapService2025,
             GeneExpressionSummaryService2025 geneExpressionService2025,
 			DataSummaryService dataSummaryService, ClusterHierarchyService clusterHierarchyService,
 			RTExpressionDataService rtExpressionDataService, RPExpressionDataService rpExpressionDataService, ParticipantService2025 participantService2025,
-                           AtlasMessageService atlasMessageService) {
+                           AtlasMessageService atlasMessageService, HubmapCellTypeMappingService hubmapCellTypeMappingService) {
 
 		this.autocompleteService = autocompleteService;
 		this.cellTypeService = cellTypeService;
@@ -62,6 +66,7 @@ public QueryController(AutocompleteService autocompleteService, CellTypeService
 		this.rpExpressionDataService = rpExpressionDataService;
         this.participantService2025 = participantService2025;
         this.atlasMessageService = atlasMessageService;
+		this.hubmapCellTypeMappingService = hubmapCellTypeMappingService;
 	}
 
     @QueryMapping
@@ -262,4 +267,9 @@ public List<AtlasMessage> getAtlasMessages() throws Exception {
 	public List<ParticipantRepoDataTypeInformation> getExperimentalStrategyCountsByParticipant(@Argument String redcapId) {
 		return participantService2025.getExperimentalStrategyCountsByParticipant(redcapId);
 	}
+
+	@QueryMapping
+	public List<HubmapOntologyCellType>  getHubmapTermMap() {
+		return hubmapCellTypeMappingService.buildHubmapIdToCellTypeMap();
+	}
 }

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();
+}

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

@@ -0,0 +1,35 @@
+package org.kpmp.cellType;
+
+import java.io.Serializable;
+
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.Id;
+import jakarta.persistence.Table;
+
+@Entity
+@Table(name = "hubmap_ontology_celltype_v")
+public class HubmapOntologyCellType implements Serializable{
+
+    @Id
+    @Column(name = "hubmap_ontology_id", nullable = false, insertable = false, updatable = false)
+    private String hubmapOntologyId;
+    private String cellType;
+
+    public String getHubmapOntologyId() {
+        return hubmapOntologyId;
+    }
+
+    public void setHubmapOntologyId(String hubmapOntologyId) {
+        this.hubmapOntologyId = hubmapOntologyId;
+    }
+
+    public String getCellType() {
+        return cellType;
+    }
+
+    public void setCellType(String cell_type) {
+        this.cellType = cell_type;
+    }
+
+}

src/main/java/org/kpmp/cellTypeSummary/ClusterHiearchyRepository.java

@@ -2,7 +2,6 @@
 
 import java.util.List;
 
-import org.kpmp.cluster.Cluster;
 import org.springframework.cache.annotation.Cacheable;
 import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.CrudRepository;

src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchy.java

@@ -11,7 +11,6 @@
 
 import org.springframework.lang.Nullable;
 import com.fasterxml.jackson.annotation.JsonProperty;
-import com.fasterxml.jackson.annotation.JsonInclude;
 
 @Entity
 @Table(name = "cluster_hierarchy_v")

src/main/java/org/kpmp/umap/SNMetadataRepository2025.java

@@ -2,7 +2,6 @@
 
 import java.util.List;
 
-import org.checkerframework.checker.units.qual.C;
 import org.springframework.cache.annotation.Cacheable;
 import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.CrudRepository;

src/main/resources/graphql/knowledge_environment.graphqls

@@ -1,10 +1,10 @@
 type Query {
   autocomplete(searchTerm: String): [AutoCompleteResult]
-    cellTypeHierarchy2025: CellTypeHierarchy
+  cellTypeHierarchy2025: CellTypeHierarchy
   geneExpressionSummary2025(dataType: String, geneSymbol: String, cellType: String, enrollmentCategory: String) : [GeneExpressionSummary2025]
-    getClusterHieararchies2025(cellType: String!): [ClusterHierarchy]
+  getClusterHieararchies2025(cellType: String!): [ClusterHierarchy]
   getUmapPlotData2025(dataType: String!, geneSymbol: String!, enrollmentCategory: String): PlotData2025
-    dataTypesForConcept2025(geneSymbol: String, clusterName: String): [String]
+  dataTypesForConcept2025(geneSymbol: String, clusterName: String): [String]
   getDataTypeSummaryInformation2025: [DataTypeSummaryInformation2025]
   getRTGeneExpressionByEnrollment(comparisonType: String, geneSymbol: String): RTGeneExpressionByEnrollment
   getRPGeneExpressionByEnrollment(geneSymbol: String!): [RPAccessionGroup]
@@ -21,6 +21,12 @@ type Query {
   getAtlasMessages: [AtlasMessages]
   getExperimentalStrategyCountsByParticipant(redcapId: String!): [ParticipantRepoDataTypeInformation]
   getParticipantClinicalDataset(redcapId: String!): ParticipantClinicalDataset
+  getHubmapTermMap: [HubmapOntologyCellType]
+}
+
+type HubmapOntologyCellType {
+  hubmapOntologyId: String
+  cellType: String
 }
 
 type AtlasMessages {

src/test/java/org/kpmp/QueryControllerTest.java

@@ -14,6 +14,7 @@
 import java.util.Arrays;
 import java.util.Date;
 import java.util.List;
+import java.util.Map;
 
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
@@ -23,6 +24,8 @@
 import org.kpmp.autocomplete.AutocompleteResult;
 import org.kpmp.autocomplete.AutocompleteService;
 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;
@@ -74,13 +77,15 @@ public class QueryControllerTest {
     private UmapDataService2025 umapDataService2025;
 
     @Mock ParticipantService2025 participantService2025;
+	@Mock
+	HubmapCellTypeMappingService hubmapCellTypeMappingService;
 
 	@BeforeEach
 	public void setUp() throws Exception {
 		MockitoAnnotations.openMocks(this);
 		query = new QueryController(autocompleteService, cellTypeService, umapDataService2025,
 				geneExpressionService2025, dataSummaryService, clusterHierarchyService, rtExpressionDataService, rpExpressionDataService, 
-        participantService2025, atlasMessageService);
+        participantService2025, atlasMessageService, hubmapCellTypeMappingService);
 	}
 
 	@AfterEach
@@ -380,4 +385,21 @@ public void testGetExperimentalStrategyCountsByParticipant() {
 
 		assertEquals(expectedResults, result);
 	}
+	@Test
+	public void testGetHubmapTermMap() {
+		HubmapOntologyCellType cellType1 = mock(HubmapOntologyCellType.class);
+		when(cellType1.getHubmapOntologyId()).thenReturn("HUBMAP:001");
+		when(cellType1.getCellType()).thenReturn("Podocyte");
+
+		HubmapOntologyCellType cellType2 = mock(HubmapOntologyCellType.class);
+		when(cellType2.getHubmapOntologyId()).thenReturn("HUBMAP:002");
+		when(cellType2.getCellType()).thenReturn("Tubule cell");
+
+		List<HubmapOntologyCellType> expectedList = Arrays.asList(cellType1, cellType2);
+		when(hubmapCellTypeMappingService.buildHubmapIdToCellTypeMap()).thenReturn(expectedList);
+
+		List<HubmapOntologyCellType> result = query.getHubmapTermMap();
+		assertEquals(expectedList, result);
+		verify(hubmapCellTypeMappingService).buildHubmapIdToCellTypeMap();
+	}
 }

src/test/java/org/kpmp/cellType/HubmapCellTypeMappingServiceTest.java

@@ -0,0 +1,46 @@
+package org.kpmp.cellType;
+
+import static org.junit.jupiter.api.Assertions.*;
+import static org.mockito.Mockito.*;
+
+import java.util.*;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+class HubmapCellTypeMappingServiceTest {
+    private HubmapOnotologyCellTypeRepository repo;
+    private HubmapCellTypeMappingService service;
+
+    @BeforeEach
+    void setUp() {
+        repo = mock(HubmapOnotologyCellTypeRepository.class);
+        service = new HubmapCellTypeMappingService(repo);
+    }
+
+    @Test
+    void testBuildHubmapIdToCellTypeMap_returnsCorrectList() {
+        HubmapOntologyCellType cellType1 = mock(HubmapOntologyCellType.class);
+        when(cellType1.getHubmapOntologyId()).thenReturn("HUBMAP:001");
+        when(cellType1.getCellType()).thenReturn("Podocyte");
+
+        HubmapOntologyCellType cellType2 = mock(HubmapOntologyCellType.class);
+        when(cellType2.getHubmapOntologyId()).thenReturn("HUBMAP:002");
+        when(cellType2.getCellType()).thenReturn("Tubule cell");
+
+        List<HubmapOntologyCellType> cellTypes = Arrays.asList(cellType1, cellType2);
+        when(repo.findAll()).thenReturn(cellTypes);
+
+        List<HubmapOntologyCellType> result = service.buildHubmapIdToCellTypeMap();
+        assertEquals(2, result.size());
+        assertTrue(result.contains(cellType1));
+        assertTrue(result.contains(cellType2));
+    }
+
+    @Test
+    void testBuildHubmapIdToCellTypeMap_emptyListReturnsEmptyList() {
+        when(repo.findAll()).thenReturn(Collections.emptyList());
+        List<HubmapOntologyCellType> result = service.buildHubmapIdToCellTypeMap();
+        assertTrue(result.isEmpty());
+    }
+}

src/test/java/org/kpmp/cellType/HubmapOntologyCellTypeTest.java

@@ -0,0 +1,24 @@
+package org.kpmp.cellType;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+import org.junit.jupiter.api.Test;
+
+class HubmapOntologyCellTypeTest {
+    @Test
+    void testGettersAndSetters() {
+        HubmapOntologyCellType cellType = new HubmapOntologyCellType();
+        cellType.setHubmapOntologyId("HUBMAP:123");
+        cellType.setCellType("Podocyte");
+
+        assertEquals("HUBMAP:123", cellType.getHubmapOntologyId());
+        assertEquals("Podocyte", cellType.getCellType());
+    }
+
+    @Test
+    void testDefaultValues() {
+        HubmapOntologyCellType cellType = new HubmapOntologyCellType();
+        assertNull(cellType.getHubmapOntologyId());
+        assertNull(cellType.getCellType());
+    }
+}